4V7H image
Deposition Date 2009-09-22
Release Date 2014-07-09
Last Version Date 2024-02-28
Entry Detail
PDB ID:
4V7H
Keywords:
RIBOSOME
Title:
Structure of the 80S rRNA and proteins and P/E tRNA for eukaryotic ribosome based on cryo-EM map of Thermomyces lanuginosus ribosome at 8.9A resolution
Biological Source:
Source Organism:
Thermomyces lanuginosus (Taxon ID: 5541)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
8.90 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
4V7H validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:P/E tRNA
Chain IDs:S (auth: A7)
Chain Length:76
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polyribonucleotide
Molecule:18S rRNA
Chain IDs:A (auth: AA)
Chain Length:1761
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S0(A)
Chain IDs:B (auth: AB)
Chain Length:193
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S3
Chain IDs:C (auth: AC)
Chain Length:188
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S9(A)
Chain IDs:D (auth: AD)
Chain Length:158
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S2
Chain IDs:E (auth: AE)
Chain Length:162
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S5
Chain IDs:F (auth: AG)
Chain Length:186
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S22(A)
Chain IDs:G (auth: AH)
Chain Length:125
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S16(A)
Chain IDs:H (auth: AI)
Chain Length:138
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S20
Chain IDs:I (auth: AJ)
Chain Length:96
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S14(A)
Chain IDs:J (auth: AK)
Chain Length:125
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S23(A)
Chain IDs:K (auth: AL)
Chain Length:118
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S18
Chain IDs:L (auth: AM)
Chain Length:130
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S29(A)
Chain IDs:M (auth: AN)
Chain Length:50
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S13
Chain IDs:N (auth: AO)
Chain Length:84
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S11
Chain IDs:O (auth: AQ)
Chain Length:80
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:RACK1 protein
Chain IDs:Q (auth: AR)
Chain Length:313
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:40S ribosomal protein S15
Chain IDs:P (auth: AS)
Chain Length:71
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:s19e protein
Chain IDs:R (auth: AT)
Chain Length:141
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L32
Chain IDs:T (auth: B0)
Chain Length:109
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L39
Chain IDs:U (auth: B1)
Chain Length:48
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L30e
Chain IDs:V (auth: B2)
Chain Length:98
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:YA (auth: B3)
Chain Length:113
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polyribonucleotide
Molecule:5.8S ribosomal RNA
Chain IDs:ZA (auth: B4)
Chain Length:157
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polyribonucleotide
Molecule:26S ribosomal RNA
Chain IDs:AB (auth: B5)
Chain Length:3170
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein LP0
Chain IDs:W (auth: B8)
Chain Length:118
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L43
Chain IDs:X (auth: B9)
Chain Length:72
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L1
Chain IDs:Y (auth: BA)
Chain Length:213
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L2
Chain IDs:Z (auth: BB)
Chain Length:243
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L3
Chain IDs:AA (auth: BC)
Chain Length:362
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L4(B)
Chain IDs:BA (auth: BD)
Chain Length:257
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L5
Chain IDs:CA (auth: BE)
Chain Length:237
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L7(A)
Chain IDs:DA (auth: BF)
Chain Length:213
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L8(A)
Chain IDs:EA (auth: BG)
Chain Length:113
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L9(A)
Chain IDs:FA (auth: BH)
Chain Length:179
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L10
Chain IDs:GA (auth: BI)
Chain Length:165
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L11(B)
Chain IDs:HA (auth: BJ)
Chain Length:151
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L12
Chain IDs:IA (auth: BK)
Chain Length:138
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L15(A)
Chain IDs:JA (auth: BL)
Chain Length:192
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L16(A)
Chain IDs:KA (auth: BM)
Chain Length:178
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L17(A)
Chain IDs:LA (auth: BN)
Chain Length:150
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L18(A)
Chain IDs:MA (auth: BO)
Chain Length:121
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L19
Chain IDs:NA (auth: BP)
Chain Length:176
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L21(A)
Chain IDs:OA (auth: BQ)
Chain Length:116
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L23
Chain IDs:PA (auth: BR)
Chain Length:131
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L24(A)
Chain IDs:QA (auth: BS)
Chain Length:45
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L25
Chain IDs:RA (auth: BT)
Chain Length:80
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L26(A)
Chain IDs:SA (auth: BU)
Chain Length:116
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L28
Chain IDs:TA (auth: BV)
Chain Length:142
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L31(A)
Chain IDs:UA (auth: BW)
Chain Length:79
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L35
Chain IDs:VA (auth: BX)
Chain Length:86
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L37(A)
Chain IDs:WA (auth: BY)
Chain Length:52
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Polymer Type:polypeptide(L)
Molecule:60S ribosomal protein L42
Chain IDs:XA (auth: BZ)
Chain Length:92
Number of Molecules:1
Biological Source:Thermomyces lanuginosus
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
1MA S A ?
2MG S G 2N-METHYLGUANOSINE-5'-MONOPHOSPHATE
5MC S C 5-METHYLCYTIDINE-5'-MONOPHOSPHATE
5MU S U 5-METHYLURIDINE 5'-MONOPHOSPHATE
7MG S G ?
H2U S U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
M2G S G N2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE
OMC S C O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
OMG S G O2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
PSU S U PSEUDOURIDINE-5'-MONOPHOSPHATE
YYG S G ?
Ligand Molecules
NA
Primary Citation
Comprehensive molecular structure of the eukaryotic ribosome.
Structure 17 1591 1604 (2009)
PMID: 20004163 DOI: 10.1016/j.str.2009.09.015

Abstact

Despite the emergence of a large number of X-ray crystallographic models of the bacterial 70S ribosome over the past decade, an accurate atomic model of the eukaryotic 80S ribosome is still not available. Eukaryotic ribosomes possess more ribosomal proteins and ribosomal RNA than do bacterial ribosomes, which are implicated in extraribosomal functions in the eukaryotic cells. By combining cryo-EM with RNA and protein homology modeling, we obtained an atomic model of the yeast 80S ribosome complete with all ribosomal RNA expansion segments and all ribosomal proteins for which a structural homolog can be identified. Mutation or deletion of 80S ribosomal proteins can abrogate maturation of the ribosome, leading to several human diseases. We have localized one such protein unique to eukaryotes, rpS19e, whose mutations are associated with Diamond-Blackfan anemia in humans. Additionally, we characterize crucial interactions between the dynamic stalk base of the ribosome with eukaryotic elongation factor 2.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
4V7H
3JYV
3JYW
3JYX