ISDA: 4UJD

Deposition Date 2014-06-18

Release Date 2014-07-30

Last Version Date 2024-10-23

Entry Detail

PDB ID:

4UJD

Keywords:

RIBOSOME

Title:

mammalian 80S HCV-IRES initiation complex with eIF5B PRE-like state

Biological Source:

Source Organism:

ORYCTOLAGUS CUNICULUS (Taxon ID: 9986)
HEPATITIS C VIRUS (Taxon ID: 11103)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

8.90 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:28S Ribosomal RNA
Chain IDs:A (auth: A2)
Chain Length:5025
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polyribonucleotide
Molecule:5.8S Ribosomal RNA
Chain IDs:B (auth: A3)
Chain Length:194
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polyribonucleotide
Molecule:5S Ribosomal RNA
Chain IDs:C (auth: A4)
Chain Length:121
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L8
Chain IDs:D (auth: AA)
Chain Length:257
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L3
Chain IDs:E (auth: AB)
Chain Length:159
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L4
Chain IDs:F (auth: AC)
Chain Length:115
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L5
Chain IDs:G (auth: AD)
Chain Length:297
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L6
Chain IDs:H (auth: AE)
Chain Length:158
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L7
Chain IDs:I (auth: AF)
Chain Length:248
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L7A
Chain IDs:J (auth: AG)
Chain Length:117
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L9
Chain IDs:K (auth: AH)
Chain Length:123
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L10
Chain IDs:L (auth: AI)
Chain Length:214
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L11
Chain IDs:M (auth: AJ)
Chain Length:178
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L13
Chain IDs:N (auth: AL)
Chain Length:51
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L14
Chain IDs:O (auth: AM)
Chain Length:215
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L15
Chain IDs:P (auth: AN)
Chain Length:204
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L13A
Chain IDs:Q (auth: AO)
Chain Length:203
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L17
Chain IDs:R (auth: AP)
Chain Length:92
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L18
Chain IDs:S (auth: AQ)
Chain Length:188
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L19
Chain IDs:T (auth: AR)
Chain Length:196
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L18A
Chain IDs:U (auth: AS)
Chain Length:176
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L21
Chain IDs:V (auth: AT)
Chain Length:160
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L22
Chain IDs:W (auth: AU)
Chain Length:210
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L23
Chain IDs:X (auth: AV)
Chain Length:140
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L24
Chain IDs:Y (auth: AW)
Chain Length:157
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L23A
Chain IDs:Z (auth: AX)
Chain Length:156
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L26
Chain IDs:AA (auth: AY)
Chain Length:145
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L27
Chain IDs:BA (auth: AZ)
Chain Length:136
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L27A
Chain IDs:CA (auth: Aa)
Chain Length:257
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L29
Chain IDs:DA (auth: Ab)
Chain Length:159
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L30
Chain IDs:EA (auth: Ac)
Chain Length:115
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L31
Chain IDs:FA (auth: Ad)
Chain Length:297
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L32
Chain IDs:GA (auth: Ae)
Chain Length:158
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L35A
Chain IDs:HA (auth: Af)
Chain Length:248
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L34
Chain IDs:IA (auth: Ag)
Chain Length:117
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L35
Chain IDs:JA (auth: Ah)
Chain Length:123
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L36
Chain IDs:KA (auth: Ai)
Chain Length:214
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L37
Chain IDs:LA (auth: Aj)
Chain Length:178
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L38
Chain IDs:MA (auth: Ak)
Chain Length:70
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L39
Chain IDs:NA (auth: Al)
Chain Length:51
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:UBIQUITIN-60S RIBOSOMAL PROTEIN L40
Chain IDs:OA (auth: Am)
Chain Length:215
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L41
Chain IDs:PA (auth: An)
Chain Length:204
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L36A
Chain IDs:QA (auth: Ao)
Chain Length:203
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L37A
Chain IDs:RA (auth: Ap)
Chain Length:92
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L28
Chain IDs:SA (auth: At)
Chain Length:160
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L10A
Chain IDs:TA (auth: Au)
Chain Length:210
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polyribonucleotide
Molecule:TRNA
Chain IDs:UA (auth: BA)
Chain Length:76
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:EIF5B
Gene (Uniprot):EIF5B
Chain IDs:VA (auth: BB)
Chain Length:627
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

UniProt ID:G1TRL5 Pfam ID:PF00009, PF11987, PF14578

Polymer Type:polyribonucleotide
Molecule:HCV-IRES
Chain IDs:WA (auth: BC)
Chain Length:504
Number of Molecules:1
Biological Source:HEPATITIS C VIRUS

Polymer Type:polyribonucleotide
Molecule:18S Ribosomal RNA
Chain IDs:XA (auth: C1)
Chain Length:1869
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN US2
Chain IDs:YA (auth: CA)
Chain Length:115
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN ES1
Chain IDs:ZA (auth: CB)
Chain Length:84
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN US5
Chain IDs:AB (auth: CC)
Chain Length:293
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN US3
Chain IDs:BB (auth: CD)
Chain Length:243
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN ES4
Chain IDs:CB (auth: CE)
Chain Length:59
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN US7
Chain IDs:DB (auth: CF)
Chain Length:204
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN ES6
Chain IDs:EB (auth: CG)
Chain Length:249
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN ES7
Chain IDs:FB (auth: CH)
Chain Length:194
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN ES8
Chain IDs:GB (auth: CI)
Chain Length:208
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN US4
Chain IDs:HB (auth: CJ)
Chain Length:194
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN ES10
Chain IDs:IB (auth: CK)
Chain Length:165
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN US17
Chain IDs:JB (auth: CL)
Chain Length:158
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN ES12
Chain IDs:KB (auth: CM)
Chain Length:132
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN ES15
Chain IDs:LB (auth: CN)
Chain Length:151
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN ES11
Chain IDs:MB (auth: CO)
Chain Length:151
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN US19
Chain IDs:NB (auth: CP)
Chain Length:145
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN US9
Chain IDs:OB (auth: CQ)
Chain Length:146
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN ES17
Chain IDs:PB (auth: CR)
Chain Length:135
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN US13
Chain IDs:QB (auth: CS)
Chain Length:152
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN ES19
Chain IDs:RB (auth: CT)
Chain Length:145
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN US10
Chain IDs:SB (auth: CU)
Chain Length:119
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN ES21
Chain IDs:TB (auth: CV)
Chain Length:83
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN US8
Chain IDs:UB (auth: CW)
Chain Length:130
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN US12
Chain IDs:VB (auth: CX)
Chain Length:143
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN ES24
Chain IDs:WB (auth: CY)
Chain Length:133
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN ES25
Chain IDs:XB (auth: CZ)
Chain Length:125
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN ES26
Chain IDs:YB (auth: Ca)
Chain Length:115
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN ES27
Chain IDs:ZB (auth: Cb)
Chain Length:84
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN ES28
Chain IDs:AC (auth: Cc)
Chain Length:293
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN US14
Chain IDs:BC (auth: Cd)
Chain Length:243
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN ES30
Chain IDs:CC (auth: Ce)
Chain Length:59
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN ES31
Chain IDs:DC (auth: Cf)
Chain Length:204
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN RACK1
Chain IDs:EC (auth: Cg)
Chain Length:249
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS

Ligand Molecules

GNP

Primary Citation

Structure of the Mammalian 80S Initiation Complex with Eif5B on Hcv Ires

Yamamoto, H, Unbehaun, A, Loerke, J, Behrmann, E, Marianne, C, Burger, J, Mielke, T, Spahn, C.M.T.Show

Nat.Struct.Mol.Biol. 21 721 ? (2014)

PMID: 25064512 DOI: 10.1038/NSMB.2859

Abstact

The universally conserved eukaryotic initiation factor (eIF) 5B, a translational GTPase, is essential for canonical translation initiation. It is also required for initiation facilitated by the internal ribosomal entry site (IRES) of hepatitis C virus (HCV) RNA. eIF5B promotes joining of 60S ribosomal subunits to 40S ribosomal subunits bound by initiator tRNA (Met-tRNAi(Met)). However, the exact molecular mechanism by which eIF5B acts has not been established. Here we present cryo-EM reconstructions of the mammalian 80S-HCV-IRES-Met-tRNAi(Met)-eIF5B-GMPPNP complex. We obtained two substates distinguished by the rotational state of the ribosomal subunits and the configuration of initiator tRNA in the peptidyl (P) site. Accordingly, a combination of conformational changes in the 80S ribosome and in initiator tRNA facilitates binding of the Met-tRNAi(Met) to the 60S P site and redefines the role of eIF5B as a tRNA-reorientation factor.

Legend

Protein

Chemical

Disease

Primary Citation of related structures