4V5Z image
Deposition Date 2008-03-27
Release Date 2014-07-09
Last Version Date 2024-03-20
Entry Detail
PDB ID:
4V5Z
Keywords:
RIBOSOMAL PROTEIN/RNA
Title:
Structure of a mammalian 80S ribosome obtained by docking homology models of the RNA and proteins into an 8.7 A cryo-EM map
Biological Source:
Source Organism:
Canis familiaris (Taxon ID: 9615)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
8.70 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
4V5Z validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:18S Ribosomal RNA
Chain IDs:A (auth: AA)
Chain Length:1563
Number of Molecules:1
Biological Source:Canis familiaris
Polymer Type:polyribonucleotide
Molecule:RNA Expansion segment ES3
Chain IDs:B (auth: AB)
Chain Length:35
Number of Molecules:1
Biological Source:Canis familiaris
Polymer Type:polyribonucleotide
Molecule:RNA Expansion segment ES4
Chain IDs:C (auth: AC)
Chain Length:243
Number of Molecules:1
Biological Source:Canis familiaris
Polymer Type:polyribonucleotide
Molecule:RNA Expansion segment ES6 part I
Chain IDs:D (auth: AD)
Chain Length:42
Number of Molecules:1
Biological Source:Canis familiaris
Polymer Type:polyribonucleotide
Molecule:RNA Expansion segment ES6 part II
Chain IDs:E (auth: AE)
Chain Length:179
Number of Molecules:1
Biological Source:Canis familiaris
Polymer Type:polyribonucleotide
Molecule:RNA Expansion segment ES9
Chain IDs:F (auth: AF)
Chain Length:31
Number of Molecules:1
Biological Source:Canis familiaris
Polymer Type:polyribonucleotide
Molecule:RNA helix
Chain IDs:G (auth: AG)
Chain Length:14
Number of Molecules:1
Biological Source:Canis familiaris
Polymer Type:polyribonucleotide
Molecule:RNA helix
Chain IDs:H (auth: AH)
Chain Length:130
Number of Molecules:1
Biological Source:Canis familiaris
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S Ribosomal protein RACK1
Chain IDs:I (auth: Aa)
Chain Length:1563
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P63244 Pfam ID:PF00400
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S Ribosomal protein SA
Chain IDs:J (auth: Ab)
Chain Length:35
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P08865 Pfam ID:PF00318, PF16122
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S Ribosomal protein S3e
Chain IDs:K (auth: Ac)
Chain Length:243
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P05750 Pfam ID:PF07650, PF00189
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S Ribosomal protein S9e
Chain IDs:L (auth: Ad)
Chain Length:42
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P0CX35 Pfam ID:PF01479
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S Ribosomal protein S2e
Chain IDs:M (auth: Ae)
Chain Length:179
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P25443 Pfam ID:PF00333, PF03719
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S Ribosomal protein S5e
Chain IDs:N (auth: Ag)
Chain Length:14
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P26783 Pfam ID:PF00177
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S Ribosomal protein S15ae
Chain IDs:O (auth: Ah)
Chain Length:130
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P0C0W1 Pfam ID:PF00410
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S Ribosomal protein S16e
Chain IDs:P (auth: Ai)
Chain Length:146
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P0CX51 Pfam ID:PF00380
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S Ribosomal protein S20e
Chain IDs:Q (auth: Aj)
Chain Length:119
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P38701 Pfam ID:PF00338
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S Ribosomal protein S14e
Chain IDs:R (auth: Ak)
Chain Length:151
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P06367 Pfam ID:PF00411
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S Ribosomal protein S23e
Chain IDs:S (auth: Al)
Chain Length:143
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P0CX29 Pfam ID:PF00164
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S Ribosomal protein S18e
Chain IDs:T (auth: Am)
Chain Length:152
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P0CX55 Pfam ID:PF00416
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S Ribosomal protein S29e
Chain IDs:U (auth: An)
Chain Length:56
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P41057 Pfam ID:PF00253
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S Ribosomal protein S13e
Chain IDs:V (auth: Ao)
Chain Length:89
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P05756 Pfam ID:PF00312
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S Ribosomal protein S11e
Chain IDs:W (auth: Aq)
Chain Length:158
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P0CX47 Pfam ID:PF16205, PF00366
Protein Blast
Polymer Type:polypeptide(L)
Molecule:40S Ribosomal protein S15e
Chain IDs:X (auth: As)
Chain Length:145
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:Q01855 Pfam ID:PF00203
Polymer Type:polyribonucleotide
Molecule:28S Ribosomal RNA
Chain IDs:Z (auth: B0)
Chain Length:2903
Number of Molecules:1
Biological Source:canis familiaris
Polymer Type:polyribonucleotide
Molecule:5.8S Ribosomal RNA
Chain IDs:Y (auth: B1)
Chain Length:123
Number of Molecules:1
Biological Source:canis familiaris
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S Ribosomal protein L37e
Chain IDs:DC (auth: B2)
Chain Length:97
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P49166 Pfam ID:PF01907
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S Ribosomal protein L39e
Chain IDs:EC (auth: B3)
Chain Length:51
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P04650 Pfam ID:PF00832
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S Ribosomal protein L44e
Chain IDs:FC (auth: B4)
Chain Length:106
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P0CX27 Pfam ID:PF00935
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S Ribosomal protein L10a
Chain IDs:GC (auth: B5)
Chain Length:212
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P0CX43 Pfam ID:PF00687
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S Ribosomal protein L30e
Chain IDs:HC (auth: B6)
Chain Length:115
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P14120 Pfam ID:PF01248
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S Ribosomal protein L19
Chain IDs:QB (auth: B7)
Chain Length:13
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P0CX82 Pfam ID:PF01280
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S Ribosomal protein L35
Chain IDs:XB (auth: B8)
Chain Length:10
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P0CX84 Pfam ID:PF00831
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S Ribosomal protein L32
Chain IDs:BC (auth: B9)
Chain Length:58
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P38061 Pfam ID:PF01655
Polymer Type:polyribonucleotide
Molecule:RNA Expansion segment ES3
Chain IDs:AA (auth: BA)
Chain Length:21
Number of Molecules:1
Biological Source:Canis familiaris
Polymer Type:polyribonucleotide
Molecule:RNA Expansion segment ES4
Chain IDs:BA (auth: BB)
Chain Length:403
Number of Molecules:1
Biological Source:Canis familiaris
Polymer Type:polyribonucleotide
Molecule:RNA Expansion segment ES5
Chain IDs:CA (auth: BC)
Chain Length:17
Number of Molecules:1
Biological Source:Canis familiaris
Polymer Type:polyribonucleotide
Molecule:RNA Expansion segment ES7 part I
Chain IDs:DA (auth: BD)
Chain Length:178
Number of Molecules:1
Biological Source:Canis familiaris
Polymer Type:polyribonucleotide
Molecule:RNA Expansion segment ES7 part II
Chain IDs:EA (auth: BE)
Chain Length:192
Number of Molecules:1
Biological Source:Canis familiaris
Polymer Type:polyribonucleotide
Molecule:RNA Expansion segment ES7 part III
Chain IDs:FA (auth: BF)
Chain Length:120
Number of Molecules:1
Biological Source:Canis familiaris
Polymer Type:polyribonucleotide
Molecule:RNA Expansion segment ES9
Chain IDs:GA (auth: BG)
Chain Length:317
Number of Molecules:1
Biological Source:Canis familiaris
Polymer Type:polyribonucleotide
Molecule:RNA Expansion segment ES12
Chain IDs:HA (auth: BH)
Chain Length:25
Number of Molecules:1
Biological Source:Canis familiaris
Polymer Type:polyribonucleotide
Molecule:RNA Expansion segment ES15 part I
Chain IDs:IA (auth: BI)
Chain Length:165
Number of Molecules:1
Biological Source:Canis familiaris
Polymer Type:polyribonucleotide
Molecule:RNA Expansion segment ES15 part II
Chain IDs:JA (auth: BJ)
Chain Length:203
Number of Molecules:1
Biological Source:Canis familiaris
Polymer Type:polyribonucleotide
Molecule:RNA Expansion segment ES19
Chain IDs:KA (auth: BK)
Chain Length:26
Number of Molecules:1
Biological Source:Canis familiaris
Polymer Type:polyribonucleotide
Molecule:RNA Expansion segment ES20
Chain IDs:LA (auth: BL)
Chain Length:148
Number of Molecules:1
Biological Source:Canis familiaris
Polymer Type:polyribonucleotide
Molecule:RNA Expansion segment ES24
Chain IDs:MA (auth: BM)
Chain Length:19
Number of Molecules:1
Biological Source:Canis familiaris
Polymer Type:polyribonucleotide
Molecule:RNA Expansion segment ES27
Chain IDs:NA (auth: BN)
Chain Length:78
Number of Molecules:1
Biological Source:Canis familiaris
Polymer Type:polyribonucleotide
Molecule:RNA Expansion segment ES30
Chain IDs:OA (auth: BO)
Chain Length:188
Number of Molecules:1
Biological Source:Canis familiaris
Polymer Type:polyribonucleotide
Molecule:RNA Expansion segment ES31 part I
Chain IDs:PA (auth: BP)
Chain Length:196
Number of Molecules:1
Biological Source:Canis familiaris
Polymer Type:polyribonucleotide
Molecule:RNA Expansion segment ES31 part II
Chain IDs:QA (auth: BQ)
Chain Length:30
Number of Molecules:1
Biological Source:Canis familiaris
Polymer Type:polyribonucleotide
Molecule:RNA Expansion segment ES39 part I
Chain IDs:RA (auth: BR)
Chain Length:184
Number of Molecules:1
Biological Source:Canis familiaris
Polymer Type:polyribonucleotide
Molecule:RNA Expansion segment ES39 part II
Chain IDs:SA (auth: BS)
Chain Length:38
Number of Molecules:1
Biological Source:Canis familiaris
Polymer Type:polyribonucleotide
Molecule:RNA Expansion segment ES39 part III
Chain IDs:TA (auth: BT)
Chain Length:30
Number of Molecules:1
Biological Source:Canis familiaris
Polymer Type:polyribonucleotide
Molecule:RNA Expansion segment ES41
Chain IDs:UA (auth: BU)
Chain Length:157
Number of Molecules:1
Biological Source:Canis familiaris
Polymer Type:polyribonucleotide
Molecule:RNA Expansion segment ES9 part2
Chain IDs:VA (auth: BV)
Chain Length:22
Number of Molecules:1
Biological Source:Canis familiaris
Polymer Type:polyribonucleotide
Molecule:RNA Expansion segment ES10
Chain IDs:WA (auth: BW)
Chain Length:270
Number of Molecules:1
Biological Source:Canis familiaris
Polymer Type:polyribonucleotide
Molecule:RNA helices
Chain IDs:XA (auth: BX)
Chain Length:125
Number of Molecules:1
Biological Source:Canis familiaris
Polymer Type:polyribonucleotide
Molecule:5S Ribosomal RNA
Chain IDs:YA (auth: BY)
Chain Length:135
Number of Molecules:1
Biological Source:Canis familiaris
Polymer Type:polyribonucleotide
Molecule:E site t-RNA
Chain IDs:ZA (auth: BZ)
Chain Length:92
Number of Molecules:1
Biological Source:Canis familiaris
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S Ribosomal protein L8
Chain IDs:AB (auth: Ba)
Chain Length:21
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P0CX45 Pfam ID:PF00181, PF03947
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S Ribosomal protein L3
Chain IDs:BB (auth: Bb)
Chain Length:403
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P14126 Pfam ID:PF00297
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S Ribosomal protein L4
Chain IDs:CB (auth: Bc)
Chain Length:17
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P10664 Pfam ID:PF00573, PF14374
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S Ribosomal protein L11
Chain IDs:DB (auth: Bd)
Chain Length:178
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P0C0W9 Pfam ID:PF00281, PF00673
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S Ribosomal protein L9
Chain IDs:EB (auth: Be)
Chain Length:192
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P05738 Pfam ID:PF00347
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S Ribosomal protein L7a
Chain IDs:FB (auth: Bf)
Chain Length:120
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P17076 Pfam ID:PF01248
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S acidic ribosomal protein P0
Chain IDs:GB (auth: Bg)
Chain Length:317
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P05317 Pfam ID:PF00466, PF17777, PF00428
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S Ribosomal protein L10
Chain IDs:HB (auth: Bh)
Chain Length:25
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P41805 Pfam ID:PF00252
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S Ribosomal protein L12
Chain IDs:IB (auth: Bi)
Chain Length:165
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P0CX53 Pfam ID:PF03946, PF00298
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L13a
Chain IDs:JB (auth: Bj)
Chain Length:203
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P26784 Pfam ID:PF00572
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S Ribosomal protein L23
Chain IDs:KB (auth: Bk)
Chain Length:26
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P0CX41 Pfam ID:PF00238
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S Ribosomal protein L27a
Chain IDs:LB (auth: Bl)
Chain Length:148
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P02406 Pfam ID:PF00828
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S Ribosomal protein L15e
Chain IDs:MB (auth: Bm)
Chain Length:19
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P05748 Pfam ID:PF00827
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S Ribosomal protein L5
Chain IDs:NB (auth: Bn)
Chain Length:78
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P26321 Pfam ID:PF17144, PF14204
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S Ribosomal protein L18
Chain IDs:OB (auth: Bo)
Chain Length:188
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P0CX49 Pfam ID:PF17135
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S Ribosomal protein L19
Chain IDs:PB (auth: Bp)
Chain Length:196
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P0CX82 Pfam ID:PF01280
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S Ribosomal protein L21
Chain IDs:RB (auth: Bq)
Chain Length:30
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:Q02753 Pfam ID:PF01157
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S Ribosomal protein L17
Chain IDs:SB (auth: Br)
Chain Length:184
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P05740 Pfam ID:PF00237
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S Ribosomal protein L23a
Chain IDs:TB (auth: Bs)
Chain Length:38
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P04456 Pfam ID:PF03939, PF00276
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S Ribosomal protein L26
Chain IDs:UB (auth: Bt)
Chain Length:30
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P05743 Pfam ID:PF16906, PF00467
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S Ribosomal protein L24
Chain IDs:VB (auth: Bu)
Chain Length:157
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P04449 Pfam ID:PF01246
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S Ribosomal protein L35
Chain IDs:WB (auth: Bv)
Chain Length:22
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P0CX84 Pfam ID:PF00831
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S Ribosomal protein L7
Chain IDs:YB (auth: Bw)
Chain Length:270
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P05737 Pfam ID:PF08079, PF00327
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S Ribosomal protein L31
Chain IDs:ZB (auth: Bx)
Chain Length:125
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P0C2H8 Pfam ID:PF01198
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S Ribosomal protein L32
Chain IDs:AC (auth: By)
Chain Length:135
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P38061 Pfam ID:PF01655
Protein Blast
Polymer Type:polypeptide(L)
Molecule:60S Ribosomal protein L37a
Chain IDs:CC (auth: Bz)
Chain Length:92
Number of Molecules:1
Biological Source:Canis familiaris
UniProt ID:P0CX25 Pfam ID:PF01780
Ligand Molecules
NA
Primary Citation
Structure of the Mammalian 80S Ribosome at 8.7 A Resolution
Structure 16 535 548 (2008)
PMID: 18400176 DOI: 10.1016/j.str.2008.01.007

Abstact

In this paper, we present a structure of the mammalian ribosome determined at approximately 8.7 A resolution by electron cryomicroscopy and single-particle methods. A model of the ribosome was created by docking homology models of subunit rRNAs and conserved proteins into the density map. We then modeled expansion segments in the subunit rRNAs and found unclaimed density for approximately 20 proteins. In general, many conserved proteins and novel proteins interact with expansion segments to form an integrated framework that may stabilize the mature ribosome. Our structure provides a snapshot of the mammalian ribosome at the beginning of translation and lends support to current models in which large movements of the small subunit and L1 stalk occur during tRNA translocation. Finally, details are presented for intersubunit bridges that are specific to the eukaryotic ribosome. We suggest that these bridges may help reset the conformation of the ribosome to prepare for the next cycle of chain elongation.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
4V5Z
2ZKQ
2ZKR
2ZKR