[English] 日本語
Yorodumi
- PDB-4rqf: human Seryl-tRNA synthetase dimer complexed with one molecule of ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4rqf
Titlehuman Seryl-tRNA synthetase dimer complexed with one molecule of tRNAsec
Components
  • Serine--tRNA ligase, cytoplasmic
  • selenocysteine tRNA
KeywordsLIGASE/RNA / aminoacyl-tRNA synthetase / classII aaRS / aminoacylation / serine / cytosol / LIGASE-RNA complex
Function / homology
Function and homology information


selenocysteine-tRNA ligase activity / negative regulation of vascular endothelial growth factor production / selenocysteine incorporation / seryl-tRNA aminoacylation / serine-tRNA ligase / serine-tRNA ligase activity / Cytosolic tRNA aminoacylation / tRNA modification / Selenocysteine synthesis / negative regulation of angiogenesis ...selenocysteine-tRNA ligase activity / negative regulation of vascular endothelial growth factor production / selenocysteine incorporation / seryl-tRNA aminoacylation / serine-tRNA ligase / serine-tRNA ligase activity / Cytosolic tRNA aminoacylation / tRNA modification / Selenocysteine synthesis / negative regulation of angiogenesis / cytoplasmic translation / tRNA binding / molecular adaptor activity / translation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / enzyme binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / extracellular exosome / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Serine-tRNA synthetase, tRNA binding domain / Serine-tRNA synthetase, type1, N-terminal / Seryl-tRNA synthetase N-terminal domain / Serine-tRNA ligase, type1 / Serine-tRNA ligase catalytic core domain / Serine-tRNA synthetase, type1, N-terminal domain superfamily / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Bira Bifunctional Protein; Domain 2 ...Serine-tRNA synthetase, tRNA binding domain / Serine-tRNA synthetase, type1, N-terminal / Seryl-tRNA synthetase N-terminal domain / Serine-tRNA ligase, type1 / Serine-tRNA ligase catalytic core domain / Serine-tRNA synthetase, type1, N-terminal domain superfamily / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / 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) / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / SERINE / RNA / RNA (> 10) / Serine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.503 Å
AuthorsXie, W. / Wang, C. / Guo, Y. / Tian, Q. / Jia, Q.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: SerRS-tRNASec complex structures reveal mechanism of the first step in selenocysteine biosynthesis.
Authors: Wang, C. / Guo, Y. / Tian, Q. / Jia, Q. / Gao, Y. / Zhang, Q. / Zhou, C. / Xie, W.
History
DepositionNov 3, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Derived calculations
Revision 1.2Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: selenocysteine tRNA
A: Serine--tRNA ligase, cytoplasmic
B: Serine--tRNA ligase, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,0407
Polymers148,8173
Non-polymers1,2234
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8340 Å2
ΔGint-45 kcal/mol
Surface area50920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.377, 108.894, 89.491
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: RNA chain selenocysteine tRNA


Mass: 28948.107 Da / Num. of mol.: 1 / Mutation: C2G, G70C / Source method: obtained synthetically / Details: in vitro synthesis / Source: (synth.) Homo sapiens (human)
#2: Protein Serine--tRNA ligase, cytoplasmic / Seryl-tRNA synthetase / SerRS / Seryl-tRNA(Ser/Sec) synthetase


Mass: 59934.441 Da / Num. of mol.: 2 / Mutation: E447K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SARS, SERS / Plasmid: pET20b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P49591, serine-tRNA ligase
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-SER / SERINE / Serine


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO3

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 18%(m/v) PEG3350, 0.1M NaCl, 0.1M Tris-HCl (pH8.0), 0.1M Sodium malonate pH7.0., VAPOR DIFFUSION, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.99 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 3.503→50 Å / Num. all: 20009 / Num. obs: 19748 / % possible obs: 98.7 % / Observed criterion σ(I): 3 / Redundancy: 5.6 % / Biso Wilson estimate: 115.87 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 12.4
Reflection shellResolution: 3.5→3.68 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.956 / % possible all: 100

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L87, 3A3A

4l87

3a3a


Resolution: 3.503→37.625 Å / SU ML: 0.47 / σ(F): 1.37 / Phase error: 34.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.314 1008 5.11 %
Rwork0.2531 --
obs0.256 19707 96.93 %
all-19707 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.503→37.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7202 1341 76 0 8619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018918
X-RAY DIFFRACTIONf_angle_d1.23812381
X-RAY DIFFRACTIONf_dihedral_angle_d15.3773499
X-RAY DIFFRACTIONf_chiral_restr0.0731432
X-RAY DIFFRACTIONf_plane_restr0.0061363
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.503-3.68770.35871410.30772313X-RAY DIFFRACTION86
3.6877-3.91850.33931350.28972727X-RAY DIFFRACTION100
3.9185-4.22070.32071490.26242703X-RAY DIFFRACTION100
4.2207-4.64470.3271770.25422684X-RAY DIFFRACTION100
4.6447-5.31520.28981310.24062744X-RAY DIFFRACTION100
5.3152-6.69050.34661540.26492764X-RAY DIFFRACTION99
6.6905-37.62710.27931210.23322764X-RAY DIFFRACTION94

+
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