› 8rdw

Electron Microscopy
2.74Å resolution

Cryo-EM structure of P. urativorans 70S ribosome in complex with hibernation factor Balon and EF-Tu(GDP) (structure 3).

Released:
DOI: 10.2210/pdb8rdw/pdb
PDB entry 8rdw coloured by chain, front view.
PDB entry 8rdw coloured by chain, side view.
PDB entry 8rdw coloured by chain, top view.
Source organism: Psychrobacter urativorans
Primary publication:
A new family of bacterial ribosome hibernation factors.
Helena-Bueno K, Rybak MY, Ekemezie CL, Sullivan R, Brown CR, Dingwall C, Baslé A, Schneider C, Connolly JPR, Blaza JN, Csörgő B, Moynihan PJ, Gagnon MG, Hill CH, Melnikov SV
OpenAccess logo Nature (2024)
PMID: 38355796
Related structures: EMD-19077

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 55-mer (preferred)
PDBe Complex ID:
PDB-CPX-241749 (preferred)
Entry contents:
52 distinct polypeptide molecules
3 distinct RNA molecules
Macromolecules (55 distinct):
Methyl-accepting chemotaxis protein Chain: B
Molecule details ›
Chain: B
Length: 369 amino acids
Theoretical weight: 41.16 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M3V8U3 (Residues: 1-369; Coverage: 100%)
Gene name: AOC03_06830
Sequence domains: Bacterial archaeo-eukaryotic release factor family 3
Large ribosomal subunit protein bL12 Chain: D
Molecule details ›
Chain: D
Length: 123 amino acids
Theoretical weight: 12.67 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M4SX69 (Residues: 1-123; Coverage: 100%)
Gene names: AOC03_04955, rplL
Sequence domains:
Small ribosomal subunit protein uS9 Chain: F
Molecule details ›
Chain: F
Length: 128 amino acids
Theoretical weight: 14.28 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M4T6M9 (Residues: 1-128; Coverage: 100%)
Gene names: AOC03_03020, rpsI
Sequence domains: Ribosomal protein S9/S16
Elongation factor Tu Chain: H
Molecule details ›
Chain: H
Length: 396 amino acids
Theoretical weight: 43.11 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M4U5B4 (Residues: 1-396; Coverage: 100%)
Gene names: AOC03_04990, AOC03_08575, tuf
Sequence domains:
Small ribosomal subunit protein bS18 Chain: R3
Molecule details ›
Chain: R3
Length: 76 amino acids
Theoretical weight: 8.97 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M5MK69 (Residues: 1-76; Coverage: 100%)
Gene names: AOC03_11085, rpsR
Sequence domains: Ribosomal protein S18
Small ribosomal subunit protein uS2 Chain: A4
Molecule details ›
Chain: A4
Length: 269 amino acids
Theoretical weight: 29.47 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M4TFJ4 (Residues: 1-269; Coverage: 100%)
Gene names: AOC03_08390, rpsB
Sequence domains: Ribosomal protein S2
Small ribosomal subunit protein uS5 Chain: E5
Molecule details ›
Chain: E5
Length: 171 amino acids
Theoretical weight: 18.19 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M3V8J0 (Residues: 1-171; Coverage: 100%)
Gene names: AOC03_03745, rpsE
Sequence domains:
Small ribosomal subunit protein uS12 Chain: L6
Molecule details ›
Chain: L6
Length: 124 amino acids
Theoretical weight: 13.75 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M4U4C3 (Residues: 1-124; Coverage: 100%)
Gene names: AOC03_05005, rpsL
Sequence domains: Ribosomal protein S12/S23
Large ribosomal subunit protein uL5 Chain: F7
Molecule details ›
Chain: F7
Length: 178 amino acids
Theoretical weight: 19.84 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M4T1L5 (Residues: 1-178; Coverage: 100%)
Gene names: AOC03_03770, rplE
Sequence domains:
Large ribosomal subunit protein uL4 Chain: E9
Molecule details ›
Chain: E9
Length: 200 amino acids
Theoretical weight: 21.97 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M4U627 (Residues: 1-200; Coverage: 100%)
Gene names: AOC03_03825, rplD
Sequence domains: Ribosomal protein L4/L1 family
Large ribosomal subunit protein bL32 Chain: aA
Molecule details ›
Chain: aA
Length: 60 amino acids
Theoretical weight: 7.17 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M4SWQ6 (Residues: 1-60; Coverage: 100%)
Gene names: AOC03_03680, rpmF
Sequence domains: Ribosomal L32p protein family
Large ribosomal subunit protein bL17 Chain: MB
Molecule details ›
Chain: MB
Length: 119 amino acids
Theoretical weight: 13.64 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M4U611 (Residues: 1-119; Coverage: 100%)
Gene names: AOC03_03700, rplQ
Sequence domains: Ribosomal protein L17
Large ribosomal subunit protein bL25 Chain: UC
Molecule details ›
Chain: UC
Length: 219 amino acids
Theoretical weight: 23.89 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M4U726 (Residues: 1-219; Coverage: 100%)
Gene names: AOC03_07335, ctc, rplY
Sequence domains:
Large ribosomal subunit protein bL28 Chain: WD
Molecule details ›
Chain: WD
Length: 78 amino acids
Theoretical weight: 9.17 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M4T6Y7 (Residues: 1-78; Coverage: 100%)
Gene names: AOC03_04030, rpmB
Sequence domains: Ribosomal L28 family
Large ribosomal subunit protein uL29 Chain: XE
Molecule details ›
Chain: XE
Length: 65 amino acids
Theoretical weight: 7.52 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M4TBX9 (Residues: 1-65; Coverage: 100%)
Gene names: AOC03_03790, rpmC
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein uL22 Chain: RF
Molecule details ›
Chain: RF
Length: 109 amino acids
Theoretical weight: 11.93 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M4SWS6 (Residues: 1-109; Coverage: 100%)
Gene names: AOC03_03805, rplV
Sequence domains: Ribosomal protein L22p/L17e
Small ribosomal subunit protein bS6 Chain: FG
Molecule details ›
Chain: FG
Length: 134 amino acids
Theoretical weight: 15.84 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M4U628 (Residues: 1-134; Coverage: 100%)
Gene names: AOC03_11090, rpsF
Sequence domains: Ribosomal protein S6
Large ribosomal subunit protein bL27 Chain: VH
Molecule details ›
Chain: VH
Length: 85 amino acids
Theoretical weight: 9.12 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M4TUE5 (Residues: 1-85; Coverage: 100%)
Gene names: AOC03_03315, rpmA
Sequence domains: Ribosomal L27 protein
Large ribosomal subunit protein uL24 Chain: TI
Molecule details ›
Chain: TI
Length: 105 amino acids
Theoretical weight: 11.47 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M4TE60 (Residues: 1-105; Coverage: 100%)
Gene names: AOC03_03775, rplX
Sequence domains:
Large ribosomal subunit protein bL31B Chain: fJ
Molecule details ›
Chain: fJ
Length: 93 amino acids
Theoretical weight: 10.71 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M4SX87 (Residues: 1-93; Coverage: 100%)
Gene names: AOC03_05100, rpmE2
Sequence domains: Ribosomal protein L31
Small ribosomal subunit protein uS14 Chain: HK
Molecule details ›
Chain: HK
Length: 101 amino acids
Theoretical weight: 11.78 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M3V8P8 (Residues: 1-101; Coverage: 100%)
Gene names: AOC03_03765, rpsN
Sequence domains: Ribosomal protein S14p/S29e
Small ribosomal subunit protein uS15 Chain: OL
Molecule details ›
Chain: OL
Length: 88 amino acids
Theoretical weight: 10.22 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M4TF29 (Residues: 1-88; Coverage: 100%)
Gene names: AOC03_06805, rpsO
Sequence domains: Ribosomal protein S15
Small ribosomal subunit protein uS13 Chain: MM
Molecule details ›
Chain: MM
Length: 118 amino acids
Theoretical weight: 13.24 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M5MJL8 (Residues: 1-118; Coverage: 100%)
Gene names: AOC03_03720, rpsM
Sequence domains: Ribosomal protein S13/S18
Large ribosomal subunit protein bL20 Chain: PO
Molecule details ›
Chain: PO
Length: 118 amino acids
Theoretical weight: 13.54 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M5MJR6 (Residues: 1-118; Coverage: 100%)
Gene names: AOC03_05530, rplT
Sequence domains: Ribosomal protein L20
Small ribosomal subunit protein uS19 Chain: SP
Molecule details ›
Chain: SP
Length: 91 amino acids
Theoretical weight: 10.34 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M4TUJ8 (Residues: 1-91; Coverage: 100%)
Gene names: AOC03_03810, rpsS
Sequence domains: Ribosomal protein S19
Small ribosomal subunit protein uS8 Chain: BQ
Molecule details ›
Chain: BQ
Length: 132 amino acids
Theoretical weight: 14.09 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M4U618 (Residues: 1-132; Coverage: 100%)
Gene names: AOC03_03760, rpsH
Sequence domains: Ribosomal protein S8
Large ribosomal subunit protein uL6 Chain: GR
Molecule details ›
Chain: GR
Length: 177 amino acids
Theoretical weight: 19.54 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M5MKV2 (Residues: 1-177; Coverage: 100%)
Gene names: AOC03_03755, rplF
Sequence domains: Ribosomal protein L6
Small ribosomal subunit protein uS7 Chain: GS
Molecule details ›
Chain: GS
Length: 157 amino acids
Theoretical weight: 17.76 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M3V8N5 (Residues: 1-157; Coverage: 100%)
Gene names: AOC03_05000, rpsG
Sequence domains: Ribosomal protein S7p/S5e
Small ribosomal subunit protein uS3 Chain: CT
Molecule details ›
Chain: CT
Length: 241 amino acids
Theoretical weight: 27.12 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M4T6V9 (Residues: 1-241; Coverage: 100%)
Gene names: AOC03_03800, rpsC
Sequence domains:
Small ribosomal subunit protein uS11 Chain: KU
Molecule details ›
Chain: KU
Length: 129 amino acids
Theoretical weight: 13.68 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M3V8P6 (Residues: 1-129; Coverage: 100%)
Gene names: AOC03_03715, rpsK
Sequence domains: Ribosomal protein S11
Small ribosomal subunit protein bS21 Chain: NV
Molecule details ›
Chain: NV
Length: 71 amino acids
Theoretical weight: 8.55 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M4SY21 (Residues: 1-71; Coverage: 100%)
Gene names: AOC03_07600, rpsU
Sequence domains: Ribosomal protein S21
Large ribosomal subunit protein uL30 Chain: YW
Molecule details ›
Chain: YW
Length: 59 amino acids
Theoretical weight: 6.62 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M4SWR7 (Residues: 1-59; Coverage: 100%)
Gene names: AOC03_03740, rpmD
Sequence domains: Ribosomal protein L30p/L7e
Large ribosomal subunit protein uL13 Chain: IX
Molecule details ›
Chain: IX
Length: 142 amino acids
Theoretical weight: 15.8 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M4TBP4 (Residues: 1-142; Coverage: 100%)
Gene names: AOC03_03015, rplM
Sequence domains: Ribosomal protein L13
Small ribosomal subunit protein uS10 Chain: JY
Molecule details ›
Chain: JY
Length: 103 amino acids
Theoretical weight: 11.64 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M4TE68 (Residues: 1-103; Coverage: 100%)
Gene names: AOC03_03835, rpsJ
Sequence domains: Ribosomal protein S10p/S20e
Small ribosomal subunit protein uS17 Chain: QZ
Molecule details ›
Chain: QZ
Length: 91 amino acids
Theoretical weight: 10.36 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M4U401 (Residues: 1-91; Coverage: 100%)
Gene names: AOC03_03785, rpsQ
Sequence domains: Ribosomal protein S17
Large ribosomal subunit protein bL34 Chain: Ba
Molecule details ›
Chain: Ba
Length: 44 amino acids
Theoretical weight: 5.29 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M4TEZ6 (Residues: 1-44; Coverage: 100%)
Gene names: AOC03_06450, rpmH
Sequence domains: Ribosomal protein L34
Large ribosomal subunit protein bL21 Chain: Qb
Molecule details ›
Chain: Qb
Length: 103 amino acids
Theoretical weight: 11.77 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M5TIS3 (Residues: 1-103; Coverage: 100%)
Gene names: AOC03_03320, rplU
Sequence domains: Ribosomal prokaryotic L21 protein
Large ribosomal subunit protein uL18 Chain: Nc
Molecule details ›
Chain: Nc
Length: 116 amino acids
Theoretical weight: 12.55 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M4TUJ2 (Residues: 1-116; Coverage: 100%)
Gene names: AOC03_03750, rplR
Sequence domains: Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
Large ribosomal subunit protein uL15 Chain: Kd
Molecule details ›
Chain: Kd
Length: 146 amino acids
Theoretical weight: 15.45 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M4T6V1 (Residues: 1-146; Coverage: 100%)
Gene names: AOC03_03735, rplO
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein uL14 Chain: Je
Molecule details ›
Chain: Je
Length: 122 amino acids
Theoretical weight: 13.42 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M5MJS2 (Residues: 1-122; Coverage: 100%)
Gene names: AOC03_03780, rplN
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein uL3 Chain: Af
Molecule details ›
Chain: Af
Length: 212 amino acids
Theoretical weight: 22.24 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M4T1M3 (Residues: 1-212; Coverage: 100%)
Gene names: AOC03_03830, rplC
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein uL16 Chain: Lg
Molecule details ›
Chain: Lg
Length: 137 amino acids
Theoretical weight: 15.63 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M3V8J3 (Residues: 1-137; Coverage: 100%)
Gene names: AOC03_03795, rplP
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein bL35 Chain: dh
Molecule details ›
Chain: dh
Length: 65 amino acids
Theoretical weight: 7.59 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M4U4I0 (Residues: 1-65; Coverage: 100%)
Gene names: AOC03_05535, rpmI
Sequence domains: Ribosomal protein L35
Large ribosomal subunit protein bL19 Chain: Oi
Molecule details ›
Chain: Oi
Length: 130 amino acids
Theoretical weight: 14.6 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M4TV08 (Residues: 1-130; Coverage: 100%)
Gene names: AOC03_05630, rplS
Sequence domains: Ribosomal protein L19
Small ribosomal subunit protein bS16 Chain: Pj
Molecule details ›
Chain: Pj
Length: 89 amino acids
Theoretical weight: 9.96 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M4T275 (Residues: 1-89; Coverage: 100%)
Gene names: AOC03_05645, rpsP
Sequence domains: Ribosomal protein S16
Large ribosomal subunit protein bL33 Chain: bk
Molecule details ›
Chain: bk
Length: 51 amino acids
Theoretical weight: 6.05 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M4SWV1 (Residues: 1-51; Coverage: 100%)
Gene names: AOC03_04035, rpmG
Sequence domains: Ribosomal protein L33
Large ribosomal subunit protein uL2 Chain: Cl
Molecule details ›
Chain: Cl
Length: 274 amino acids
Theoretical weight: 30.26 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M3V8Q0 (Residues: 1-274; Coverage: 100%)
Gene names: AOC03_03815, rplB
Sequence domains:
Small ribosomal subunit protein uS4 Chain: Dm
Molecule details ›
Chain: Dm
Length: 213 amino acids
Theoretical weight: 24.28 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M4TE52 (Residues: 1-213; Coverage: 100%)
Gene names: AOC03_03710, rpsD
Sequence domains:
Large ribosomal subunit protein uL23 Chain: Sn
Molecule details ›
Chain: Sn
Length: 116 amino acids
Theoretical weight: 12.82 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M5MJH9 (Residues: 1-116; Coverage: 100%)
Gene names: AOC03_03820, rplW
Sequence domains: Ribosomal protein L23
Small ribosomal subunit protein bS20 Chain: To
Molecule details ›
Chain: To
Length: 88 amino acids
Theoretical weight: 9.98 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M4T3R2 (Residues: 1-88; Coverage: 100%)
Gene names: AOC03_10865, rpsT
Sequence domains: Ribosomal protein S20
Large ribosomal subunit protein bL36 Chain: ep
Molecule details ›
Chain: ep
Length: 38 amino acids
Theoretical weight: 4.33 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M4U3Z5 (Residues: 1-38; Coverage: 100%)
Gene names: AOC03_03725, rpmJ
Sequence domains: Ribosomal protein L36
Large ribosomal subunit protein bL9 Chain: C1
Molecule details ›
Chain: C1
Length: 166 amino acids
Theoretical weight: 18.2 KDa
Source organism: Psychrobacter urativorans
UniProt:
  • Canonical: A0A0M3V9E8 (Residues: 1-166; Coverage: 100%)
Gene names: AOC03_11080, rplI
Sequence domains:
23S ribosomal RNA Chain: Z2
Molecule details ›
Chain: Z2
Length: 2882 nucleotides
Theoretical weight: 933.56 KDa
Sequence domains: Bacterial large subunit ribosomal RNA
5S ribosomal RNA Chain: D8
Molecule details ›
Chain: D8
Length: 115 nucleotides
Theoretical weight: 36.95 KDa
Sequence domains: 5S ribosomal RNA
16S ribosomal RNA Chain: iN
Molecule details ›
Chain: iN
Length: 1590 nucleotides
Theoretical weight: 514.95 KDa
Sequence domains: Bacterial small subunit ribosomal RNA

Ligands and Environments

2 bound ligands:
Ligand GDP 1 x GDP
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 2.74Å
Relevant EMDB volumes: EMD-19077

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