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- PDB-5w6m: Crystal structure of the human histidyl-tRNA synthetase mutant D175E -

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Basic information

Entry
Database: PDB / ID: 5w6m
TitleCrystal structure of the human histidyl-tRNA synthetase mutant D175E
ComponentsHistidine--tRNA ligase, cytoplasmic
KeywordsLIGASE / tRNA-synthetase / CMT mutant
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 / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Histidine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.696 Å
AuthorsBlocquel, D. / Yang, X.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: CMT disease severity correlates with mutation-induced open conformation of histidyl-tRNA synthetase, not aminoacylation loss, in patient cells.
Authors: Blocquel, D. / Sun, L. / Matuszek, Z. / Li, S. / Weber, T. / Kuhle, B. / Kooi, G. / Wei, N. / Baets, J. / Pan, T. / Schimmel, P. / Yang, X.L.
History
DepositionJun 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histidine--tRNA ligase, cytoplasmic
B: Histidine--tRNA ligase, cytoplasmic


Theoretical massNumber of molelcules
Total (without water)101,8452
Polymers101,8452
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7800 Å2
ΔGint-43 kcal/mol
Surface area35350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.360, 93.360, 254.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 50922.695 Da / Num. of mol.: 2 / Fragment: UNP residues 54-503 / Mutation: D175E
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

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M Tris pH 8, 0.2 M MgCl2 and 20% PEG 2000 / PH range: 7-9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.696→38.591 Å / Num. obs: 12712 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 12.586 % / Biso Wilson estimate: 134.07 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Rrim(I) all: 0.096 / Χ2: 0.99 / Net I/σ(I): 21.03
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.696-3.7912.6050.8173.719040.9430.85198.6
3.79-3.913.2480.5785.229070.9740.60199.8
3.9-4.0113.4770.4526.438510.9870.4799.5
4.01-4.1313.2130.3468.298350.9920.3699.8
4.13-4.2713.050.2999.558440.9920.31199.9
4.27-4.4212.5190.21412.457840.9960.22399.9
4.42-4.5811.2210.14316.987700.9970.1599.9
4.58-4.7713.3920.133197390.9980.138100
4.77-4.9813.5670.10721.517200.9990.111100
4.98-5.2313.3050.12120.676960.9980.126100
5.23-5.5113.0210.11521.686640.9980.12100
5.51-5.8412.9760.11521.296210.9980.12100
5.84-6.2512.350.124.855860.9980.104100
6.25-6.7510.8130.08426.65570.9980.08899.8
6.75-7.3912.3730.06238.395090.9990.06599.8
7.39-8.2612.40.04348.984730.9990.04599.8
8.26-9.5412.0850.03557.1842310.037100
9.54-11.6910.970.03260.5836910.033100
11.69-16.539.5920.03455.942940.9990.035100
16.53-38.5919.5360.03556.31660.9990.03689.7

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4G84

4g84


Resolution: 3.696→38.591 Å / SU ML: 0.59 / Cross valid method: NONE / σ(F): 1.36 / Phase error: 36.53
RfactorNum. reflection% reflection
Rfree0.3107 635 5.01 %
Rwork0.2498 --
obs0.2528 12679 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 327.23 Å2 / Biso mean: 152.9919 Å2 / Biso min: 102.15 Å2
Refinement stepCycle: final / Resolution: 3.696→38.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6261 0 0 0 6261
Num. residues----784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046348
X-RAY DIFFRACTIONf_angle_d0.6858532
X-RAY DIFFRACTIONf_chiral_restr0.046972
X-RAY DIFFRACTIONf_plane_restr0.0041088
X-RAY DIFFRACTIONf_dihedral_angle_d13.573906
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.6961-3.98120.39871230.28682327245099
3.9812-4.38130.30731240.25192350247499
4.3813-5.01410.28591240.21323692493100
5.0141-6.31280.33211280.269124332561100
6.3128-38.59340.29451360.248625652701100
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)
11.2928-1.119-1.28831.0211-0.8009-0.0658-0.24550.02980.298-0.10570.1409-0.289-0.29260.28150.00011.4955-0.29430.02581.4748-0.06871.3841219.3392-30.4774262.3778
20.7629-0.7978-0.70230.72770.10291.2241-0.0387-0.2444-0.06690.07990.2055-0.10880.37130.7731-01.42230.0311-0.08161.5159-0.05531.3788222.932-49.8198272.2921
30.59430.39420.00331.08410.2890.94190.2684-0.2526-0.4384-0.7229-0.21660.5912-0.1027-0.25850.00011.65350.0818-0.05361.3835-0.00721.4583188.3638-35.5287232.5088
4-0.18070.77221.2607-2.34580.5148-0.1447-0.1255-0.13370.0173-0.4831-0.26660.1335-0.36660.2954-0.00011.6711-0.13220.04551.50530.10641.5459212.7005-21.2894252.2429
50.25510.04350.3486-0.114-0.19790.135-0.2276-0.68350.13710.37430.48150.7345-0.4563-0.20590.00031.80840.162-0.13841.2186-0.11881.6542194.1185-13.0229239.5965
60.54280.73460.74020.30590.54960.60940.80240.27670.9707-0.4495-0.1361-1.0034-2.4230.52970.00082.3076-0.0976-0.07151.210.25331.6264203.3818-11.5415240.9552
70.7285-0.40540.42490.1409-0.36960.3417-0.0588-0.5370.5007-0.07150.11240.5502-0.1299-0.27470.00031.58610.19230.04441.3692-0.27991.6491196.4088-22.0072265.043
81.97580.8512-0.761.3128-0.71680.5937-0.1878-0.2872-0.4549-0.18470.01540.3870.0639-0.2882-01.31390.00750.01731.4289-0.04161.4252193.0303-48.0526281.2942
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 54 through 169 )A54 - 169
2X-RAY DIFFRACTION2chain 'A' and (resid 170 through 411 )A170 - 411
3X-RAY DIFFRACTION3chain 'A' and (resid 412 through 503 )A412 - 503
4X-RAY DIFFRACTION4chain 'B' and (resid 54 through 185 )B54 - 185
5X-RAY DIFFRACTION5chain 'B' and (resid 186 through 312 )B186 - 312
6X-RAY DIFFRACTION6chain 'B' and (resid 313 through 379 )B313 - 379
7X-RAY DIFFRACTION7chain 'B' and (resid 380 through 410 )B380 - 410
8X-RAY DIFFRACTION8chain 'B' and (resid 411 through 502 )B411 - 502

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