[English] 日本語
Yorodumi
- PDB-8hyr: Crystal structure of human KARS apo -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8hyr
TitleCrystal structure of human KARS apo
ComponentsLysine--tRNA ligase
KeywordsBIOSYNTHETIC PROTEIN / Lysyl-tRNA synthetase / KARS
Function / homology
Function and homology information


basophil activation involved in immune response / positive regulation of inflammatory response to antigenic stimulus / ATP:ADP adenylyltransferase activity / Mitochondrial tRNA aminoacylation / lysine-tRNA ligase / Selenoamino acid metabolism / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / Cytosolic tRNA aminoacylation ...basophil activation involved in immune response / positive regulation of inflammatory response to antigenic stimulus / ATP:ADP adenylyltransferase activity / Mitochondrial tRNA aminoacylation / lysine-tRNA ligase / Selenoamino acid metabolism / lysine-tRNA ligase activity / lysyl-tRNA aminoacylation / diadenosine tetraphosphate biosynthetic process / Cytosolic tRNA aminoacylation / aminoacyl-tRNA synthetase multienzyme complex / positive regulation of macrophage activation / tRNA processing / amino acid binding / response to X-ray / Transcriptional and post-translational regulation of MITF-M expression and activity / ERK1 and ERK2 cascade / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / tRNA binding / mitochondrial matrix / positive regulation of DNA-templated transcription / protein homodimerization activity / mitochondrion / extracellular space / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysine-tRNA ligase, class II / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. ...Bacterial/eukaryotic lysine-tRNA ligase, class II / Lysine-tRNA ligase, class II, N-terminal / Lysine-tRNA ligase, class II / Lysyl-tRNA synthetase, class II, C-terminal / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / 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) / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsZhang, X. / Wang, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870751 China
Ministry of Science and Technology (MoST, China)2018YFE0204500 China
CitationJournal: To Be Published
Title: Crystal structure of human KARS apo
Authors: Zhang, X. / Wang, Y. / Ouyang, Z.
History
DepositionJan 7, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lysine--tRNA ligase
B: Lysine--tRNA ligase


Theoretical massNumber of molelcules
Total (without water)120,3942
Polymers120,3942
Non-polymers00
Water3,297183
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8270 Å2
ΔGint-42 kcal/mol
Surface area43950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.331, 107.664, 130.516
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 70 and (name N or name...
d_2ens_1(chain "B" and ((resid 70 and (name N or name...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERGLUGLUAA70 - 5662 - 498
d_21SERSERLYSLYSBB70 - 5172 - 449
d_22PHEPHEGLUGLUBB528 - 566460 - 498

NCS oper: (Code: givenMatrix: (-0.999978102251, -0.00653717132516, 0.00102976222449), (-0.00654785426751, 0.999920918381, -0.0107369729668), (-0.000959491357428, -0.0107434805843, -0.999941826809) ...NCS oper: (Code: given
Matrix: (-0.999978102251, -0.00653717132516, 0.00102976222449), (-0.00654785426751, 0.999920918381, -0.0107369729668), (-0.000959491357428, -0.0107434805843, -0.999941826809)
Vector: -0.0160336185251, 0.0791000865951, 28.230642563)

-
Components

#1: Protein Lysine--tRNA ligase / Lysyl-tRNA synthetase / LysRS


Mass: 60197.199 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KARS1, KARS, KIAA0070 / Production host: Escherichia phage EcSzw-2 (virus)
References: UniProt: Q15046, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases, lysine-tRNA ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.64 Å3/Da / Density % sol: 53.33 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.06M Morpheus Divalents, 0.1M Morpheus Buffer system 1, pH 6.5, 30% Morpheus Precipitant Mix 2

-
Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 42172 / % possible obs: 99.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 39.66 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.064 / Rrim(I) all: 0.165 / Net I/σ(I): 13.5
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.93 / Num. unique obs: 4151 / CC1/2: 0.865 / Rpim(I) all: 0.383 / Rrim(I) all: 0.961 / % possible all: 99.71

-
Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→46.24 Å / SU ML: 0.2824 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.9554
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2453 1995 4.74 %
Rwork0.2147 40133 -
obs0.2162 42128 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.37 Å2
Refinement stepCycle: LAST / Resolution: 2.55→46.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8111 0 0 183 8294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00478303
X-RAY DIFFRACTIONf_angle_d0.666311213
X-RAY DIFFRACTIONf_chiral_restr0.04511215
X-RAY DIFFRACTIONf_plane_restr0.00651451
X-RAY DIFFRACTIONf_dihedral_angle_d13.7743177
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.515430016446 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.610.33481390.28092804X-RAY DIFFRACTION98.69
2.61-2.680.31191420.26352822X-RAY DIFFRACTION99.9
2.68-2.760.3141400.25942848X-RAY DIFFRACTION99.8
2.76-2.850.32721410.25992825X-RAY DIFFRACTION99.9
2.85-2.950.31511410.25412831X-RAY DIFFRACTION99.93
2.95-3.070.28521410.23882853X-RAY DIFFRACTION99.9
3.07-3.210.27551420.22622835X-RAY DIFFRACTION99.87
3.21-3.380.24711410.22942863X-RAY DIFFRACTION99.87
3.38-3.590.29571430.22222870X-RAY DIFFRACTION99.9
3.59-3.870.2561420.20372857X-RAY DIFFRACTION99.87
3.87-4.260.19391440.18192882X-RAY DIFFRACTION99.9
4.26-4.870.17011430.16062897X-RAY DIFFRACTION99.8
4.87-6.140.19951470.20572934X-RAY DIFFRACTION99.94
6.14-46.240.23651490.21913012X-RAY DIFFRACTION98.11
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.746811911311.118229956370.6607424648555.784825395370.4598579829052.05449500919-0.0787055626765-0.02259618974-0.09658214029740.2633138811250.14085327835-0.1921954345490.1971773894080.192692438464-0.06873808866970.3461620081150.053415107323-0.03730650401520.3503058243540.06368546094190.25571427081929.9380253638-9.6592688682836.5546182028
22.516090629130.07265778234520.693070632440.7022822249020.1285239014341.56375401634-0.125847751055-0.1604700139210.2127404512860.0279428950298-0.04094138958830.0181180638337-0.12453491384-0.1185102565840.1165043725860.2335420506390.004160045708330.02847740463390.246800260796-0.007825577622310.214498690267-2.358092505724.5044939301320.4142296718
34.50514886157-2.1872521893-0.3946219499863.429432221890.9182600827492.03997036127-0.25312571436-0.0284267736066-0.1470166457530.1187701077450.0962310386220.376069375911-0.118382221388-0.2265064415520.1507670931340.2738374680350.007735770328570.06720348801660.3544608543770.07446283695670.29623699998-26.40675137980.28262142584329.8826832217
42.0043446241-0.777788556171.403463784150.6077016216780.3834585710943.9578232182-0.2853189503060.1135387740970.3412335588760.07311494013650.006624661788820.124580614605-0.507943174167-0.2915200902730.291404217210.3142585452820.003110343089540.004038690155370.3399573481030.03501348898460.409355705728-15.58762260476.0820287533918.1805472126
51.73085282725-0.1653079813210.9446652459180.329260056211-0.0841638008781.433190172170.02736201245920.173320670267-0.163599478312-0.141915919553-0.03807831750960.01313140377270.126330837174-0.00494223876110.003983677378140.313521697784-0.003548286194340.03873528299250.289205438303-0.01126522278040.275257879643-10.3675611061-3.49458440897-0.261331063637
62.214558042860.1291609891450.5743710366030.1317116861690.5344202197681.45813377938-0.2271909218180.7010901713430.427474084042-0.1283934273530.0545111690558-0.203761556968-0.333878364350.5487233393320.1292629613010.440787441024-0.07178769265150.007874168330370.6380738853960.1712877978710.48714932702623.98184572114.842352745063.79235981841
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 70 through 207 )AA70 - 2071 - 138
22chain 'A' and (resid 208 through 346 )AA208 - 346139 - 277
33chain 'A' and (resid 347 through 484 )AA347 - 484278 - 415
44chain 'A' and (resid 485 through 576 )AA485 - 576416 - 499
55chain 'B' and (resid 70 through 382 )BB70 - 3821 - 313
66chain 'B' and (resid 383 through 576 )BB383 - 576314 - 500

+
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://pdbjlvh1.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