[English] 日本語
Yorodumi
- PDB-3e20: Crystal structure of S.pombe eRF1/eRF3 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3.0E+20
TitleCrystal structure of S.pombe eRF1/eRF3 complex
Components
  • Eukaryotic peptide chain release factor GTP-binding subunit
  • Eukaryotic peptide chain release factor subunit 1
KeywordsTRANSLATION / Sup35 / Sup45 / translation termination / peptide release / GTP-binding / Nucleotide-binding / Phosphoprotein / Protein biosynthesis
Function / homology
Function and homology information


Eukaryotic Translation Termination / Protein hydroxylation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translation release factor complex / GTPase regulator activity / cytoplasmic translational termination / translation release factor activity, codon specific / translation release factor activity / sequence-specific mRNA binding ...Eukaryotic Translation Termination / Protein hydroxylation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translation release factor complex / GTPase regulator activity / cytoplasmic translational termination / translation release factor activity, codon specific / translation release factor activity / sequence-specific mRNA binding / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / translation / GTPase activity / GTP binding / magnesium ion binding / cytosol
Similarity search - Function
Helix Hairpins - #2070 / Translation, Eukaryotic Peptide Chain Release Factor Subunit 1; Chain A / eRF1 domain 1 / Eukaryotic peptide chain release factor GTP-binding subunit / Peptide chain release factor eRF1/aRF1 / eRF1, domain 1 / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1/Pelota-like / eRF1 domain 3 ...Helix Hairpins - #2070 / Translation, Eukaryotic Peptide Chain Release Factor Subunit 1; Chain A / eRF1 domain 1 / Eukaryotic peptide chain release factor GTP-binding subunit / Peptide chain release factor eRF1/aRF1 / eRF1, domain 1 / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 1 / eRF1 domain 3 / eRF1_1 / : / GTP-eEF1A C-terminal domain-like / : / Ribosomal protein L30/S12 / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / Helix Hairpins / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / 60s Ribosomal Protein L30; Chain: A; / Elongation Factor Tu (Ef-tu); domain 3 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Helix non-globular / Special / 50S ribosomal protein L30e-like / Translation protein, beta-barrel domain superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Eukaryotic peptide chain release factor GTP-binding subunit / Eukaryotic peptide chain release factor subunit 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsCheng, Z. / Lim, M. / Kong, C. / Song, H.
CitationJournal: Genes Dev. / Year: 2009
Title: Structural insights into eRF3 and stop codon recognition by eRF1
Authors: Cheng, Z. / Saito, K. / Pisarev, A.V. / Wada, M. / Pisareva, V.P. / Pestova, T.V. / Gajda, M. / Round, A. / Kong, C. / Lim, M. / Nakamura, Y. / Svergun, D.I. / Ito, K. / Song, H.
History
DepositionAug 5, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Eukaryotic peptide chain release factor GTP-binding subunit
C: Eukaryotic peptide chain release factor subunit 1
D: Eukaryotic peptide chain release factor GTP-binding subunit
B: Eukaryotic peptide chain release factor subunit 1
E: Eukaryotic peptide chain release factor GTP-binding subunit
H: Eukaryotic peptide chain release factor subunit 1
J: Eukaryotic peptide chain release factor GTP-binding subunit
K: Eukaryotic peptide chain release factor subunit 1


Theoretical massNumber of molelcules
Total (without water)288,6408
Polymers288,6408
Non-polymers00
Water00
1
A: Eukaryotic peptide chain release factor GTP-binding subunit
B: Eukaryotic peptide chain release factor subunit 1


Theoretical massNumber of molelcules
Total (without water)72,1602
Polymers72,1602
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Eukaryotic peptide chain release factor subunit 1
D: Eukaryotic peptide chain release factor GTP-binding subunit


Theoretical massNumber of molelcules
Total (without water)72,1602
Polymers72,1602
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Eukaryotic peptide chain release factor GTP-binding subunit
H: Eukaryotic peptide chain release factor subunit 1


Theoretical massNumber of molelcules
Total (without water)72,1602
Polymers72,1602
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: Eukaryotic peptide chain release factor GTP-binding subunit
K: Eukaryotic peptide chain release factor subunit 1


Theoretical massNumber of molelcules
Total (without water)72,1602
Polymers72,1602
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)129.848, 129.848, 332.638
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22C
13B
23C
14E
24J
15H
25K

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A467 - 662
2111D467 - 662
1121B2 - 137
2121C2 - 137
1131B274 - 425
2131C274 - 425
1141E467 - 662
2141J467 - 662
1151H274 - 425
2151K274 - 425

NCS ensembles :
ID
1
2
3
4
5

-
Components

#1: Protein
Eukaryotic peptide chain release factor GTP-binding subunit / ERF2 / ERF-3 / ERF3 / Translation release factor 3 / Polypeptide release factor 3 / Sup35


Mass: 22208.695 Da / Num. of mol.: 4 / Fragment: UNP residues 467-662
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: sup35, SPCC584.04 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 (DE3) / References: UniProt: O74718
#2: Protein
Eukaryotic peptide chain release factor subunit 1 / Eukaryotic release factor 1 / eRF1 / Sup45


Mass: 49951.340 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: sup45, SPAC1834.01 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 (DE3) / References: UniProt: P79063

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.86 Å3/Da / Density % sol: 74.68 %
Crystal growTemperature: 288 K / Method: evaporation / pH: 7
Details: 50mM MOPS, pH7.0, 500mM KCl, 12% PEG4000, 20% Glycerol, EVAPORATION, temperature 288K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 30, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.5→30 Å / Num. obs: 69011 / % possible obs: 99.9 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 8
Reflection shellResolution: 3.5→3.62 Å / Rmerge(I) obs: 0.56

-
Processing

Software
NameVersionClassification
REFMAC5.4.0077refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DT9, 1R5B

1dt9

1r5b


Resolution: 3.5→30 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.881 / SU B: 49.215 / SU ML: 0.338 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(I): 1.9 / ESU R: 0.93 / ESU R Free: 0.447 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27987 3474 5.1 %RANDOM
Rwork0.25808 ---
obs0.25915 65207 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.544 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å2-0 Å2-0 Å2
2--0.03 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 3.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13096 0 0 0 13096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02213276
X-RAY DIFFRACTIONr_angle_refined_deg1.111.97817862
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.57951624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.96224.845582
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.853152536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5961572
X-RAY DIFFRACTIONr_chiral_restr0.0770.22068
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219636
X-RAY DIFFRACTIONr_mcbond_it0.2361.58204
X-RAY DIFFRACTIONr_mcangle_it0.457213268
X-RAY DIFFRACTIONr_scbond_it0.57235072
X-RAY DIFFRACTIONr_scangle_it1.0774.54594
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1524TIGHT POSITIONAL0.020.05
1A1524TIGHT THERMAL0.010.5
2B1066TIGHT POSITIONAL0.040.05
2B1066TIGHT THERMAL0.010.5
3B1005TIGHT POSITIONAL0.040.05
3B1005TIGHT THERMAL0.010.5
4E1524TIGHT POSITIONAL0.050.05
4E1524TIGHT THERMAL0.010.5
5H1005TIGHT POSITIONAL0.060.05
5H1005TIGHT THERMAL0.010.5
LS refinement shellResolution: 3.5→3.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 261 -
Rwork0.335 4616 -
obs--97.31 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.559-1.5827-0.490810.36660.82462.6447-0.0231-0.08280.04650.22820.12830.0855-0.28620.2807-0.10530.7085-0.1223-0.13660.03220.04820.4049117.3172-1.74045.9966
210.6204-1.54590.96221.4665-0.50822.82880.08910.22170.0574-0.05160.01220.07160.2831-0.3237-0.10130.0182-0.11230.03660.7095-0.15360.389866.6472-52.404836.041
32.79221.80890.86510.1369-0.72592.588-0.10210.1065-0.1193-0.78240.1027-0.0690.18250.254-0.00060.62050.14640.12580.24870.01670.4359118.3661-57.54439.6364
410.31291.6812-0.64562.64760.97752.51940.1305-0.7741-0.0140.0693-0.1243-0.09620.29370.1883-0.00620.2490.1390.01810.62120.12630.433122.4777-53.463632.374
53.062-0.74162.47414.1568-3.008211.45410.11380.1003-0.0877-1.03080.0548-0.14250.9379-0.2922-0.16860.6776-0.06230.01950.67510.00960.5601110.25559.810857.6867
67.43180.79840.33368.11352.166810.1674-0.20360.1443-0.2421-0.6023-0.00060.3405-0.0125-0.22820.20420.23090.038-0.0150.9043-0.050.49737.6336-45.243713.3339
74.3236-0.6889-3.14233.21622.455611.63040.0549-0.9656-0.12810.10.1516-0.1072-0.30450.9215-0.20650.6772-0.0633-0.01910.68380.0030.552155.1063-45.363-15.6796
87.66861.00091.87027.88940.286910.02310.0017-0.67960.31180.2135-0.1931-0.2293-0.1463-0.07750.19140.87650.0261-0.07760.2302-0.01640.4794110.156427.290628.6862
94.0427-1.20833.56612.8513-2.14757.60830.37290.6539-0.2621-1.0465-0.26390.34260.3086-0.5379-0.10911.77820.1436-0.40810.4826-0.03920.814995.0801-83.0274-12.4181
103.016-1.2212-1.98994.15343.95077.856-0.2485-0.98160.38340.62060.2978-0.1584-0.47360.277-0.04930.45880.14050.00391.7601-0.40020.8131147.9783-30.164354.3289
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA467 - 6626 - 201
2X-RAY DIFFRACTION2DC467 - 6626 - 201
3X-RAY DIFFRACTION3EE467 - 6626 - 201
4X-RAY DIFFRACTION4JG467 - 6626 - 201
5X-RAY DIFFRACTION5BD4 - 13712 - 145
6X-RAY DIFFRACTION6CB274 - 425282 - 433
7X-RAY DIFFRACTION7CB4 - 13712 - 145
8X-RAY DIFFRACTION8BD274 - 425282 - 433
9X-RAY DIFFRACTION9HF274 - 425282 - 433
10X-RAY DIFFRACTION10KH274 - 425282 - 433

+
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