[English] 日本語
Yorodumi
- PDB-3wxm: Crystal structure of archaeal Pelota and GTP-bound EF1 alpha complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wxm
TitleCrystal structure of archaeal Pelota and GTP-bound EF1 alpha complex
Components
  • Elongation factor 1-alpha
  • Protein pelota homolog
KeywordsTRANSLATION/HYDROLASE / mRNA surveillance / Ribosome / TRANSLATION-HYDROLASE complex
Function / homology
Function and homology information


RNA surveillance / nuclear-transcribed mRNA catabolic process, no-go decay / nuclear-transcribed mRNA catabolic process, non-stop decay / translation elongation factor activity / endonuclease activity / Hydrolases; Acting on ester bonds / GTPase activity / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
Translation release factor pelota, archaea / Pelota, domain A / eRF1 domain 2 / Translation release factor pelota / Pelota/DOM34, N-terminal domain / Translation elongation factor EF1A, eukaryotic/archaeal / eRF1 domain 1 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily ...Translation release factor pelota, archaea / Pelota, domain A / eRF1 domain 2 / Translation release factor pelota / Pelota/DOM34, N-terminal domain / Translation elongation factor EF1A, eukaryotic/archaeal / eRF1 domain 1 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 3 / eRF1_1 / Ribosomal protein L30/S12 / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / 60s Ribosomal Protein L30; Chain: A; / Translation elongation factor EFTu-like, domain 2 / 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 (Ef-tu); domain 3 / 50S ribosomal protein L30e-like / SH3 type barrels. / Small GTP-binding protein domain / Nucleotidyltransferase; domain 5 / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Roll / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Elongation factor 1-alpha / Protein pelota homolog
Similarity search - Component
Biological speciesAeropyrum pernix K1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsKobayashi, K. / Ishitani, R. / Nureki, O.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural basis for mRNA surveillance by archaeal Pelota and GTP-bound EF1 alpha complex
Authors: Kobayashi, K. / Kikuno, I. / Kuroha, K. / Saito, K. / Ito, K. / Ishitani, R. / Inada, T. / Nureki, O.
History
DepositionAug 4, 2014Deposition site: PDBJ / Processing site: PDBJ
SupersessionSep 3, 2014ID: 3AGJ
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Elongation factor 1-alpha
B: Protein pelota homolog
C: Elongation factor 1-alpha
D: Protein pelota homolog
E: Elongation factor 1-alpha
F: Protein pelota homolog
G: Elongation factor 1-alpha
H: Protein pelota homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)366,72316
Polymers364,5338
Non-polymers2,1908
Water24,3021349
1
A: Elongation factor 1-alpha
B: Protein pelota homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,6814
Polymers91,1332
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-22 kcal/mol
Surface area32280 Å2
MethodPISA
2
C: Elongation factor 1-alpha
D: Protein pelota homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,6814
Polymers91,1332
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-23 kcal/mol
Surface area32410 Å2
MethodPISA
3
E: Elongation factor 1-alpha
F: Protein pelota homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,6814
Polymers91,1332
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-18 kcal/mol
Surface area32510 Å2
MethodPISA
4
G: Elongation factor 1-alpha
H: Protein pelota homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,6814
Polymers91,1332
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-20 kcal/mol
Surface area32420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.926, 158.944, 427.236
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-712-

HOH

-
Components

#1: Protein
Elongation factor 1-alpha / GTP-bound aEF1 alpha / EF-1-alpha / Elongation factor Tu / EF-Tu


Mass: 49662.559 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix K1 (archaea) / Gene: tuf, APE_1844 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): CodonPlus / References: UniProt: Q9YAV0
#2: Protein
Protein pelota homolog


Mass: 41470.602 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix K1 (archaea) / Gene: pelA, APE_1800.1 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): CodonPlus
References: UniProt: Q9YAZ5, Hydrolases; Acting on ester bonds
#3: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1349 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.47 Å3/Da / Density % sol: 64.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2.2M NaCl, 100mM imidazole, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 216696 / % possible obs: 95.8 % / Redundancy: 4.8 % / Biso Wilson estimate: 38.36 Å2

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
PHENIX(phenix.refine: 1.8.3_1479)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→32.433 Å / FOM work R set: 0.793 / SU ML: 0.41 / σ(F): 1.48 / Phase error: 28.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2609 10902 5.04 %
Rwork0.1983 --
obs0.2015 216119 96.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.52 Å2 / Biso mean: 45.73 Å2 / Biso min: 15.61 Å2
Refinement stepCycle: LAST / Resolution: 2.3→32.433 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24215 0 132 1349 25696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00924796
X-RAY DIFFRACTIONf_angle_d1.27533624
X-RAY DIFFRACTIONf_chiral_restr0.0543873
X-RAY DIFFRACTIONf_plane_restr0.0054343
X-RAY DIFFRACTIONf_dihedral_angle_d19.0579368
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.32610.38993430.3416466680992
2.3261-2.35350.38543390.32896444678393
2.3535-2.38220.34933300.31396521685193
2.3822-2.41230.35743460.31586565691193
2.4123-2.44410.36383710.31056500687193
2.4441-2.47750.35253780.30036567694593
2.4775-2.51290.34893530.30436499685294
2.5129-2.55040.34823300.30436648697894
2.5504-2.59020.35343470.28556667701495
2.5902-2.63270.33143640.26956628699295
2.6327-2.67810.3463650.26496755712096
2.6781-2.72670.3153420.24136807714996
2.7267-2.77920.33810.25156723710496
2.7792-2.83580.34623590.25386797715697
2.8358-2.89750.3073360.23966867720397
2.8975-2.96480.30123540.23796888724298
2.9648-3.03890.33223480.23346984733298
3.0389-3.1210.29893740.23016979735399
3.121-3.21280.31943280.21737004733299
3.2128-3.31640.26543700.20857000737099
3.3164-3.43480.27534090.19926956736599
3.4348-3.57220.27413730.193670327405100
3.5722-3.73450.26583770.176470897466100
3.7345-3.93110.22223910.16470187409100
3.9311-4.17690.21553790.153670927471100
4.1769-4.49860.20733550.138270787433100
4.4986-4.94990.18163930.128271187511100
4.9499-5.66290.21563480.154371537501100
5.6629-7.12220.22643920.162371837575100
7.1222-32.43650.18494270.15037189761697

+
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