[English] 日本語
Yorodumi
- PDB-2uz8: The crystal structure of p18, human translation elongation factor... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2uz8
TitleThe crystal structure of p18, human translation elongation factor 1 epsilon 1
ComponentsEUKARYOTIC TRANSLATION ELONGATION FACTOR 1 EPSILON-1
KeywordsRNA BINDING PROTEIN / PROTEIN BIOSYNTHESIS / AMINOACYL-TRNA SYNTHETASE / P18 / GST / NUCLEAR PROTEIN / ELONGATION FACTOR / RNA-BINDING PROTEIN
Function / homology
Function and homology information


Selenoamino acid metabolism / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / tRNA aminoacylation for protein translation / positive regulation of DNA damage response, signal transduction by p53 class mediator / Transcriptional and post-translational regulation of MITF-M expression and activity / positive regulation of cellular senescence / positive regulation of apoptotic process / negative regulation of cell population proliferation / nucleoplasm ...Selenoamino acid metabolism / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / tRNA aminoacylation for protein translation / positive regulation of DNA damage response, signal transduction by p53 class mediator / Transcriptional and post-translational regulation of MITF-M expression and activity / positive regulation of cellular senescence / positive regulation of apoptotic process / negative regulation of cell population proliferation / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Glutaredoxin - #90 / Eukaryotic translation elongation factor 1 epsilon-1 / : / : / Nuclear-export cofactor Arc1p / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. ...Glutaredoxin - #90 / Eukaryotic translation elongation factor 1 epsilon-1 / : / : / Nuclear-export cofactor Arc1p / Glutathione S-transferase, C-terminal domain / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #10 / Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 / Glutathione S-transferase, C-terminal-like / Soluble glutathione S-transferase C-terminal domain profile. / Glutathione S-transferase, C-terminal domain superfamily / Glutaredoxin / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Eukaryotic translation elongation factor 1 epsilon-1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKang, B.S. / Kim, K.J. / Kim, M.H. / Oh, Y.S. / Kim, S.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Determination of Three-Dimensional Structure and Residues of the Novel Tumor Suppressor Aimp3/P18 Required for the Interaction with Atm.
Authors: Kim, K.J. / Park, M.C. / Choi, S.J. / Oh, Y.S. / Choi, E.C. / Cho, H.J. / Kim, M.H. / Kim, S.H. / Kim, D.W. / Kim, S. / Kang, B.S.
History
DepositionApr 26, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EUKARYOTIC TRANSLATION ELONGATION FACTOR 1 EPSILON-1
B: EUKARYOTIC TRANSLATION ELONGATION FACTOR 1 EPSILON-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3334
Polymers40,1492
Non-polymers1842
Water2,774154
1
A: EUKARYOTIC TRANSLATION ELONGATION FACTOR 1 EPSILON-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1662
Polymers20,0741
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: EUKARYOTIC TRANSLATION ELONGATION FACTOR 1 EPSILON-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1662
Polymers20,0741
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.336, 77.915, 194.784
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein EUKARYOTIC TRANSLATION ELONGATION FACTOR 1 EPSILON-1 / EUKARYOTIC TRANSLATION ELONGATION FACTOR 1 EPSILON 1 / MULTISYNTHETASE COMPLEX AUXILIARY COMPONENT ...EUKARYOTIC TRANSLATION ELONGATION FACTOR 1 EPSILON 1 / MULTISYNTHETASE COMPLEX AUXILIARY COMPONENT P18 / ELONGATION FACTOR P18


Mass: 20074.275 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: FIVE RESIDUES AT C-TERMINUS ARE DELETED / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PPROEX-HTA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: O43324
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, THR 42 TO MET ENGINEERED RESIDUE IN CHAIN A, ILE 70 TO MET ...ENGINEERED RESIDUE IN CHAIN A, THR 42 TO MET ENGINEERED RESIDUE IN CHAIN A, ILE 70 TO MET ENGINEERED RESIDUE IN CHAIN A, LYS 96 TO MET ENGINEERED RESIDUE IN CHAIN B, THR 42 TO MET ENGINEERED RESIDUE IN CHAIN B, ILE 70 TO MET ENGINEERED RESIDUE IN CHAIN B, LYS 96 TO MET
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 44.86 % / Description: NONE

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.2399
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2399 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 22902 / % possible obs: 93.6 % / Observed criterion σ(I): 4 / Redundancy: 6.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 31.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 4 / % possible all: 82.7

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→33.41 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.336 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1156 5.1 %RANDOM
Rwork0.204 ---
obs0.206 21697 93.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→33.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2617 0 12 154 2783
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222689
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.9623645
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6785328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47524.426122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.02315471
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.181512
X-RAY DIFFRACTIONr_chiral_restr0.1050.2418
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021996
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.21161
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21833
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2177
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6671.51690
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.97822623
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.92931156
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2144.51020
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→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.352 65
Rwork0.236 1358

+
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