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- PDB-4ujd: mammalian 80S HCV-IRES initiation complex with eIF5B PRE-like state -

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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
  • TRNATransfer RNA
  • 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


translation initiation factor activity / GTPase activity / GTP binding
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]

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Structure visualization

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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
Water0
1


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

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Components

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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 / Transfer RNA


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)

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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)

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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

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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)

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Non-polymers , 2 types, 2 molecules

#84: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


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

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

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Experimental details

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Experiment

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

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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,

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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 FIELDBright-field microscopy / 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

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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

RefinementHighest resolution: 8.9 Å
Refinement stepCycle: LAST / Highest resolution: 8.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 83360 0 0 83360

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