[English] 日本語
Yorodumi
- PDB-4bl7: Crystal structure of the AIMP3-MRS N-terminal domain complex in d... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bl7
TitleCrystal structure of the AIMP3-MRS N-terminal domain complex in different space group
Components
  • EUKARYOTIC TRANSLATION ELONGATION FACTOR 1 EPSILON-1
  • METHIONINE--TRNA LIGASE, CYTOPLASMIC
KeywordsTRANSLATION / LIGASE
Function / homology
Function and homology information


Selenoamino acid metabolism / methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / 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 / rRNA transcription ...Selenoamino acid metabolism / methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / 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 / rRNA transcription / cellular response to platelet-derived growth factor stimulus / Transcriptional and post-translational regulation of MITF-M expression and activity / cellular response to epidermal growth factor stimulus / cellular response to leukemia inhibitory factor / positive regulation of apoptotic signaling pathway / positive regulation of cellular senescence / tRNA binding / positive regulation of apoptotic process / translation / negative regulation of cell population proliferation / nucleolus / extracellular exosome / nucleoplasm / ATP binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Glutaredoxin - #90 / Eukaryotic translation elongation factor 1 epsilon-1 / : / Methionine--tRNA ligase, N-terminal / Glutathione S-transferase, N-terminal domain / Methionine-tRNA ligase, type 1 / Methionyl-tRNA synthetase, Zn-domain / : / Nuclear-export cofactor Arc1p / WHEP-TRS domain ...Glutaredoxin - #90 / Eukaryotic translation elongation factor 1 epsilon-1 / : / Methionine--tRNA ligase, N-terminal / Glutathione S-transferase, N-terminal domain / Methionine-tRNA ligase, type 1 / Methionyl-tRNA synthetase, Zn-domain / : / Nuclear-export cofactor Arc1p / WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / Anticodon binding domain of methionyl tRNA ligase / Methionyl-tRNA synthetase / Methioninyl-tRNA synthetase core domain / Methionyl-tRNA synthetase, anticodon-binding domain / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Glutathione S-transferase, C-terminal domain / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / Glutathione S-transferase, C-terminal / 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 / Rossmann-like alpha/beta/alpha sandwich fold / Glutaredoxin / Glutaredoxin / S15/NS1, RNA-binding / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Eukaryotic translation elongation factor 1 epsilon-1 / Methionine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.892 Å
AuthorsCho, H.Y. / Seo, W.W. / Cho, H.J. / Kang, B.S.
CitationJournal: To be Published
Title: Crystal Structure of the Aimp3-Mrs N-Terminal Domain Complex in Different Space Group
Authors: Cho, H.Y. / Seo, W.W. / Cho, H.J. / Kang, B.S.
History
DepositionMay 2, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
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
A: METHIONINE--TRNA LIGASE, CYTOPLASMIC
B: EUKARYOTIC TRANSLATION ELONGATION FACTOR 1 EPSILON-1


Theoretical massNumber of molelcules
Total (without water)47,1122
Polymers47,1122
Non-polymers00
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-7.5 kcal/mol
Surface area17530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.685, 72.029, 123.417
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-2054-

HOH

21A-2055-

HOH

-
Components

#1: Protein METHIONINE--TRNA LIGASE, CYTOPLASMIC / METHIONYL-TRNA SYNTHETASE / METRS


Mass: 25886.238 Da / Num. of mol.: 1 / Fragment: N-TERMINAL DOMAIN, RESIDUES 1-224
Source method: isolated from a genetically manipulated source
Details: M1 TO E224 OF MRS N-TERMINUS DOMAIN / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 / References: UniProt: P56192, methionine-tRNA ligase
#2: Protein EUKARYOTIC TRANSLATION ELONGATION FACTOR 1 EPSILON-1 / AMINOACYL TRNA SYNTHETASE COMPLEX-INTERACTING MULTIFUNCTIONAL PROTEIN 3 / ELONGATION FACTOR P18 / ...AMINOACYL TRNA SYNTHETASE COMPLEX-INTERACTING MULTIFUNCTIONAL PROTEIN 3 / ELONGATION FACTOR P18 / MULTISYNTHASE COMPLEX AUXILIARY COMPONENT P18 / AIMP3


Mass: 21226.016 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: M1 TO H174 OF AIMP3 WITH ADDITIONAL S SEQUENCE AT THE N-TERMINUS DUE TO CLONING PROCEDURE
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O43324
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.32 Å3/Da / Density % sol: 46.97 % / Description: NONE
Crystal growpH: 6.5
Details: PROTEIN WAS CRYSTALLIZED FROM 25% PEG 3350, 100 MM BIS-TRIS, PH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97954
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97954 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 29322 / % possible obs: 92 % / Observed criterion σ(I): -2 / Redundancy: 11.2 % / Biso Wilson estimate: 18.92 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 53
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 4.14 / % possible all: 60.2

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BJW

4bjw
PDB Unreleased entry


Resolution: 1.892→37.352 Å / SU ML: 0.2 / σ(F): 0.13 / Phase error: 21.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2294 1949 6.9 %
Rwork0.1804 --
obs0.1837 28425 89.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.892→37.352 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2963 0 0 153 3116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073031
X-RAY DIFFRACTIONf_angle_d1.1094125
X-RAY DIFFRACTIONf_dihedral_angle_d14.2761104
X-RAY DIFFRACTIONf_chiral_restr0.075469
X-RAY DIFFRACTIONf_plane_restr0.005526
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8924-1.93970.2835760.24271004X-RAY DIFFRACTION48
1.9397-1.99210.286980.22381296X-RAY DIFFRACTION62
1.9921-2.05070.26871160.20631549X-RAY DIFFRACTION75
2.0507-2.11690.22961260.18691729X-RAY DIFFRACTION83
2.1169-2.19260.21781390.18041894X-RAY DIFFRACTION90
2.1926-2.28040.2411490.17422006X-RAY DIFFRACTION96
2.2804-2.38410.24741470.18282044X-RAY DIFFRACTION98
2.3841-2.50980.24681520.18982084X-RAY DIFFRACTION99
2.5098-2.6670.26831540.18942100X-RAY DIFFRACTION99
2.667-2.87290.24661550.19392116X-RAY DIFFRACTION100
2.8729-3.16180.25691550.2042113X-RAY DIFFRACTION99
3.1618-3.6190.22021580.17982137X-RAY DIFFRACTION100
3.619-4.55830.18381590.14872156X-RAY DIFFRACTION99
4.5583-37.35940.20951650.16652248X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -18.4083 Å / Origin y: 18.919 Å / Origin z: -19.7389 Å
111213212223313233
T0.0975 Å2-0.0358 Å20.0017 Å2-0.0472 Å20.0058 Å2--0.0687 Å2
L0.457 °20.0899 °2-0.1894 °2-1.2283 °2-0.1684 °2--0.5308 °2
S0.0466 Å °0.0369 Å °-0.062 Å °0.3205 Å °-0.0735 Å °-0.0004 Å °-0.0693 Å °0.0994 Å °0.0177 Å °
Refinement TLS groupSelection details: ALL

+
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