4V88 image
Entry Detail
PDB ID:
4V88
Keywords:
Title:
The structure of the eukaryotic ribosome at 3.0 A resolution.
Biological Source:
PDB Version:
Deposition Date:
2011-10-11
Release Date:
2014-07-09
Method Details:
Experimental Method:
Resolution:
3.00 Å
R-Value Free:
0.22
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polyribonucleotide
Description:25S rRNA
Chain IDs:JA (auth: A1), KD (auth: A5)
Chain Length:3396
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Description:18S RIBOSOMAL RNA
Chain IDs:A (auth: A2)
Chain Length:1800
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Description:5S rRNA
Chain IDs:KA (auth: A3), LD (auth: A7)
Chain Length:121
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Description:5.8S rRNA
Chain IDs:LA (auth: A4), MD (auth: A8)
Chain Length:158
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polyribonucleotide
Description:18S rRNA
Chain IDs:BC (auth: A6)
Chain Length:1800
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S0-A
Chain IDs:B (auth: AA), CC (auth: CA)
Chain Length:119
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S1-A
Chain IDs:C (auth: AB), DC (auth: CB)
Chain Length:82
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S2
Chain IDs:D (auth: AC), EC (auth: CC)
Chain Length:254
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S3
Chain IDs:E (auth: AD), FC (auth: CD)
Chain Length:56
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S4-A
Chain IDs:F (auth: AE), GC (auth: CE)
Chain Length:63
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S5
Chain IDs:G (auth: AF), HC (auth: CF)
Chain Length:152
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S6-A
Chain IDs:H (auth: AG), IC (auth: CG)
Chain Length:236
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S7-A
Chain IDs:I (auth: AH), JC (auth: CH)
Chain Length:273
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S8-A
Chain IDs:J (auth: AI), KC (auth: CI)
Chain Length:200
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S9-A
Chain IDs:K (auth: AJ), LC (auth: CJ)
Chain Length:197
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S10-A
Chain IDs:L (auth: AK), MC (auth: CK)
Chain Length:105
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S11-A
Chain IDs:M (auth: AL), NC (auth: CL)
Chain Length:156
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S12
Chain IDs:N (auth: AM), OC (auth: CM)
Chain Length:143
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S13
Chain IDs:O (auth: AN), PC (auth: CN)
Chain Length:151
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S14-A
Chain IDs:P (auth: AO), QC (auth: CO)
Chain Length:137
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S15
Chain IDs:Q (auth: AP), RC (auth: CP)
Chain Length:142
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S16-A
Chain IDs:R (auth: AQ), SC (auth: CQ)
Chain Length:143
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S17-A
Chain IDs:S (auth: AR), TC (auth: CR)
Chain Length:136
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S18-A
Chain IDs:T (auth: AS), UC (auth: CS)
Chain Length:146
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S19-A
Chain IDs:U (auth: AT), VC (auth: CT)
Chain Length:144
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S20
Chain IDs:V (auth: AU), WC (auth: CU)
Chain Length:121
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S21-A
Chain IDs:W (auth: AV), XC (auth: CV)
Chain Length:87
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S22-A
Chain IDs:X (auth: AW), YC (auth: CW)
Chain Length:130
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S23-A
Chain IDs:Y (auth: AX), ZC (auth: CX)
Chain Length:145
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S24-A
Chain IDs:Z (auth: AY), AD (auth: CY)
Chain Length:135
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S25-A
Chain IDs:AA (auth: AZ), BD (auth: CZ)
Chain Length:108
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S26-A
Chain IDs:BA (auth: Aa), CD (auth: Ca)
Chain Length:119
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S27-A
Chain IDs:CA (auth: Ab), DD (auth: Cb)
Chain Length:82
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S28-A
Chain IDs:DA (auth: Ac), ED (auth: Cc)
Chain Length:254
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S29-A
Chain IDs:EA (auth: Ad), FD (auth: Cd)
Chain Length:56
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S30-A
Chain IDs:FA (auth: Ae), GD (auth: Ce)
Chain Length:63
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:40S ribosomal protein S31
Chain IDs:GA (auth: Af), HD (auth: Cf)
Chain Length:152
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:Guanine nucleotide-binding protein subunit beta-like protein (ASC1, RACK1)
Chain IDs:HA (auth: Ag), ID (auth: Cg)
Chain Length:236
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:Suppressor protein STM1
Chain IDs:IA (auth: Ah)
Chain Length:273
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L2-A
Chain IDs:MA (auth: BA), ND (auth: DA)
Chain Length:254
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L3
Chain IDs:NA (auth: BB), OD (auth: DB)
Chain Length:387
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L4-A
Chain IDs:OA (auth: BC), PD (auth: DC)
Chain Length:105
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L5
Chain IDs:PA (auth: BD), QD (auth: DD)
Chain Length:113
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L6-A
Chain IDs:QA (auth: BE), RD (auth: DE)
Chain Length:130
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L7-A
Chain IDs:RA (auth: BF), SD (auth: DF)
Chain Length:107
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L8-A
Chain IDs:SA (auth: BG), TD (auth: DG)
Chain Length:256
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L9-A
Chain IDs:TA (auth: BH), UD (auth: DH)
Chain Length:120
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L10
Chain IDs:UA (auth: BI), VD (auth: DI)
Chain Length:100
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L11-A
Chain IDs:VA (auth: BJ), WD (auth: DJ)
Chain Length:174
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L13-A
Chain IDs:WA (auth: BL), YD (auth: DL)
Chain Length:51
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L14-A
Chain IDs:XA (auth: BM), ZD (auth: DM)
Chain Length:128
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L15-A
Chain IDs:YA (auth: BN), AE (auth: DN)
Chain Length:25
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L16-A, 60S ribosomal protein L16-B
Chain IDs:ZA (auth: BO), BE (auth: DO)
Chain Length:106
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L17-A
Chain IDs:AB (auth: BP), CE (auth: DP)
Chain Length:92
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L18-A
Chain IDs:BB (auth: BQ), DE (auth: DQ)
Chain Length:186
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L19-A
Chain IDs:CB (auth: BR), EE (auth: DR)
Chain Length:189
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L20-A
Chain IDs:DB (auth: BS), FE (auth: DS)
Chain Length:172
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L21-A
Chain IDs:EB (auth: BT), GE (auth: DT)
Chain Length:160
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L22-A
Chain IDs:FB (auth: BU), HE (auth: DU)
Chain Length:121
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L23-A
Chain IDs:GB (auth: BV), IE (auth: DV)
Chain Length:137
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L24-A
Chain IDs:HB (auth: BW), JE (auth: DW)
Chain Length:155
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L25
Chain IDs:IB (auth: BX), KE (auth: DX)
Chain Length:142
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L26-A
Chain IDs:JB (auth: BY), LE (auth: DY)
Chain Length:127
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L27-A
Chain IDs:KB (auth: BZ), ME (auth: DZ)
Chain Length:136
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L28
Chain IDs:LB (auth: Ba), NE (auth: Da)
Chain Length:254
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L29
Chain IDs:MB (auth: Bb), OE (auth: Db)
Chain Length:387
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L30
Chain IDs:NB (auth: Bc), PE (auth: Dc)
Chain Length:105
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L31-A
Chain IDs:OB (auth: Bd), QE (auth: Dd)
Chain Length:113
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L32
Chain IDs:PB (auth: Be), RE (auth: De)
Chain Length:130
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L33-A
Chain IDs:QB (auth: Bf), SE (auth: Df)
Chain Length:107
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L34-A
Chain IDs:RB (auth: Bg), TE (auth: Dg)
Chain Length:256
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L35-A
Chain IDs:SB (auth: Bh), UE (auth: Dh)
Chain Length:120
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L36-A
Chain IDs:TB (auth: Bi), VE (auth: Di)
Chain Length:100
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L37-A
Chain IDs:UB (auth: Bj), WE (auth: Dj)
Chain Length:174
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L38
Chain IDs:VB (auth: Bk), XE (auth: Dk)
Chain Length:78
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L39
Chain IDs:WB (auth: Bl), YE (auth: Dl)
Chain Length:51
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L40
Chain IDs:XB (auth: Bm), ZE (auth: Dm)
Chain Length:128
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L41-A
Chain IDs:YB (auth: Bn), AF (auth: Dn)
Chain Length:25
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L42-A
Chain IDs:ZB (auth: Bo), BF (auth: Do)
Chain Length:106
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S ribosomal protein L43-A
Chain IDs:AC (auth: Bp), CF (auth: Dp)
Chain Length:92
Number of Molecules:2
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:Ribosomal protein L12
Chain IDs:XD (auth: DK)
Chain Length:78
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:60S acidic ribosomal protein P0
Chain IDs:DF (auth: Dq)
Chain Length:312
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:Ribosomal protein P1 alpha
Chain IDs:EF (auth: Dr)
Chain Length:189
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Polymer Type:polypeptide(L)
Description:Ribosomal protein P2 beta
Chain IDs:FF (auth: Ds)
Chain Length:46
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
Primary Citation
The structure of the eukaryotic ribosome at 3.0 angstrom resolution.
Science 334 1524 1529 (2011)
PMID: 22096102

Abstact

Ribosomes translate genetic information encoded by messenger RNA into proteins. Many aspects of translation and its regulation are specific to eukaryotes, whose ribosomes are much larger and intricate than their bacterial counterparts. We report the crystal structure of the 80S ribosome from the yeast Saccharomyces cerevisiae--including nearly all ribosomal RNA bases and protein side chains as well as an additional protein, Stm1--at a resolution of 3.0 angstroms. This atomic model reveals the architecture of eukaryote-specific elements and their interaction with the universally conserved core, and describes all eukaryote-specific bridges between the two ribosomal subunits. It forms the structural framework for the design and analysis of experiments that explore the eukaryotic translation apparatus and the evolutionary forces that shaped it.

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Primary Citation of related structures