[English] 日本語
Yorodumi
- PDB-5e6m: Crystal structure of human wild type GlyRS bound with tRNAGly -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5e6m
TitleCrystal structure of human wild type GlyRS bound with tRNAGly
Components
  • Glycine--tRNA ligase
  • tRNA(Gly)
KeywordsLIGASE/RNA / Aminoacyl-tRNA syntheses / glycyl-tRNA synthetase / tRNA / LIGASE-RNA complex
Function / homology
Function and homology information


mitochondrial glycyl-tRNA aminoacylation / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / glycine-tRNA ligase / glycine-tRNA ligase activity / Mitochondrial tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / secretory granule / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases ...mitochondrial glycyl-tRNA aminoacylation / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / glycine-tRNA ligase / glycine-tRNA ligase activity / Mitochondrial tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / secretory granule / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / transferase activity / protein dimerization activity / mitochondrial matrix / axon / mitochondrion / extracellular exosome / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Glycyl-tRNA synthetase / Glycyl-tRNA synthetase-like core domain / Glycyl-tRNA synthetase/DNA polymerase subunit gamma-2 / WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) ...Glycyl-tRNA synthetase / Glycyl-tRNA synthetase-like core domain / Glycyl-tRNA synthetase/DNA polymerase subunit gamma-2 / WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Anticodon-binding / Anticodon binding domain / Anticodon-binding domain superfamily / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / S15/NS1, RNA-binding
Similarity search - Domain/homology
GLYCYL-ADENOSINE-5'-PHOSPHATE / NICKEL (II) ION / : / RNA / RNA (> 10) / Glycine--tRNA ligase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.927 Å
AuthorsXie, W. / Qin, X. / Deng, X. / Chen, L. / Liu, Y.
Funding support China, 3items
OrganizationGrant numberCountry
National Sciences Foundation of China31100579 China
Guangdong Innovative Research Team Program2011Y038 China
The Fundamental Research Funds for the Central Universities15lgjc15 China
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Crystal Structure of the Wild-Type Human GlyRS Bound with tRNA(Gly) in a Productive Conformation
Authors: Qin, X. / Deng, X. / Chen, L. / Xie, W.
History
DepositionOct 10, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycine--tRNA ligase
B: Glycine--tRNA ligase
C: tRNA(Gly)
E: tRNA(Gly)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,2329
Polymers205,2104
Non-polymers1,0225
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19720 Å2
ΔGint-132 kcal/mol
Surface area58510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)206.864, 122.200, 84.727
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-822-

HOH

-
Components

-
Protein / RNA chain , 2 types, 4 molecules ABCE

#1: Protein Glycine--tRNA ligase / Diadenosine tetraphosphate synthetase / AP-4-A synthetase / Glycyl-tRNA synthetase / GlyRS


Mass: 78704.828 Da / Num. of mol.: 2 / Fragment: UNP residues 55-739
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HELA CELLS / Gene: GARS / Plasmid: pET21b(+) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P41250, glycine-tRNA ligase
#2: RNA chain tRNA(Gly)


Mass: 23899.998 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: GenBank: 174921

-
Non-polymers , 4 types, 77 molecules

#3: Chemical ChemComp-GAP / GLYCYL-ADENOSINE-5'-PHOSPHATE


Mass: 404.273 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H17N6O8P
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.55 Å3/Da / Density % sol: 51.8 % / Description: rod crystals
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 32% PEG 600, 0.1 M NaCl, and 0.1 M MES (pH 6.5) with additives

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.997 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.997 Å / Relative weight: 1
ReflectionResolution: 2.927→50 Å / Num. obs: 46845 / % possible obs: 96.6 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 11.7
Reflection shellResolution: 2.927→3.06 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.878 / Mean I/σ(I) obs: 1.8 / % possible all: 96.2

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RK3

4rk3
PDB Unreleased entry


Resolution: 2.927→49.558 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2431 2283 5.05 %Random selection
Rwork0.1935 ---
obs0.1959 45184 95.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.927→49.558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7885 3160 61 72 11178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411643
X-RAY DIFFRACTIONf_angle_d0.85116506
X-RAY DIFFRACTIONf_dihedral_angle_d15.7134753
X-RAY DIFFRACTIONf_chiral_restr0.0551955
X-RAY DIFFRACTIONf_plane_restr0.0041589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9275-2.99110.30851460.24882338X-RAY DIFFRACTION86
2.9911-3.06070.33891440.23992632X-RAY DIFFRACTION96
3.0607-3.13720.34141590.23232608X-RAY DIFFRACTION95
3.1372-3.2220.29751420.22062667X-RAY DIFFRACTION97
3.222-3.31680.27441580.20272651X-RAY DIFFRACTION96
3.3168-3.42390.29121290.19912664X-RAY DIFFRACTION96
3.4239-3.54620.27371480.19732665X-RAY DIFFRACTION96
3.5462-3.68810.28041310.20862681X-RAY DIFFRACTION96
3.6881-3.85590.24011330.18732707X-RAY DIFFRACTION97
3.8559-4.05910.26411360.17182704X-RAY DIFFRACTION97
4.0591-4.31330.21911390.16372714X-RAY DIFFRACTION97
4.3133-4.64610.19241660.15252687X-RAY DIFFRACTION97
4.6461-5.11330.18591300.15782723X-RAY DIFFRACTION97
5.1133-5.85220.22381460.17922749X-RAY DIFFRACTION97
5.8522-7.36920.22441250.21142832X-RAY DIFFRACTION98
7.3692-49.5650.23181510.22552879X-RAY DIFFRACTION96

+
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