› 7r7a

Electron Microscopy
3.04Å resolution

State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model

Released:
DOI: 10.2210/pdb7r7a/pdb
PDB entry 7r7a coloured by chain, front view.
PDB entry 7r7a coloured by chain, side view.
PDB entry 7r7a coloured by chain, top view.
Source organism: Saccharomyces cerevisiae BY4741
Primary publication:
Sequence-specific remodeling of a topologically complex RNP substrate by Spb4.
Cruz VE, Sekulski K, Peddada N, Sailer C, Balasubramanian S, Weirich CS, Stengel F, Erzberger JP
Nat Struct Mol Biol (2022)
PMID: 36482249
Related structures: EMD-24296

Function and Biology Details

Reactions catalysed: 
S-adenosyl-L-methionine + cytosine(2870) in 25S rRNA = S-adenosyl-L-homocysteine + 5-methylcytosine(2870) in 25S rRNA
ATP + H(2)O = ADP + phosphate
S-adenosyl-L-methionine + guanosine(2922) in 27S pre-rRNA = S-adenosyl-L-homocysteine + 2'-O-methylguanosine(2922) in 27S pre-rRNA
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 57-mer (preferred)
PDBe Complex ID:
PDB-CPX-216271 (preferred)
Entry contents:
54 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (57 distinct):
60S ribosomal subunit assembly/export protein LOC1 Chain: 7
Molecule details ›
Chain: 7
Length: 204 amino acids
Theoretical weight: 23.65 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P43586 (Residues: 1-204; Coverage: 100%)
Gene names: LOC1, YFR001W
Ribosome biogenesis protein BRX1 Chain: A
Molecule details ›
Chain: A
Length: 291 amino acids
Theoretical weight: 33.59 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: Q08235 (Residues: 1-291; Coverage: 100%)
Gene names: BRX1, YOL077C
Sequence domains: Brix domain
Large ribosomal subunit protein uL3 Chain: B
Molecule details ›
Chain: B
Length: 387 amino acids
Theoretical weight: 43.85 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P14126 (Residues: 1-387; Coverage: 100%)
Gene names: MAK8, RPL3, TCM1, YOR063W, YOR29-14
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL4A Chain: C
Molecule details ›
Chain: C
Length: 362 amino acids
Theoretical weight: 39.16 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P10664 (Residues: 1-362; Coverage: 100%)
Gene names: RPL2, RPL2A, RPL4A, YBR0315, YBR031W
Sequence domains:
Large ribosomal subunit protein eL6A Chain: E
Molecule details ›
Chain: E
Length: 175 amino acids
Theoretical weight: 19.89 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: Q02326 (Residues: 1-176; Coverage: 99%)
Gene names: RPL17A, RPL6A, YL16A, YML073C
Sequence domains: Ribosomal protein L6e
Large ribosomal subunit protein uL30A Chain: F
Molecule details ›
Chain: F
Length: 244 amino acids
Theoretical weight: 27.69 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P05737 (Residues: 1-244; Coverage: 100%)
Gene names: RPL6A, RPL7A, RPL8A, YGL076C, YL8A
Sequence domains:
Large ribosomal subunit protein uL6A Chain: H
Molecule details ›
Chain: H
Length: 191 amino acids
Theoretical weight: 21.61 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P05738 (Residues: 1-191; Coverage: 100%)
Gene names: RPL8A, RPL9, RPL9A, YGL147C
Sequence domains: Ribosomal protein L6
rRNA-processing protein EBP2 Chain: J
Molecule details ›
Chain: J
Length: 427 amino acids
Theoretical weight: 49.84 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P36049 (Residues: 1-427; Coverage: 100%)
Gene names: EBP2, YKL172W, YKL636
Sequence domains: Eukaryotic rRNA processing protein EBP2
Large ribosomal subunit protein eL13A Chain: L
Molecule details ›
Chain: L
Length: 199 amino acids
Theoretical weight: 22.6 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: Q12690 (Residues: 1-199; Coverage: 100%)
Gene names: RPL13A, YDL082W
Sequence domains: Ribosomal protein L13e
Large ribosomal subunit protein eL14A Chain: M
Molecule details ›
Chain: M
Length: 138 amino acids
Theoretical weight: 15.2 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P36105 (Residues: 1-138; Coverage: 100%)
Gene names: RPL14A, YKL006W, YKL153
Sequence domains:
Large ribosomal subunit protein eL15A Chain: N
Molecule details ›
Chain: N
Length: 204 amino acids
Theoretical weight: 24.48 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P05748 (Residues: 1-204; Coverage: 100%)
Gene names: RPL10A, RPL13A, RPL15A, YL10A, YLR029C
Sequence domains: Ribosomal L15
Large ribosomal subunit protein uL13A Chain: O
Molecule details ›
Chain: O
Length: 199 amino acids
Theoretical weight: 22.25 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P26784 (Residues: 1-199; Coverage: 100%)
Gene names: RPL13, RPL16A, RPL21A, YIL133C
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL22A Chain: P
Molecule details ›
Chain: P
Length: 184 amino acids
Theoretical weight: 20.59 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P05740 (Residues: 1-184; Coverage: 100%)
Gene names: RPL17, RPL17A, RPL20A, YKL180W
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein eL18A Chain: Q
Molecule details ›
Chain: Q
Length: 186 amino acids
Theoretical weight: 20.61 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P0CX49 (Residues: 1-186; Coverage: 100%)
Gene names: RP28A, RPL18A, YOL120C
Sequence domains: Ribosomal protein 60S L18 and 50S L18e
Large ribosomal subunit protein eL20A Chain: S
Molecule details ›
Chain: S
Length: 172 amino acids
Theoretical weight: 20.48 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P0CX23 (Residues: 1-172; Coverage: 100%)
Gene names: RPL18A, RPL18A2, RPL20A, YM9408.04C, YMR242C
Sequence domains: Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
Large ribosomal subunit protein eL21A Chain: T
Molecule details ›
Chain: T
Length: 160 amino acids
Theoretical weight: 18.28 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: Q02753 (Residues: 1-160; Coverage: 100%)
Gene names: RPL21A, URP1, YBR1401, YBR191W
Sequence domains: Ribosomal protein L21e
Ribosome assembly factor MRT4 Chain: W
Molecule details ›
Chain: W
Length: 236 amino acids
Theoretical weight: 27.1 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P33201 (Residues: 1-236; Coverage: 100%)
Gene names: MRT4, YKL009W, YKL160
Sequence domains:
Large ribosomal subunit protein uL23 Chain: X
Molecule details ›
Chain: X
Length: 142 amino acids
Theoretical weight: 15.79 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P04456 (Residues: 1-142; Coverage: 100%)
Gene names: RPL25, YOL127W
Sequence domains:
Large ribosomal subunit protein uL24A Chain: Y
Molecule details ›
Chain: Y
Length: 127 amino acids
Theoretical weight: 14.27 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P05743 (Residues: 1-127; Coverage: 100%)
Gene names: L8300.4, RPL26, RPL26A, RPL33A, YLR344W
Sequence domains:
Nucleolar GTP-binding protein 1 Chain: b
Molecule details ›
Chain: b
Length: 647 amino acids
Theoretical weight: 74.53 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: Q02892 (Residues: 1-647; Coverage: 100%)
Gene names: LPG15W, NOG1, YPL093W
Sequence domains:
Large ribosomal subunit protein eL31A Chain: d
Molecule details ›
Chain: d
Length: 113 amino acids
Theoretical weight: 12.98 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P0C2H8 (Residues: 1-113; Coverage: 100%)
Gene names: D2478, RPL31A, RPL34, RPL34A, YDL075W
Sequence domains: Ribosomal protein L31e
Large ribosomal subunit protein eL32 Chain: e
Molecule details ›
Chain: e
Length: 130 amino acids
Theoretical weight: 14.81 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P38061 (Residues: 1-130; Coverage: 100%)
Gene names: RPL32, YBL0838, YBL092W
Sequence domains: Ribosomal protein L32
Large ribosomal subunit protein eL33A Chain: f
Molecule details ›
Chain: f
Length: 107 amino acids
Theoretical weight: 12.18 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P05744 (Residues: 1-107; Coverage: 100%)
Gene names: LPI4W, P2625, RPL33A, RPL37A, YPL143W
Sequence domains: Ribosomal protein L35Ae
Large ribosomal subunit protein uL29A Chain: h
Molecule details ›
Chain: h
Length: 120 amino acids
Theoretical weight: 13.94 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P0CX84 (Residues: 1-120; Coverage: 100%)
Gene names: D1249, RPL35A, SOS1, YDL191W
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein eL36A Chain: i
Molecule details ›
Chain: i
Length: 100 amino acids
Theoretical weight: 11.15 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P05745 (Residues: 1-100; Coverage: 100%)
Gene names: RPL36A, RPL39A, YM9646.06, YMR194W
Sequence domains: Ribosomal protein L36e
Large ribosomal subunit protein eL37A Chain: j
Molecule details ›
Chain: j
Length: 88 amino acids
Theoretical weight: 9.88 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P49166 (Residues: 1-88; Coverage: 100%)
Gene names: L9470.6, RPL35A, RPL37A, YLR185W
Sequence domains: Ribosomal protein L37e
60S ribosome subunit biogenesis protein NIP7 Chain: l
Molecule details ›
Chain: l
Length: 181 amino acids
Theoretical weight: 20.41 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: Q08962 (Residues: 1-181; Coverage: 100%)
Gene names: NIP7, YPL211W
Sequence domains:
Ribosome biogenesis protein ERB1 Chain: m
Molecule details ›
Chain: m
Length: 807 amino acids
Theoretical weight: 91.77 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: Q04660 (Residues: 1-807; Coverage: 100%)
Gene names: ERB1, YM9796.02C, YMR049C
Sequence domains:
25S rRNA (cytosine(2870)-C(5))-methyltransferase Chain: q
Molecule details ›
Chain: q
Length: 618 amino acids
Theoretical weight: 69.91 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P40991 (Residues: 1-618; Coverage: 100%)
Gene names: N2428, NOP2, YNA1, YNL061W, YNL2428W
Sequence domains: 16S rRNA methyltransferase RsmB/F
Ribosome biogenesis protein NSA2 Chain: r
Molecule details ›
Chain: r
Length: 261 amino acids
Theoretical weight: 29.79 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P40078 (Residues: 1-261; Coverage: 100%)
Gene names: NSA2, SYGP-ORF47, YER126C
Sequence domains: Ribosomal protein S8e
Nuclear GTP-binding protein NUG1 Chain: s
Molecule details ›
Chain: s
Length: 520 amino acids
Theoretical weight: 57.8 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P40010 (Residues: 1-520; Coverage: 100%)
Gene names: NUG1, YER006W
Sequence domains:
Ribosome biogenesis protein RLP24 Chain: u
Molecule details ›
Chain: u
Length: 199 amino acids
Theoretical weight: 24.03 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: Q07915 (Residues: 1-199; Coverage: 100%)
Gene names: RLP24, YLR009W
Sequence domains: Ribosomal protein L24e
Nucleolar protein 16 Chain: v
Molecule details ›
Chain: v
Length: 231 amino acids
Theoretical weight: 26.95 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P40007 (Residues: 1-231; Coverage: 100%)
Gene names: NOP16, YER002W
Sequence domains: Ribosome biogenesis protein Nop16
Eukaryotic translation initiation factor 6 Chain: y
Molecule details ›
Chain: y
Length: 245 amino acids
Theoretical weight: 26.48 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: Q12522 (Residues: 1-245; Coverage: 100%)
Gene names: CDC95, LPZ15C, TIF6, YPR016C
Sequence domains: eIF-6 family
UPF0642 protein YBL028C Chain: z
Molecule details ›
Chain: z
Length: 106 amino acids
Theoretical weight: 12.44 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P38202 (Residues: 1-106; Coverage: 100%)
Gene names: YBL028C, YBL0423
Sequence domains: YBL028C ribosome biogenesis factor, N-terminal domain
Nucleolar complex protein 2 Chain: 8
Molecule details ›
Chain: 8
Length: 710 amino acids
Theoretical weight: 81.72 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P39744 (Residues: 1-710; Coverage: 100%)
Gene names: NOC2, YOR206W, YOX001
Sequence domains: Noc2p family
Nucleolar complex-associated protein 3 Chain: I
Molecule details ›
Chain: I
Length: 663 amino acids
Theoretical weight: 75.69 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: Q07896 (Residues: 1-663; Coverage: 100%)
Gene names: NOC3, YLR002C
Sequence domains:
Proteasome-interacting protein CIC1 Chain: K
Molecule details ›
Chain: K
Length: 376 amino acids
Theoretical weight: 42.6 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P38779 (Residues: 1-376; Coverage: 100%)
Gene names: CIC1, NSA3, YHR052W
Sequence domains: Ribosomal protein L1p/L10e family
Large ribosomal subunit protein uL14A Chain: V
Molecule details ›
Chain: V
Length: 137 amino acids
Theoretical weight: 14.49 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P0CX41 (Residues: 1-137; Coverage: 100%)
Gene names: RPL17A, RPL17AA, RPL23A, YBL0713, YBL087C
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein eL19A Chain: R
Molecule details ›
Chain: R
Length: 189 amino acids
Theoretical weight: 21.76 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P0CX82 (Residues: 1-189; Coverage: 100%)
Gene names: RPL19A, RPL23A, YBR084BC, YBR084C-A, YL14A
Sequence domains: Ribosomal protein L19e
Large ribosomal subunit protein eL8A Chain: G
Molecule details ›
Chain: G
Length: 256 amino acids
Theoretical weight: 28.18 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P17076 (Residues: 1-256; Coverage: 100%)
Gene names: MAK7, RPL4A, RPL8A, YHL033C
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Large ribosomal subunit protein eL27A Chain: Z
Molecule details ›
Chain: Z
Length: 136 amino acids
Theoretical weight: 15.57 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P0C2H6 (Residues: 1-136; Coverage: 100%)
Gene names: RPL27, RPL27A, YHR010W
Sequence domains: Ribosomal L27e protein family
Large ribosomal subunit protein eL22A Chain: U
Molecule details ›
Chain: U
Length: 121 amino acids
Theoretical weight: 13.71 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P05749 (Residues: 1-121; Coverage: 100%)
Gene names: L2168, RPL22A, YLR061W
Sequence domains: Ribosomal L22e protein family
Large ribosomal subunit protein eL30 Chain: c
Molecule details ›
Chain: c
Length: 105 amino acids
Theoretical weight: 11.43 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P14120 (Residues: 1-105; Coverage: 100%)
Gene names: RPL30, RPL32, YGL030W
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Large ribosomal subunit protein eL34A Chain: g
Molecule details ›
Chain: g
Length: 121 amino acids
Theoretical weight: 13.67 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P87262 (Residues: 1-121; Coverage: 100%)
Gene names: RPL34A, YER056BC, YER056C-A
Sequence domains: Ribosomal protein L34e
Large ribosomal subunit protein eL38 Chain: k
Molecule details ›
Chain: k
Length: 78 amino acids
Theoretical weight: 8.85 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P49167 (Residues: 1-78; Coverage: 100%)
Gene names: L8543.2, RPL38, YLR325C
Sequence domains: Ribosomal L38e protein family
Pescadillo homolog Chain: n
Molecule details ›
Chain: n
Length: 605 amino acids
Theoretical weight: 69.98 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P53261 (Residues: 1-605; Coverage: 100%)
Gene names: NOP7, RRP13, YGR103W, YPH1
Sequence domains:
Ribosome biogenesis protein YTM1 Chain: p
Molecule details ›
Chain: p
Length: 460 amino acids
Theoretical weight: 51.43 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: Q12024 (Residues: 1-460; Coverage: 100%)
Gene names: YOR272W, YTM1
Sequence domains:
Ribosome biogenesis protein RLP7 Chain: t
Molecule details ›
Chain: t
Length: 322 amino acids
Theoretical weight: 36.62 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P40693 (Residues: 1-322; Coverage: 100%)
Gene names: N2014, RLP7, RPL7, YNL002C
Sequence domains: Ribosomal protein L30p/L7e
ATP-dependent RNA helicase HAS1 Chain: D
Molecule details ›
Chain: D
Length: 505 amino acids
Theoretical weight: 56.8 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: Q03532 (Residues: 1-505; Coverage: 100%)
Gene names: HAS1, YMR290C
Sequence domains:
Ribosome biogenesis protein 15 Chain: o
Molecule details ›
Chain: o
Length: 220 amino acids
Theoretical weight: 25.5 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P53927 (Residues: 1-220; Coverage: 100%)
Gene names: N1954, NOP15, YNL110C
Sequence domains: RNA recognition motif
27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase Chain: w
Molecule details ›
Chain: w
Length: 841 amino acids
Theoretical weight: 96.66 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P25582 (Residues: 1-841; Coverage: 100%)
Gene names: SPB1, YCL054W, YCL431, YCL54W
Sequence domains:
Large ribosomal subunit protein uL1A Chain: a
Molecule details ›
Chain: a
Length: 217 amino acids
Theoretical weight: 24.52 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P0CX43 (Residues: 1-217; Coverage: 100%)
Gene names: RPL1A, SSM1, SSM1A, YPL220W
Sequence domains: Ribosomal protein L1p/L10e family
ATP-dependent rRNA helicase SPB4 Chain: x
Molecule details ›
Chain: x
Length: 606 amino acids
Theoretical weight: 69.49 KDa
Source organism: Saccharomyces cerevisiae BY4741
UniProt:
  • Canonical: P25808 (Residues: 1-606; Coverage: 100%)
Gene names: SPB4, YFL002C
Sequence domains:
25S ribosomal RNA Chain: 1
Molecule details ›
Chain: 1
Length: 3396 nucleotides
Theoretical weight: 1097.53 KDa
Sequence domains: Eukaryotic large subunit ribosomal RNA
5.8S ribosomal RNA Chain: 2
Molecule details ›
Chain: 2
Length: 158 nucleotides
Theoretical weight: 50.68 KDa
Sequence domains: 5.8S ribosomal RNA
5.8S ribosomal RNA gene and internal transcribed spacer 2 Chain: 6
Molecule details ›
Chain: 6
Length: 87 nucleotides
Theoretical weight: 27.79 KDa

Ligands and Environments

1 bound ligand:
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.04Å
Relevant EMDB volumes: EMD-24296

Quick links

Citations

2 review citations

Cellular functions of eukaryotic RNA helicases and their links to human diseases.
Bohnsack et al. (2023)
1 more

2 mentions without citation

Sequence-specific remodeling of a topologically complex RNP substrate by Spb4.
Cruz et al. (2022)
1 more