4UJC image
Deposition Date 2014-06-18
Release Date 2014-07-30
Last Version Date 2024-11-13
Entry Detail
PDB ID:
4UJC
Keywords:
RIBOSOME
Title:
mammalian 80S HCV-IRES initiation complex with eIF5B POST-like state
Biological Source:
Source Organism:
ORYCTOLAGUS CUNICULUS (Taxon ID: 9986)
HEPATITIS C VIRUS (Taxon ID: 11103)
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
9.50 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
4UJC validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:28S RIBOSOMAL RNA
Chain IDs:D (auth: A2)
Chain Length:5025
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polyribonucleotide
Molecule:5.8S RIBOSOMAL RNA
Chain IDs:E (auth: A3)
Chain Length:194
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polyribonucleotide
Molecule:5S RIBOSOMAL RNA
Chain IDs:F (auth: A4)
Chain Length:121
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polyribonucleotide
Molecule:TRNA
Chain IDs:A (auth: AA)
Chain Length:76
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Protein Blast
Polymer Type:polypeptide(L)
Molecule:EIF5B
Gene (Uniprot):EIF5B
Chain IDs:B (auth: AB)
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:C (auth: AC)
Chain Length:504
Number of Molecules:1
Biological Source:HEPATITIS C VIRUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L8
Chain IDs:G (auth: BA)
Chain Length:257
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L3
Chain IDs:H (auth: BB)
Chain Length:403
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L4
Chain IDs:I (auth: BC)
Chain Length:115
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L5
Chain IDs:J (auth: BD)
Chain Length:125
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L6
Chain IDs:K (auth: BE)
Chain Length:158
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L7
Chain IDs:L (auth: BF)
Chain Length:248
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L7A
Chain IDs:M (auth: BG)
Chain Length:117
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L9
Chain IDs:N (auth: BH)
Chain Length:192
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L10
Chain IDs:O (auth: BI)
Chain Length:105
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L11
Chain IDs:P (auth: BJ)
Chain Length:97
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L13
Chain IDs:Q (auth: BL)
Chain Length:51
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L14
Chain IDs:R (auth: BM)
Chain Length:128
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L15
Chain IDs:S (auth: BN)
Chain Length:204
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L13A
Chain IDs:T (auth: BO)
Chain Length:203
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L17
Chain IDs:U (auth: BP)
Chain Length:92
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L18
Chain IDs:V (auth: BQ)
Chain Length:188
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L19
Chain IDs:W (auth: BR)
Chain Length:196
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L18A
Chain IDs:X (auth: BS)
Chain Length:176
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L21
Chain IDs:Y (auth: BT)
Chain Length:137
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L22
Chain IDs:Z (auth: BU)
Chain Length:210
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L23
Chain IDs:AA (auth: BV)
Chain Length:140
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L24
Chain IDs:BA (auth: BW)
Chain Length:157
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L23A
Chain IDs:CA (auth: BX)
Chain Length:156
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L26
Chain IDs:DA (auth: BY)
Chain Length:145
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L27
Chain IDs:EA (auth: BZ)
Chain Length:136
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L27A
Chain IDs:FA (auth: Ba)
Chain Length:257
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L29
Chain IDs:GA (auth: Bb)
Chain Length:403
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L30
Chain IDs:HA (auth: Bc)
Chain Length:115
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L31
Chain IDs:IA (auth: Bd)
Chain Length:125
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L32
Chain IDs:JA (auth: Be)
Chain Length:158
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L35A
Chain IDs:KA (auth: Bf)
Chain Length:248
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L34
Chain IDs:LA (auth: Bg)
Chain Length:117
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN UL29
Chain IDs:MA (auth: Bh)
Chain Length:192
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L36
Chain IDs:NA (auth: Bi)
Chain Length:105
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L37
Chain IDs:OA (auth: Bj)
Chain Length:97
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L38
Chain IDs:PA (auth: Bk)
Chain Length:70
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L39
Chain IDs:QA (auth: Bl)
Chain Length:51
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:UBIQUITIN-60S RIBOSOMAL PROTEIN L40
Chain IDs:RA (auth: Bm)
Chain Length:128
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L41
Chain IDs:SA (auth: Bn)
Chain Length:204
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L36A
Chain IDs:TA (auth: Bo)
Chain Length:203
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L37A
Chain IDs:UA (auth: Bp)
Chain Length:92
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L28
Chain IDs:VA (auth: Bt)
Chain Length:137
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:60S RIBOSOMAL PROTEIN L10A
Chain IDs:WA (auth: Bu)
Chain Length:210
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
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:69
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN US3
Chain IDs:BB (auth: CD)
Chain Length:56
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:317
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 US15
Chain IDs:LB (auth: CN)
Chain Length:151
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN US11
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:69
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Polymer Type:polypeptide(L)
Molecule:40S RIBOSOMAL PROTEIN US14
Chain IDs:BC (auth: Cd)
Chain Length:56
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:317
Number of Molecules:1
Biological Source:ORYCTOLAGUS CUNICULUS
Ligand Molecules
GNP
MG
Primary Citation
Structure of the Mammalian 80S Initiation Complex with Initiation Factor 5B on Hcv-Ires RNA.
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
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