[English] 日本語
Yorodumi
- PDB-3zwl: Structure of eukaryotic translation initiation factor eIF3i compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zwl
TitleStructure of eukaryotic translation initiation factor eIF3i complex with eIF3b C-terminus (655-700)
Components
  • EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT B
  • EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT I
KeywordsTRANSLATION
Function / homology
Function and homology information


eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / multi-eIF complex / cytoplasmic translational initiation / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation ...eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / eukaryotic translation initiation factor 3 complex / formation of cytoplasmic translation initiation complex / multi-eIF complex / cytoplasmic translational initiation / eukaryotic 43S preinitiation complex / eukaryotic 48S preinitiation complex / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / L13a-mediated translational silencing of Ceruloplasmin expression / translation initiation factor binding / translation initiation factor activity / translational initiation / cytoplasmic stress granule / RNA binding / identical protein binding
Similarity search - Function
Eukaryotic translation initiation factor 3 subunit I / Eukaryotic translation initiation factor 3 subunit B / eIF3B, RNA recognition motif / Translation initiation factor, beta propellor-like domain / Eukaryotic translation initiation factor eIF2A / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / RNA recognition motif / RNA recognition motif ...Eukaryotic translation initiation factor 3 subunit I / Eukaryotic translation initiation factor 3 subunit B / eIF3B, RNA recognition motif / Translation initiation factor, beta propellor-like domain / Eukaryotic translation initiation factor eIF2A / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Eukaryotic translation initiation factor 3 subunit B / Eukaryotic translation initiation factor 3 subunit I
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.2 Å
AuthorsDaujotyte, D. / Lukavsky, P.J.
CitationJournal: Nucleic Acids Res. / Year: 2012
Title: Structural Analysis of an Eif3 Subcomplex Reveals Conserved Interactions Required for a Stable and Proper Translation Pre-Initiation Complex Assembly.
Authors: Herrmannova, A. / Daujotyte, D. / Yang, J.C. / Cuchalova, L. / Gorrec, F. / Wagner, S. / Danyi, I. / Lukavsky, P.J. / Shivaya Valasek, L.
History
DepositionAug 1, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2011Group: Database references
Revision 1.2Apr 18, 2012Group: Other
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT I
D: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT I
E: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT B
F: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT B


Theoretical massNumber of molelcules
Total (without water)94,7324
Polymers94,7324
Non-polymers00
Water4,252236
1
B: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT I
E: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT B


Theoretical massNumber of molelcules
Total (without water)47,3662
Polymers47,3662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-16 kcal/mol
Surface area17760 Å2
MethodPISA
2
D: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT I
F: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT B


Theoretical massNumber of molelcules
Total (without water)47,3662
Polymers47,3662
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-15.1 kcal/mol
Surface area18610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.469, 126.469, 105.741
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT I / EIF3I / EUKARYOTIC TRANSLATION INITIATION FACTOR 3 39 KDA SUBUNIT / EIF-3 39 KDA SUBUNIT / EIF3 P39 / TIF34


Mass: 41302.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P40217
#2: Protein/peptide EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT B / EIF3B / CELL CYCLE REGULATION AND TRANSLATION INITIATION PROTEIN / EUKARYOTIC TRANSLATION ...EIF3B / CELL CYCLE REGULATION AND TRANSLATION INITIATION PROTEIN / EUKARYOTIC TRANSLATION INITIATION FACTOR 3 90 KDA SUBUNIT / EIF3 P90 / TRANSLATION INITIATION FACTOR EIF3 P90 SUBUNIT / PRT1


Mass: 6062.861 Da / Num. of mol.: 2 / Fragment: RESIDUES 693-739
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06103
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 236 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL HIS TAG AND TEV PROTEASE CLEAVAGE SITE ARE PRESENT. THREE RESIDUES GSH FROM TEV PROTEASE ...N-TERMINAL HIS TAG AND TEV PROTEASE CLEAVAGE SITE ARE PRESENT. THREE RESIDUES GSH FROM TEV PROTEASE CLEAVAGE SITE ARE PRESENT.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.45 % / Description: NONE
Crystal growpH: 8.8
Details: 0.1 M TRIS PH 8.8, 0.1 M LI2SO4, 30% PEG4000, 8% DIAMINOPENTANE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 24, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→54.7 Å / Num. obs: 49844 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 10.2
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 2.2 / % possible all: 100

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
BUCCANEERphasing
REFMAC5.5.0109refinement
RefinementMethod to determine structure: MIR
Starting model: NONE

Resolution: 2.2→109.53 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.545 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES B260-271 ARE OMITTED FROM THE PDB FILE DUE TO THE LACK OF ELECTRON DENSITY AROUND THEM.
RfactorNum. reflection% reflectionSelection details
Rfree0.24706 2524 5.1 %RANDOM
Rwork0.18871 ---
obs0.19166 47261 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.941 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20.4 Å20 Å2
2--0.8 Å20 Å2
3----1.2 Å2
Refinement stepCycle: LAST / Resolution: 2.2→109.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6145 0 0 236 6381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0226290
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8821.9428498
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2165764
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.9524.751301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.14151097
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.4051522
X-RAY DIFFRACTIONr_chiral_restr0.1280.2914
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214764
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2631.53807
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.43426150
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.77532483
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.2034.52348
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 195 -
Rwork0.251 3454 -
obs--99.97 %

+
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