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- PDB-2lw7: NMR solution structure of human HisRS splice variant -

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Basic information

Entry
Database: PDB / ID: 2lw7
TitleNMR solution structure of human HisRS splice variant
ComponentsHistidine--tRNA ligase, cytoplasmic
KeywordsLIGASE / synthetase
Function / homology
Function and homology information


histidine-tRNA ligase / histidine-tRNA ligase activity / histidyl-tRNA aminoacylation / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / mitochondrial translation / translation / protein homodimerization activity / mitochondrion / RNA binding ...histidine-tRNA ligase / histidine-tRNA ligase activity / histidyl-tRNA aminoacylation / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / mitochondrial translation / translation / protein homodimerization activity / mitochondrion / RNA binding / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Histidyl-anticodon-binding / Histidine-tRNA ligase / Histidine-tRNA ligase/ATP phosphoribosyltransferase regulatory subunit / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase / WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS ...Histidyl-anticodon-binding / Histidine-tRNA ligase / Histidine-tRNA ligase/ATP phosphoribosyltransferase regulatory subunit / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase / WHEP-TRS domain / WHEP-TRS domain / WHEP-TRS domain signature. / WHEP-TRS domain profile. / WHEP-TRS / Anticodon-binding domain / S15/NS1, RNA-binding / 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) / Helix Hairpins / S15/NS1, RNA-binding / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Histidine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
Model detailslowest energy, model1
AuthorsYe, F. / Wei, Z. / Wu, J. / Schimmel, P. / Zhang, M.
CitationJournal: To be Published
Title: NMR solution structure of human HisRS splice variant
Authors: Ye, F. / Wei, Z. / Wu, J. / Schimmel, P. / Zhang, M.
History
DepositionJul 24, 2012Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _struct_ref_seq_dif.details
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histidine--tRNA ligase, cytoplasmic


Theoretical massNumber of molelcules
Total (without water)19,2081
Polymers19,2081
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 94structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Histidine--tRNA ligase, cytoplasmic / Histidyl-tRNA synthetase / HisRS


Mass: 19208.338 Da / Num. of mol.: 1 / Fragment: UNP residues 2-59, UNP residues 399-509
Mutation: Deletion (UNP residues 61-398), W432Q, C507S, C509S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HARS, HRS / Production host: Escherichia coli (E. coli) / References: UniProt: P12081, histidine-tRNA ligase
Sequence detailsAMINO ACIDS (UNP RESIDUES 61-398) ARE MISSING BECAUSE OF DELETION MUTATION.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D HN(CA)CB
1412D 1H-1H NOESY
1513D 1H-13C NOESY
1613D 1H-15N NOESY

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Sample preparation

DetailsContents: 0.8 mM [U-100% 13C; U-100% 15N] entity-1, 100% D2O
Solvent system: 100% D2O
SampleConc.: 0.8 mM / Component: entity-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 100 / pH: 6.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSrefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 94 / Conformers submitted total number: 20 / Representative conformer: 1

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