[English] 日本語
Yorodumi
- PDB-4ujd: mammalian 80S HCV-IRES initiation complex with eIF5B PRE-like state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ujd
Titlemammalian 80S HCV-IRES initiation complex with eIF5B PRE-like state
Components
  • (40S RIBOSOMAL PROTEIN ...) x 33
  • (60S RIBOSOMAL PROTEIN ...) x 42
  • 18S Ribosomal RNA
  • 28S Ribosomal RNA
  • 5.8S Ribosomal RNA
  • 5S Ribosomal RNA
  • EIF5B
  • HCV-IRES
  • TRNA
  • UBIQUITIN-60S RIBOSOMAL PROTEIN L40
KeywordsRIBOSOME / TRANSLATION INITIATION / HEPATITIS C VIRUS INTERNAL RIBOSOME ENTRY SITE / EUKARYOTIC INITIATION FACTOR 5B
Function / homology
Function and homology information


protein-synthesizing GTPase / translation initiation factor activity / GTPase activity / GTP binding / mitochondrion
Similarity search - Function
Elongation factor Tu-type domain / Elongation factor Tu domain 4 / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. ...Elongation factor Tu-type domain / Elongation factor Tu domain 4 / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / RNA / RNA (> 10) / RNA (> 100) / RNA (> 1000) / Eukaryotic translation initiation factor 5B
Similarity search - Component
Biological speciesORYCTOLAGUS CUNICULUS (rabbit)
HEPATITIS C VIRUS
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.9 Å
AuthorsYamamoto, H. / Unbehaun, A. / Loerke, J. / Behrmann, E. / Marianne, C. / Burger, J. / Mielke, T. / Spahn, C.M.T.
CitationJournal: Nat Struct Mol Biol / Year: 2014
Title: Structure of the mammalian 80S initiation complex with initiation factor 5B on HCV-IRES RNA.
Authors: Hiroshi Yamamoto / Anett Unbehaun / Justus Loerke / Elmar Behrmann / Marianne Collier / Jörg Bürger / Thorsten Mielke / Christian M T Spahn /
Abstract: 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 ...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.
History
DepositionJun 18, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
SupersessionDec 10, 2014ID: 4UPW, 4UPX, 4UPY, 4UQ5 / Details: supersedes the associated split entries
Revision 1.1Jun 8, 2016Group: Other / Source and taxonomy
Revision 2.0Aug 23, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / em_image_scans ...atom_site / em_image_scans / em_software / pdbx_validate_close_contact / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _em_software.image_processing_id / _pdbx_validate_close_contact.auth_atom_id_1
Revision 2.1Dec 18, 2019Group: Other / Category: atom_sites
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3]
Revision 2.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-2682
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A2: 28S Ribosomal RNA
A3: 5.8S Ribosomal RNA
A4: 5S Ribosomal RNA
AA: 60S RIBOSOMAL PROTEIN L8
AB: 60S RIBOSOMAL PROTEIN L3
AC: 60S RIBOSOMAL PROTEIN L4
AD: 60S RIBOSOMAL PROTEIN L5
AE: 60S RIBOSOMAL PROTEIN L6
AF: 60S RIBOSOMAL PROTEIN L7
AG: 60S RIBOSOMAL PROTEIN L7A
AH: 60S RIBOSOMAL PROTEIN L9
AI: 60S RIBOSOMAL PROTEIN L10
AJ: 60S RIBOSOMAL PROTEIN L11
AL: 60S RIBOSOMAL PROTEIN L13
AM: 60S RIBOSOMAL PROTEIN L14
AN: 60S RIBOSOMAL PROTEIN L15
AO: 60S RIBOSOMAL PROTEIN L13A
AP: 60S RIBOSOMAL PROTEIN L17
AQ: 60S RIBOSOMAL PROTEIN L18
AR: 60S RIBOSOMAL PROTEIN L19
AS: 60S RIBOSOMAL PROTEIN L18A
AT: 60S RIBOSOMAL PROTEIN L21
AU: 60S RIBOSOMAL PROTEIN L22
AV: 60S RIBOSOMAL PROTEIN L23
AW: 60S RIBOSOMAL PROTEIN L24
AX: 60S RIBOSOMAL PROTEIN L23A
AY: 60S RIBOSOMAL PROTEIN L26
AZ: 60S RIBOSOMAL PROTEIN L27
Aa: 60S RIBOSOMAL PROTEIN L27A
Ab: 60S RIBOSOMAL PROTEIN L29
Ac: 60S RIBOSOMAL PROTEIN L30
Ad: 60S RIBOSOMAL PROTEIN L31
Ae: 60S RIBOSOMAL PROTEIN L32
Af: 60S RIBOSOMAL PROTEIN L35A
Ag: 60S RIBOSOMAL PROTEIN L34
Ah: 60S RIBOSOMAL PROTEIN L35
Ai: 60S RIBOSOMAL PROTEIN L36
Aj: 60S RIBOSOMAL PROTEIN L37
Ak: 60S RIBOSOMAL PROTEIN L38
Al: 60S RIBOSOMAL PROTEIN L39
Am: UBIQUITIN-60S RIBOSOMAL PROTEIN L40
An: 60S RIBOSOMAL PROTEIN L41
Ao: 60S RIBOSOMAL PROTEIN L36A
Ap: 60S RIBOSOMAL PROTEIN L37A
At: 60S RIBOSOMAL PROTEIN L28
Au: 60S RIBOSOMAL PROTEIN L10A
BA: TRNA
BB: EIF5B
BC: HCV-IRES
C1: 18S Ribosomal RNA
CA: 40S RIBOSOMAL PROTEIN US2
CB: 40S RIBOSOMAL PROTEIN ES1
CC: 40S RIBOSOMAL PROTEIN US5
CD: 40S RIBOSOMAL PROTEIN US3
CE: 40S RIBOSOMAL PROTEIN ES4
CF: 40S RIBOSOMAL PROTEIN US7
CG: 40S RIBOSOMAL PROTEIN ES6
CH: 40S RIBOSOMAL PROTEIN ES7
CI: 40S RIBOSOMAL PROTEIN ES8
CJ: 40S RIBOSOMAL PROTEIN US4
CK: 40S RIBOSOMAL PROTEIN ES10
CL: 40S RIBOSOMAL PROTEIN US17
CM: 40S RIBOSOMAL PROTEIN ES12
CN: 40S RIBOSOMAL PROTEIN ES15
CO: 40S RIBOSOMAL PROTEIN ES11
CP: 40S RIBOSOMAL PROTEIN US19
CQ: 40S RIBOSOMAL PROTEIN US9
CR: 40S RIBOSOMAL PROTEIN ES17
CS: 40S RIBOSOMAL PROTEIN US13
CT: 40S RIBOSOMAL PROTEIN ES19
CU: 40S RIBOSOMAL PROTEIN US10
CV: 40S RIBOSOMAL PROTEIN ES21
CW: 40S RIBOSOMAL PROTEIN US8
CX: 40S RIBOSOMAL PROTEIN US12
CY: 40S RIBOSOMAL PROTEIN ES24
CZ: 40S RIBOSOMAL PROTEIN ES25
Ca: 40S RIBOSOMAL PROTEIN ES26
Cb: 40S RIBOSOMAL PROTEIN ES27
Cc: 40S RIBOSOMAL PROTEIN ES28
Cd: 40S RIBOSOMAL PROTEIN US14
Ce: 40S RIBOSOMAL PROTEIN ES30
Cf: 40S RIBOSOMAL PROTEIN ES31
Cg: 40S RIBOSOMAL PROTEIN RACK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,044,60385
Polymers4,044,05683
Non-polymers5472
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

-
Components

-
RNA chain , 6 types, 6 molecules A2A3A4BABCC1

#1: RNA chain 28S Ribosomal RNA


Mass: 1625917.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#2: RNA chain 5.8S Ribosomal RNA


Mass: 62616.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#3: RNA chain 5S Ribosomal RNA


Mass: 38998.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#47: RNA chain TRNA


Mass: 24485.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#49: RNA chain HCV-IRES


Mass: 162190.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) HEPATITIS C VIRUS
#50: RNA chain 18S Ribosomal RNA


Mass: 602776.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)

+
60S RIBOSOMAL PROTEIN ... , 42 types, 42 molecules AAABACADAEAFAGAHAIAJALAMANAOAPAQARASATAUAVAWAXAYAZAaAbAcAdAe...

#4: Protein 60S RIBOSOMAL PROTEIN L8 / 60S RIBOSOMAL PROTEIN UL2


Mass: 28088.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#5: Protein 60S RIBOSOMAL PROTEIN L3 / HIV-1 TAR RNA-BINDING PROTEIN B / TARBP-B / 60S RIBOSOMAL PROTEIN UL3


Mass: 46211.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#6: Protein 60S RIBOSOMAL PROTEIN L4 / 60S RIBOSOMAL PROTEIN L1 / 60S RIBOSOMAL PROTEIN UL4


Mass: 47804.621 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#7: Protein 60S RIBOSOMAL PROTEIN L5 / 60S RIBOSOMAL PROTEIN UL18


Mass: 34426.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#8: Protein 60S RIBOSOMAL PROTEIN L6 / NEOPLASM-RELATED PROTEIN C140 / TAX-RESPONSIVE ENHANCER ELEMENT-BINDING PROTEIN 107 / TAXREB107 / ...NEOPLASM-RELATED PROTEIN C140 / TAX-RESPONSIVE ENHANCER ELEMENT-BINDING PROTEIN 107 / TAXREB107 / 60S RIBOSOMAL PROTEIN EL6


Mass: 18219.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#9: Protein 60S RIBOSOMAL PROTEIN L7 / 60S RIBOSOMAL PROTEIN UL30


Mass: 29290.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#10: Protein 60S RIBOSOMAL PROTEIN L7A / PLA-X POLYPEPTIDE / SURFEIT LOCUS PROTEIN 3 / 60S RIBOSOMAL PROTEIN EL8


Mass: 30061.785 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#11: Protein 60S RIBOSOMAL PROTEIN L9 / 60S RIBOSOMAL PROTEIN UL6


Mass: 21899.471 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#12: Protein 60S RIBOSOMAL PROTEIN L10 / LAMININ RECEPTOR HOMOLOG / PROTEIN QM / TUMOR SUPPRESSOR QM / 60S RIBOSOMAL PROTEIN UL16


Mass: 24657.084 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#13: Protein 60S RIBOSOMAL PROTEIN L11 / CLL-ASSOCIATED ANTIGEN KW-12 / 60S RIBOSOMAL PROTEIN UL5


Mass: 20288.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#14: Protein 60S RIBOSOMAL PROTEIN L13 / BREAST BASIC CONSERVED PROTEIN 1 / 60S RIBOSOMAL PROTEIN EL13


Mass: 24321.682 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#15: Protein 60S RIBOSOMAL PROTEIN L14 / CAG-ISL 7 / 60S RIBOSOMAL PROTEIN EL14


Mass: 23485.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#16: Protein 60S RIBOSOMAL PROTEIN L15 / 60S RIBOSOMAL PROTEIN EL15


Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#17: Protein 60S RIBOSOMAL PROTEIN L13A / 23 KDA HIGHLY BASIC PROTEIN / 60S RIBOSOMAL PROTEIN UL13


Mass: 23633.412 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#18: Protein 60S RIBOSOMAL PROTEIN L17 / 60S RIBOSOMAL PROTEIN L23 / PD-1 / 60S RIBOSOMAL PROTEIN UL22


Mass: 21443.170 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#19: Protein 60S RIBOSOMAL PROTEIN L18 / 60S RIBOSOMAL PROTEIN EL18


Mass: 21687.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#20: Protein 60S RIBOSOMAL PROTEIN L19 / 60S RIBOSOMAL PROTEIN EL19


Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#21: Protein 60S RIBOSOMAL PROTEIN L18A / 60S RIBOSOMAL PROTEIN EL20


Mass: 20808.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#22: Protein 60S RIBOSOMAL PROTEIN L21 / 60S RIBOSOMAL PROTEIN EL21


Mass: 18609.988 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#23: Protein 60S RIBOSOMAL PROTEIN L22 / EBER-ASSOCIATED PROTEIN / EAP / EPSTEIN-BARR VIRUS SMALL RNA-ASSOCIATED PROTEIN / HEPARIN-BINDING ...EBER-ASSOCIATED PROTEIN / EAP / EPSTEIN-BARR VIRUS SMALL RNA-ASSOCIATED PROTEIN / HEPARIN-BINDING PROTEIN HBP15 / 60S RIBOSOMAL PROTEIN EL22


Mass: 14813.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#24: Protein 60S RIBOSOMAL PROTEIN L23 / 60S RIBOSOMAL PROTEIN L17 / 60S RIBOSOMAL PROTEIN UL14


Mass: 14892.505 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#25: Protein 60S RIBOSOMAL PROTEIN L24 / 60S RIBOSOMAL PROTEIN L30 / 60S RIBOSOMAL PROTEIN EL24


Mass: 17825.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#26: Protein 60S RIBOSOMAL PROTEIN L23A / 60S RIBOSOMAL PROTEIN UL23


Mass: 17740.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#27: Protein 60S RIBOSOMAL PROTEIN L26 / 60S RIBOSOMAL PROTEIN UL24


Mass: 17303.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#28: Protein 60S RIBOSOMAL PROTEIN L27 / 60S RIBOSOMAL PROTEIN EL27


Mass: 15835.831 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#29: Protein 60S RIBOSOMAL PROTEIN L27A / 60S RIBOSOMAL PROTEIN UL15


Mass: 16604.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#30: Protein 60S RIBOSOMAL PROTEIN L29 / CELL SURFACE HEPARIN-BINDING PROTEIN HIP / 60S RIBOSOMAL PROTEIN EL29


Mass: 17804.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#31: Protein 60S RIBOSOMAL PROTEIN L30 / 60S RIBOSOMAL PROTEIN EL30


Mass: 12805.092 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#32: Protein 60S RIBOSOMAL PROTEIN L31 / 60S RIBOSOMAL PROTEIN EL31


Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#33: Protein 60S RIBOSOMAL PROTEIN L32 / 60S RIBOSOMAL PROTEIN EL32


Mass: 15898.932 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#34: Protein 60S RIBOSOMAL PROTEIN L35A / CELL GROWTH-INHIBITING GENE 33 PROTEIN / 60S RIBOSOMAL PROTEIN EL33


Mass: 12564.743 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#35: Protein 60S RIBOSOMAL PROTEIN L34 / 60S RIBOSOMAL PROTEIN EL34


Mass: 13326.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#36: Protein 60S RIBOSOMAL PROTEIN L35 / 60S RIBOSOMAL PROTEIN UL29


Mass: 14593.624 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#37: Protein 60S RIBOSOMAL PROTEIN L36


Mass: 12290.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#38: Protein 60S RIBOSOMAL PROTEIN L37 / G1.16


Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#39: Protein 60S RIBOSOMAL PROTEIN L38


Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#40: Protein 60S RIBOSOMAL PROTEIN L39


Mass: 6426.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#42: Protein/peptide 60S RIBOSOMAL PROTEIN L41 / HG12


Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#43: Protein 60S RIBOSOMAL PROTEIN L36A / 60S RIBOSOMAL PROTEIN L44 / CELL GROWTH-INHIBITING GENE 15 PROTEIN / CELL MIGRATION-INDUCING GENE 6 PROTEIN


Mass: 12476.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#44: Protein 60S RIBOSOMAL PROTEIN L37A


Mass: 10299.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#45: Protein 60S RIBOSOMAL PROTEIN L28


Mass: 15784.622 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#46: Protein 60S RIBOSOMAL PROTEIN L10A


Mass: 23174.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)

-
Protein , 2 types, 2 molecules AmBB

#41: Protein UBIQUITIN-60S RIBOSOMAL PROTEIN L40 / CEP52 / UBIQUITIN A-52 RESIDUE RIBOSOMAL PROTEIN FUSION PRODUCT 1


Mass: 14758.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#48: Protein EIF5B


Mass: 70788.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: G1TRL5

+
40S RIBOSOMAL PROTEIN ... , 33 types, 33 molecules CACBCCCDCECFCGCHCICJCKCLCMCNCOCPCQCRCSCTCUCVCWCXCYCZCaCbCcCd...

#51: Protein 40S RIBOSOMAL PROTEIN US2


Mass: 32883.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#52: Protein 40S RIBOSOMAL PROTEIN ES1


Mass: 30002.061 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#53: Protein 40S RIBOSOMAL PROTEIN US5


Mass: 31376.516 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#54: Protein 40S RIBOSOMAL PROTEIN US3


Mass: 26729.369 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#55: Protein 40S RIBOSOMAL PROTEIN ES4


Mass: 29512.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#56: Protein 40S RIBOSOMAL PROTEIN US7


Mass: 22913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#57: Protein 40S RIBOSOMAL PROTEIN ES6


Mass: 28751.906 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#58: Protein 40S RIBOSOMAL PROTEIN ES7


Mass: 22168.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#59: Protein 40S RIBOSOMAL PROTEIN ES8


Mass: 24263.387 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#60: Protein 40S RIBOSOMAL PROTEIN US4


Mass: 22641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#61: Protein 40S RIBOSOMAL PROTEIN ES10


Mass: 18933.846 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#62: Protein 40S RIBOSOMAL PROTEIN US17


Mass: 18468.826 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#63: Protein 40S RIBOSOMAL PROTEIN ES12


Mass: 14538.987 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#64: Protein 40S RIBOSOMAL PROTEIN ES15


Mass: 17259.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#65: Protein 40S RIBOSOMAL PROTEIN ES11


Mass: 16302.772 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#66: Protein 40S RIBOSOMAL PROTEIN US19


Mass: 17076.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#67: Protein 40S RIBOSOMAL PROTEIN US9


Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#68: Protein 40S RIBOSOMAL PROTEIN ES17


Mass: 15578.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#69: Protein 40S RIBOSOMAL PROTEIN US13


Mass: 17759.777 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#70: Protein 40S RIBOSOMAL PROTEIN ES19


Mass: 16091.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#71: Protein 40S RIBOSOMAL PROTEIN US10


Mass: 13398.763 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#72: Protein 40S RIBOSOMAL PROTEIN ES21


Mass: 9124.389 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#73: Protein 40S RIBOSOMAL PROTEIN US8


Mass: 14865.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#74: Protein 40S RIBOSOMAL PROTEIN US12


Mass: 15844.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#75: Protein 40S RIBOSOMAL PROTEIN ES24


Mass: 15463.333 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#76: Protein 40S RIBOSOMAL PROTEIN ES25


Mass: 13776.224 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#77: Protein 40S RIBOSOMAL PROTEIN ES26


Mass: 13047.532 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#78: Protein 40S RIBOSOMAL PROTEIN ES27


Mass: 9480.186 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#79: Protein 40S RIBOSOMAL PROTEIN ES28


Mass: 7855.052 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#80: Protein 40S RIBOSOMAL PROTEIN US14


Mass: 6690.821 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#81: Protein 40S RIBOSOMAL PROTEIN ES30


Mass: 6668.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#82: Protein 40S RIBOSOMAL PROTEIN ES31


Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)
#83: Protein 40S RIBOSOMAL PROTEIN RACK1


Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit)

-
Non-polymers , 2 types, 2 molecules

#84: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#85: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

-
Details

Has protein modificationY
Sequence detailsCHAIN 2 1-5025 GB M11167 1-5025 CHAIN 3 1-181 GB CR749662 1-181 CHAIN 4 1-121 GB X51545 274-394

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: HCV-IRES 80S INITIATION COMPLEX WITH EIF5B PRE- LIKE STATE
Type: RIBOSOME
Buffer solutionName: 20MM TRIS-HCL, 5MM MGCL2, 100MM KCL, 0.2MM SPERMIDINE, 2MM DTT
pH: 7.6
Details: 20MM TRIS-HCL, 5MM MGCL2, 100MM KCL, 0.2MM SPERMIDINE, 2MM DTT
SpecimenConc.: 0.15 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 93, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT FOR 2-4 SECONDS BEFORE PLUNGING,

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30 / Date: Dec 22, 2012 / Details: AUTOMATED DATA COLLECTION USING LEGINON
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 115000 X / Calibrated magnification: 194805 X / Nominal defocus max: 4500 nm / Nominal defocus min: 2000 nm / Cs: 2 mm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k)
Radiation wavelengthRelative weight: 1

-
Processing

EM software
IDNameCategory
1SPARX3D reconstruction
2SPIDER3D reconstruction
CTF correctionDetails: CTFFIND3
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 8.9 Å / Num. of particles: 541570 / Nominal pixel size: 2.37 Å / Actual pixel size: 2.37 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2682. (DEPOSITION ID: 12562).
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Details: METHOD--RIGID BODY
Atomic model buildingPDB-ID: 4CXC

4cxc
PDB Unreleased entry


Accession code: 4CXC / Source name: PDB / Type: experimental model
RefinementHighest resolution: 8.9 Å
Refinement stepCycle: LAST / Highest resolution: 8.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 83360 0 0 83360

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more