PDB 7rr5 structure summary ‹ Protein Data Bank in Europe (PDBe)

Function and Biology Details

Biochemical function:

structural constituent of ribosome

Biological process:

translation

Cellular component:

ribosome

Sequence domains:

282 more domains

Structure analysis Details

Assembly composition:

hetero 87-mer (preferred)

PDBe Complex ID:

PDB-CPX-249481 (preferred)

Entry contents:

80 distinct polypeptide molecules
7 distinct RNA molecules

Macromolecules (87 distinct):

60S ribosomal protein L2-B Chain: LA

Molecule details ›

Chain: LA
Length: 254 amino acids
Theoretical weight: 27.46 KDa
Source organism: Saccharomyces cerevisiae

RPL3 isoform 1 Chain: LB

Molecule details ›

Chain: LB
Length: 387 amino acids
Theoretical weight: 43.85 KDa
Source organism: Saccharomyces cerevisiae

RPL4A isoform 1 Chain: LC

Molecule details ›

Chain: LC
Length: 362 amino acids
Theoretical weight: 39.16 KDa
Source organism: Saccharomyces cerevisiae

RPL5 isoform 1 Chain: LD

Molecule details ›

Chain: LD
Length: 297 amino acids
Theoretical weight: 33.76 KDa
Source organism: Saccharomyces cerevisiae

60S ribosomal protein L6 Chain: LE

Molecule details ›

Chain: LE
Length: 176 amino acids
Theoretical weight: 20.02 KDa
Source organism: Saccharomyces cerevisiae

60S ribosomal protein L7-A Chain: LF

Molecule details ›

Chain: LF
Length: 244 amino acids
Theoretical weight: 27.69 KDa
Source organism: Saccharomyces cerevisiae

Large ribosomal subunit protein eL8A Chain: LG

Molecule details ›

Chain: LG
Length: 256 amino acids
Theoretical weight: 28.18 KDa
Source organism: Saccharomyces cerevisiae
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 uL6A Chain: LH

Molecule details ›

Chain: LH
Length: 191 amino acids
Theoretical weight: 21.61 KDa
Source organism: Saccharomyces cerevisiae
UniProt:

Canonical: P05738 (Residues: 1-191; Coverage: 100%)

Gene names: RPL8A, RPL9, RPL9A, YGL147C
Sequence domains: Ribosomal protein L6

RPL10 isoform 1 Chain: LI

Molecule details ›

Chain: LI
Length: 221 amino acids
Theoretical weight: 25.41 KDa
Source organism: Saccharomyces cerevisiae

RPL11B isoform 1 Chain: LJ

Molecule details ›

Chain: LJ
Length: 174 amino acids
Theoretical weight: 19.79 KDa
Source organism: Saccharomyces cerevisiae

60S ribosomal protein L13 Chain: LL

Molecule details ›

Chain: LL
Length: 199 amino acids
Theoretical weight: 22.6 KDa
Source organism: Saccharomyces cerevisiae

Large ribosomal subunit protein eL14A Chain: LM

Molecule details ›

Chain: LM
Length: 138 amino acids
Theoretical weight: 15.2 KDa
Source organism: Saccharomyces cerevisiae
UniProt:

Canonical: P36105 (Residues: 1-138; Coverage: 100%)

Gene names: RPL14A, YKL006W, YKL153
Sequence domains:

Large ribosomal subunit protein eL15A Chain: LN

Molecule details ›

Chain: LN
Length: 204 amino acids
Theoretical weight: 24.48 KDa
Source organism: Saccharomyces cerevisiae
UniProt:

Canonical: P05748 (Residues: 1-204; Coverage: 100%)

Gene names: RPL10A, RPL13A, RPL15A, YL10A, YLR029C
Sequence domains: Ribosomal L15

60S ribosomal protein L16-A Chain: LO

Molecule details ›

Chain: LO
Length: 199 amino acids
Theoretical weight: 22.25 KDa
Source organism: Saccharomyces cerevisiae

60S ribosomal protein L17-A Chain: LP

Molecule details ›

Chain: LP
Length: 184 amino acids
Theoretical weight: 20.59 KDa
Source organism: Saccharomyces cerevisiae

60S ribosomal protein L18-B Chain: LQ

Molecule details ›

Chain: LQ
Length: 186 amino acids
Theoretical weight: 20.61 KDa
Source organism: Saccharomyces cerevisiae

Large ribosomal subunit protein eL19A Chain: LR

Molecule details ›

Chain: LR
Length: 189 amino acids
Theoretical weight: 21.76 KDa
Source organism: Saccharomyces cerevisiae
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 eL20A Chain: LS

Molecule details ›

Chain: LS
Length: 172 amino acids
Theoretical weight: 20.48 KDa
Source organism: Saccharomyces cerevisiae
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

60S ribosomal protein L21-A Chain: LT

Molecule details ›

Chain: LT
Length: 160 amino acids
Theoretical weight: 18.28 KDa
Source organism: Saccharomyces cerevisiae

60S ribosomal protein L22-A Chain: LU

Molecule details ›

Chain: LU
Length: 121 amino acids
Theoretical weight: 13.71 KDa
Source organism: Saccharomyces cerevisiae

60S ribosomal protein L23-B Chain: LV

Molecule details ›

Chain: LV
Length: 137 amino acids
Theoretical weight: 14.49 KDa
Source organism: Saccharomyces cerevisiae

RPL24A isoform 1 Chain: LW

Molecule details ›

Chain: LW
Length: 155 amino acids
Theoretical weight: 17.66 KDa
Source organism: Saccharomyces cerevisiae

60S ribosomal protein L25 Chain: LX

Molecule details ›

Chain: LX
Length: 142 amino acids
Theoretical weight: 15.79 KDa
Source organism: Saccharomyces cerevisiae

Large ribosomal subunit protein uL24A Chain: LY

Molecule details ›

Chain: LY
Length: 127 amino acids
Theoretical weight: 14.27 KDa
Source organism: Saccharomyces cerevisiae
UniProt:

Canonical: P05743 (Residues: 1-127; Coverage: 100%)

Gene names: L8300.4, RPL26, RPL26A, RPL33A, YLR344W
Sequence domains:

60S ribosomal protein L27 Chain: LZ

Molecule details ›

Chain: LZ
Length: 136 amino acids
Theoretical weight: 15.57 KDa
Source organism: Saccharomyces cerevisiae

60S ribosomal protein L28 Chain: La

Molecule details ›

Chain: La
Length: 149 amino acids
Theoretical weight: 16.76 KDa
Source organism: Saccharomyces cerevisiae

RPL29 isoform 1 Chain: Lb

Molecule details ›

Chain: Lb
Length: 59 amino acids
Theoretical weight: 6.69 KDa
Source organism: Saccharomyces cerevisiae

Large ribosomal subunit protein eL30 Chain: Lc

Molecule details ›

Chain: Lc
Length: 105 amino acids
Theoretical weight: 11.43 KDa
Source organism: Saccharomyces cerevisiae
UniProt:

Canonical: P14120 (Residues: 1-105; Coverage: 100%)

Gene names: RPL30, RPL32, YGL030W
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family

60S ribosomal protein L31-A Chain: Ld

Molecule details ›

Chain: Ld
Length: 113 amino acids
Theoretical weight: 12.98 KDa
Source organism: Saccharomyces cerevisiae

RPL32 isoform 1 Chain: Le

Molecule details ›

Chain: Le
Length: 130 amino acids
Theoretical weight: 14.81 KDa
Source organism: Saccharomyces cerevisiae

60S ribosomal protein L33-A Chain: Lf

Molecule details ›

Chain: Lf
Length: 107 amino acids
Theoretical weight: 12.18 KDa
Source organism: Saccharomyces cerevisiae

60S ribosomal protein L34-A Chain: Lg

Molecule details ›

Chain: Lg
Length: 121 amino acids
Theoretical weight: 13.67 KDa
Source organism: Saccharomyces cerevisiae

60S ribosomal protein L35-A Chain: Lh

Molecule details ›

Chain: Lh
Length: 120 amino acids
Theoretical weight: 13.94 KDa
Source organism: Saccharomyces cerevisiae

Large ribosomal subunit protein eL36A Chain: Li

Molecule details ›

Chain: Li
Length: 100 amino acids
Theoretical weight: 11.15 KDa
Source organism: Saccharomyces cerevisiae
UniProt:

Canonical: P05745 (Residues: 1-100; Coverage: 100%)

Gene names: RPL36A, RPL39A, YM9646.06, YMR194W
Sequence domains: Ribosomal protein L36e

Ribosomal protein L37 Chain: Lj

Molecule details ›

Chain: Lj
Length: 88 amino acids
Theoretical weight: 9.88 KDa
Source organism: Saccharomyces cerevisiae

RPL38 isoform 1 Chain: Lk

Molecule details ›

Chain: Lk
Length: 78 amino acids
Theoretical weight: 8.85 KDa
Source organism: Saccharomyces cerevisiae

60S ribosomal protein L39 Chain: Ll

Molecule details ›

Chain: Ll
Length: 51 amino acids
Theoretical weight: 6.36 KDa
Source organism: Saccharomyces cerevisiae

Ubiquitin-60S ribosomal protein L40 Chain: Lm

Molecule details ›

Chain: Lm
Length: 128 amino acids
Theoretical weight: 14.58 KDa
Source organism: Saccharomyces cerevisiae

Small ribosomal subunit protein eS32A Chain: Ln

Molecule details ›

Chain: Ln
Length: 25 amino acids
Theoretical weight: 3.35 KDa
Source organism: Saccharomyces cerevisiae
UniProt:

Canonical: P0CX86 (Residues: 1-25; Coverage: 100%)

Gene names: D1290, RPL41A, RPL47A, YDL184C, YL41A
Sequence domains: Ribosomal protein L41

60S ribosomal protein L42-A Chain: Lo

Molecule details ›

Chain: Lo
Length: 106 amino acids
Theoretical weight: 12.25 KDa
Source organism: Saccharomyces cerevisiae

Large ribosomal subunit protein eL43A Chain: Lp

Molecule details ›

Chain: Lp
Length: 92 amino acids
Theoretical weight: 10.11 KDa
Source organism: Saccharomyces cerevisiae
UniProt:

Canonical: P0CX25 (Residues: 1-92; Coverage: 100%)

Gene names: RPL43A, YP9499.02, YPR043W
Sequence domains: Ribosomal L37ae protein family

RPP0 isoform 1 Chain: P0

Molecule details ›

Chain: P0
Length: 312 amino acids
Theoretical weight: 33.75 KDa
Source organism: Saccharomyces cerevisiae

RPL12A isoform 1 Chain: P2

Molecule details ›

Chain: P2
Length: 165 amino acids
Theoretical weight: 17.85 KDa
Source organism: Saccharomyces cerevisiae

40S ribosomal protein S0 Chain: SA

Molecule details ›

Chain: SA
Length: 252 amino acids
Theoretical weight: 28.05 KDa
Source organism: Saccharomyces cerevisiae

RPS1A isoform 1 Chain: SB

Molecule details ›

Chain: SB
Length: 255 amino acids
Theoretical weight: 28.8 KDa
Source organism: Saccharomyces cerevisiae

RPS2 isoform 1 Chain: SC

Molecule details ›

Chain: SC
Length: 254 amino acids
Theoretical weight: 27.49 KDa
Source organism: Saccharomyces cerevisiae

RPS3 isoform 1 Chain: SD

Molecule details ›

Chain: SD
Length: 240 amino acids
Theoretical weight: 26.54 KDa
Source organism: Saccharomyces cerevisiae

40S ribosomal protein S4 Chain: SE

Molecule details ›

Chain: SE
Length: 261 amino acids
Theoretical weight: 29.47 KDa
Source organism: Saccharomyces cerevisiae

Rps5p Chain: SF

Molecule details ›

Chain: SF
Length: 225 amino acids
Theoretical weight: 25.07 KDa
Source organism: Saccharomyces cerevisiae
UniProt:

Canonical: A0A1L4AA68 (Residues: 1-225; Coverage: 100%)

Gene name: RPS5
Sequence domains: Ribosomal protein S7p/S5e

40S ribosomal protein S6 Chain: SG

Molecule details ›

Chain: SG
Length: 236 amino acids
Theoretical weight: 27.05 KDa
Source organism: Saccharomyces cerevisiae

40S ribosomal protein S7 Chain: SH

Molecule details ›

Chain: SH
Length: 190 amino acids
Theoretical weight: 21.66 KDa
Source organism: Saccharomyces cerevisiae

RPS8A isoform 1 Chain: SI

Molecule details ›

Chain: SI
Length: 200 amino acids
Theoretical weight: 22.54 KDa
Source organism: Saccharomyces cerevisiae

40S ribosomal protein S9-A Chain: SJ

Molecule details ›

Chain: SJ
Length: 197 amino acids
Theoretical weight: 22.49 KDa
Source organism: Saccharomyces cerevisiae

40S ribosomal protein S10-A Chain: SK

Molecule details ›

Chain: SK
Length: 105 amino acids
Theoretical weight: 12.76 KDa
Source organism: Saccharomyces cerevisiae

40S ribosomal protein S11-B Chain: SL

Molecule details ›

Chain: SL
Length: 156 amino acids
Theoretical weight: 17.79 KDa
Source organism: Saccharomyces cerevisiae

40S ribosomal protein S12 Chain: SM

Molecule details ›

Chain: SM
Length: 143 amino acids
Theoretical weight: 15.49 KDa
Source organism: Saccharomyces cerevisiae

40S ribosomal protein S13 Chain: SN

Molecule details ›

Chain: SN
Length: 151 amino acids
Theoretical weight: 17.06 KDa
Source organism: Saccharomyces cerevisiae

40S ribosomal protein S14-B Chain: SO

Molecule details ›

Chain: SO
Length: 138 amino acids
Theoretical weight: 14.68 KDa
Source organism: Saccharomyces cerevisiae

RPS15 isoform 1 Chain: SP

Molecule details ›

Chain: SP
Length: 142 amino acids
Theoretical weight: 16.03 KDa
Source organism: Saccharomyces cerevisiae

40S ribosomal protein S16-A Chain: SQ

Molecule details ›

Chain: SQ
Length: 143 amino acids
Theoretical weight: 15.88 KDa
Source organism: Saccharomyces cerevisiae

40S ribosomal protein S17-A Chain: SR

Molecule details ›

Chain: SR
Length: 136 amino acids
Theoretical weight: 15.82 KDa
Source organism: Saccharomyces cerevisiae

40S ribosomal protein S18-B Chain: SS

Molecule details ›

Chain: SS
Length: 146 amino acids
Theoretical weight: 17.07 KDa
Source organism: Saccharomyces cerevisiae

40S ribosomal protein S19-A Chain: ST

Molecule details ›

Chain: ST
Length: 144 amino acids
Theoretical weight: 15.94 KDa
Source organism: Saccharomyces cerevisiae

RPS20 isoform 1 Chain: SU

Molecule details ›

Chain: SU
Length: 121 amino acids
Theoretical weight: 13.93 KDa
Source organism: Saccharomyces cerevisiae

Small ribosomal subunit protein eS21A Chain: SV

Molecule details ›

Chain: SV
Length: 87 amino acids
Theoretical weight: 9.76 KDa
Source organism: Saccharomyces cerevisiae
UniProt:

Canonical: P0C0V8 (Residues: 1-87; Coverage: 100%)

Gene names: RPS21A, RPS25, RPS25A, RPS26A, YKR057W
Sequence domains: Ribosomal protein S21e

RPS22A isoform 1 Chain: SW

Molecule details ›

Chain: SW
Length: 130 amino acids
Theoretical weight: 14.65 KDa
Source organism: Saccharomyces cerevisiae

40S ribosomal protein S23 Chain: SX

Molecule details ›

Chain: SX
Length: 145 amino acids
Theoretical weight: 16.07 KDa
Source organism: Saccharomyces cerevisiae

40S ribosomal protein S24 Chain: SY

Molecule details ›

Chain: SY
Length: 135 amino acids
Theoretical weight: 15.36 KDa
Source organism: Saccharomyces cerevisiae

RPS25A isoform 1 Chain: SZ

Molecule details ›

Chain: SZ
Length: 108 amino acids
Theoretical weight: 12.07 KDa
Source organism: Saccharomyces cerevisiae

RPS26B isoform 1 Chain: Sa

Molecule details ›

Chain: Sa
Length: 119 amino acids
Theoretical weight: 13.48 KDa
Source organism: Saccharomyces cerevisiae

Small ribosomal subunit protein eS27A Chain: Sb

Molecule details ›

Chain: Sb
Length: 82 amino acids
Theoretical weight: 8.89 KDa
Source organism: Saccharomyces cerevisiae
UniProt:

Canonical: P35997 (Residues: 1-82; Coverage: 100%)

Gene names: RPS27A, YKL156W
Sequence domains: Ribosomal protein S27

RPS28A isoform 1 Chain: Sc

Molecule details ›

Chain: Sc
Length: 67 amino acids
Theoretical weight: 7.61 KDa
Source organism: Saccharomyces cerevisiae

RPS29A isoform 1 Chain: Sd

Molecule details ›

Chain: Sd
Length: 56 amino acids
Theoretical weight: 6.68 KDa
Source organism: Saccharomyces cerevisiae

40S ribosomal protein S30 Chain: Se

Molecule details ›

Chain: Se
Length: 63 amino acids
Theoretical weight: 7.14 KDa
Source organism: Saccharomyces cerevisiae

Ubiquitin-40S ribosomal protein S31 Chain: Sf

Molecule details ›

Chain: Sf
Length: 152 amino acids
Theoretical weight: 17.25 KDa
Source organism: Saccharomyces cerevisiae

Guanine nucleotide-binding protein subunit beta-like protein Chain: Sg

Molecule details ›

Chain: Sg
Length: 319 amino acids
Theoretical weight: 34.84 KDa
Source organism: Saccharomyces cerevisiae

Eukaryotic translation initiation factor 5A Chain: 5

Molecule details ›

Chain: 5
Length: 157 amino acids
Theoretical weight: 17.22 KDa
Source organism: Saccharomyces cerevisiae

Ribosome-interacting GTPase 1 Chain: R

Molecule details ›

Chain: R
Length: 410 amino acids
Theoretical weight: 45.47 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae

Translation machinery-associated protein 46 Chain: T

Molecule details ›

Chain: T
Length: 345 amino acids
Theoretical weight: 39.59 KDa
Source organism: Saccharomyces cerevisiae

60S ribosomal protein L1 Chain: L1

Molecule details ›

Chain: L1
Length: 210 amino acids
Theoretical weight: 17.89 KDa
Source organism: Saccharomyces cerevisiae

25S ribosomal RNA Chain: C1

Molecule details ›

Chain: C1
Length: 3396 nucleotides
Theoretical weight: 1097.49 KDa
Sequence domains: Eukaryotic large subunit ribosomal RNA

5S ribosomal RNA Chain: C4

Molecule details ›

Chain: C4
Length: 121 nucleotides
Theoretical weight: 38.95 KDa
Sequence domains: 5S ribosomal RNA

5.8S ribosomal RNA Chain: C3

Molecule details ›

Chain: C3
Length: 158 nucleotides
Theoretical weight: 50.68 KDa
Sequence domains: 5.8S ribosomal RNA

18S Ribosomal RNA Chain: C2

Molecule details ›

Chain: C2
Length: 1800 nucleotides
Theoretical weight: 579.76 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA

A-tRNA Chain: A

Molecule details ›

Chain: A
Length: 76 nucleotides
Theoretical weight: 24.36 KDa
Sequence domains: tRNA

P-tRNA Chain: P

Molecule details ›

Chain: P
Length: 76 nucleotides
Theoretical weight: 24.45 KDa
Sequence domains: tRNA

Messenger RNA Chain: m

Molecule details ›

Chain: m
Length: 16 nucleotides
Theoretical weight: 5.23 KDa

Ligands and Environments

3 bound ligands:

1 modified residue:

Experiments and Validation Details

Resolution: 3.23Å

Relevant EMDB volumes: EMD-24652

Expression system: Saccharomyces cerevisiae

Protein Data Bank in Europe

Structure of ribosomal complex bound with Rbg1/Tma46

Function and Biology Details

Structure analysis Details

Ligands and Environments

Experiments and Validation Details

Quick links

Citations

1 review citation

2 mentions without citation

PDBe › 7rr5

Structure of ribosomal complex bound with Rbg1/Tma46

Function and Biology Details

Structure analysis Details

Ligands and Environments

Experiments and Validation Details

Quick links

Citations

1 review citation

2 mentions without citation