[English] 日本語
Yorodumi
- PDB-2hsn: Structural basis of yeast aminoacyl-tRNA synthetase complex forma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2hsn
TitleStructural basis of yeast aminoacyl-tRNA synthetase complex formation revealed by crystal structures of two binary sub-complexes
Components
  • GU4 nucleic-binding protein 1
  • Methionyl-tRNA synthetase, cytoplasmicMethionine—tRNA ligase
KeywordsLigase/RNA Binding Protein / protein complex protein interaction GST-fold / Ligase-RNA Binding Protein COMPLEX
Function / homology
Function and homology information


methionyl glutamyl tRNA synthetase complex / glutamyl-tRNA aminoacylation / methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / tRNA aminoacylation for protein translation / phosphatidylinositol-3-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / enzyme activator activity / cytoplasmic stress granule ...methionyl glutamyl tRNA synthetase complex / glutamyl-tRNA aminoacylation / methionine-tRNA ligase / methionine-tRNA ligase activity / methionyl-tRNA aminoacylation / tRNA aminoacylation for protein translation / phosphatidylinositol-3-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / enzyme activator activity / cytoplasmic stress granule / tRNA binding / ATP binding / cytosol / cytoplasm
Similarity search - Function
Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #110 / Glutaredoxin - #170 / Methionyl-tRNA synthetase, N-terminal heteromerisation domain / MetRS-N binding domain / Methionine-tRNA ligase, type 1 / Methionyl-tRNA synthetase, Zn-domain / Methionyl-tRNA synthetase / Methioninyl-tRNA synthetase core domain / Methionyl-tRNA synthetase, anticodon-binding domain / tRNA-binding domain ...Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 - #110 / Glutaredoxin - #170 / Methionyl-tRNA synthetase, N-terminal heteromerisation domain / MetRS-N binding domain / Methionine-tRNA ligase, type 1 / Methionyl-tRNA synthetase, Zn-domain / Methionyl-tRNA synthetase / Methioninyl-tRNA synthetase core domain / Methionyl-tRNA synthetase, anticodon-binding domain / tRNA-binding domain / Putative tRNA binding domain / tRNA-binding domain profile. / Methionyl/Leucyl tRNA synthetase / tRNA synthetases class I (M) / Aminoacyl-tRNA synthetase, class Ia, anticodon-binding / Aminoacyl-tRNA synthetase, class I, conserved site / Aminoacyl-transfer RNA synthetases class-I signature. / 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 domain superfamily / Rossmann-like alpha/beta/alpha sandwich fold / Glutaredoxin / Nucleic acid-binding, OB-fold / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Methionine--tRNA ligase, cytoplasmic / tRNA-aminoacylation cofactor ARC1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSimader, H. / Koehler, C. / Basquin, J. / Suck, D.
CitationJournal: Nucleic Acids Res. / Year: 2006
Title: Structural basis of yeast aminoacyl-tRNA synthetase complex formation revealed by crystal structures of two binary sub-complexes.
Authors: Simader, H. / Hothorn, M. / Kohler, C. / Basquin, J. / Simos, G. / Suck, D.
History
DepositionJul 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). According to authors:This crystal structure reveals domain swapping of the N-terminal 55 residues between neighbouring molecules of MetRS-N (chain A of this entry) related by a true crystallographic 2-fold axis, effectively generating a tetramer of 2:2 composition. As discussed in detail in the literature reference of this entry, this phenomenon is an artifact of heterologous recombinant overexpression of MetRS-N in E. coli. Full-length MetRS purified from yeast is a monomer and engages in a 1:1 interaction with Arc1p (Deinert et al. (2001) JBC 276, 6000-6008).

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methionyl-tRNA synthetase, cytoplasmic
B: GU4 nucleic-binding protein 1


Theoretical massNumber of molelcules
Total (without water)32,2062
Polymers32,2062
Non-polymers00
Water2,738152
1
A: Methionyl-tRNA synthetase, cytoplasmic
B: GU4 nucleic-binding protein 1

A: Methionyl-tRNA synthetase, cytoplasmic
B: GU4 nucleic-binding protein 1


Theoretical massNumber of molelcules
Total (without water)64,4124
Polymers64,4124
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Unit cell
Length a, b, c (Å)94.480, 94.480, 88.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe biological unit is a heterodimer. The asymmetric unit contains a domain-swapped heterodimer.

-
Components

#1: Protein Methionyl-tRNA synthetase, cytoplasmic / Methionine—tRNA ligase / Methionine-tRNA ligase / MetRS


Mass: 18202.875 Da / Num. of mol.: 1 / Fragment: residues 1-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MES1 / Plasmid: pETm-derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 Star / References: UniProt: P00958, methionine-tRNA ligase
#2: Protein GU4 nucleic-binding protein 1 / G4p1 protein / P42 / ARC1 protein


Mass: 14002.878 Da / Num. of mol.: 1 / Fragment: residues 1-122
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ARC1 / Plasmid: pETm-derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 Star / References: UniProt: P46672
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.86 %
Crystal growTemperature: 293 K / pH: 9
Details: 8 - 14 % PEG 20.000, 1 - 3 % dioxane, 100 mM BICINE, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 9.00

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.54179
SYNCHROTRONESRF ID14-420.9395
Detector
TypeIDDetectorDate
MAR scanner 345 mm plate1IMAGE PLATEFeb 7, 2006
ADSC QUANTUM 3152CCDFeb 26, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1mirrorsSINGLE WAVELENGTHMx-ray1
2Si111 or Si311 crystals, LN2 cooledSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.541791
20.93951
ReflectionResolution: 2.2→50 Å / Num. obs: 20772 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 11 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 21.5
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.263 / Mean I/σ(I) obs: 4.96 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
SOLVEphasing
RESOLVEphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CHAIN C FROM PDB ENTRY 2HQT

2hqt


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.924 / SU B: 7.439 / SU ML: 0.183 / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.246 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1039 5 %RANDOM
Rwork0.225 ---
obs0.228 19731 99.3 %-
all-19862 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.68 Å2
Baniso -1Baniso -2Baniso -3
1--1.43 Å20 Å20 Å2
2---1.43 Å20 Å2
3---2.87 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2203 0 0 152 2355
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222265
X-RAY DIFFRACTIONr_bond_other_d0.0020.021458
X-RAY DIFFRACTIONr_angle_refined_deg1.2671.9643081
X-RAY DIFFRACTIONr_angle_other_deg0.93333604
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1515278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.31325.45599
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.87215380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.659155
X-RAY DIFFRACTIONr_chiral_restr0.0690.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022474
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02421
X-RAY DIFFRACTIONr_nbd_refined0.2380.2594
X-RAY DIFFRACTIONr_nbd_other0.1910.21448
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21106
X-RAY DIFFRACTIONr_nbtor_other0.0910.21086
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2146
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2560.234
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2610.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2340.213
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9051.51811
X-RAY DIFFRACTIONr_mcbond_other0.1081.5549
X-RAY DIFFRACTIONr_mcangle_it1.02722274
X-RAY DIFFRACTIONr_scbond_it1.4243990
X-RAY DIFFRACTIONr_scangle_it2.1144.5807
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 72 -
Rwork0.317 1442 -
obs--100 %

+
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