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- PDB-8yp1: Crystal structure of HARS WHEP domain fused with Fc -

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Basic information

Entry
Database: PDB / ID: 8yp1
TitleCrystal structure of HARS WHEP domain fused with Fc
ComponentsImmunoglobulin heavy constant gamma 1,Histidine--tRNA ligase, cytoplasmic
KeywordsSPLICING-IMMUNE SYSTEM / His-tRNA Synthetase / Splice Variant
Function / homology
Function and homology information


histidine-tRNA ligase / histidine-tRNA ligase activity / histidyl-tRNA aminoacylation / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / mitochondrial translation ...histidine-tRNA ligase / histidine-tRNA ligase activity / histidyl-tRNA aminoacylation / Cytosolic tRNA aminoacylation / tRNA aminoacylation for protein translation / Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / mitochondrial translation / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / complement activation, classical pathway / Role of phospholipids in phagocytosis / antigen binding / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / blood microparticle / adaptive immune response / translation / protein homodimerization activity / mitochondrion / extracellular space / RNA binding / extracellular exosome / extracellular region / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
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 / 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) / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / S15/NS1, RNA-binding / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Immunoglobulin heavy constant gamma 1 / Histidine--tRNA ligase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsGeng, Y. / Zhai, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Transl Med / Year: 2025
Title: A human histidyl-tRNA synthetase splice variant therapeutic targets NRP2 to resolve lung inflammation and fibrosis.
Authors: Nangle, L.A. / Xu, Z. / Siefker, D. / Burkart, C. / Chong, Y.E. / Zhai, L. / Geng, Y. / Polizzi, C. / Guy, L. / Eide, L. / Tong, Y. / Klopp-Savino, S. / Ferrer, M. / Rauch, K. / Wang, A. / ...Authors: Nangle, L.A. / Xu, Z. / Siefker, D. / Burkart, C. / Chong, Y.E. / Zhai, L. / Geng, Y. / Polizzi, C. / Guy, L. / Eide, L. / Tong, Y. / Klopp-Savino, S. / Ferrer, M. / Rauch, K. / Wang, A. / Hamel, K. / Crampton, S. / Paz, S. / Chiang, K.P. / Do, M.H. / Burman, L. / Lee, D. / Zhang, M. / Ogilvie, K. / King, D. / Adams, R.A. / Schimmel, P.
History
DepositionMar 15, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Immunoglobulin heavy constant gamma 1,Histidine--tRNA ligase, cytoplasmic
B: Immunoglobulin heavy constant gamma 1,Histidine--tRNA ligase, cytoplasmic
C: Immunoglobulin heavy constant gamma 1,Histidine--tRNA ligase, cytoplasmic
D: Immunoglobulin heavy constant gamma 1,Histidine--tRNA ligase, cytoplasmic


Theoretical massNumber of molelcules
Total (without water)129,2804
Polymers129,2804
Non-polymers00
Water00
1
A: Immunoglobulin heavy constant gamma 1,Histidine--tRNA ligase, cytoplasmic
B: Immunoglobulin heavy constant gamma 1,Histidine--tRNA ligase, cytoplasmic


Theoretical massNumber of molelcules
Total (without water)64,6402
Polymers64,6402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-14 kcal/mol
Surface area28350 Å2
MethodPISA
2
C: Immunoglobulin heavy constant gamma 1,Histidine--tRNA ligase, cytoplasmic
D: Immunoglobulin heavy constant gamma 1,Histidine--tRNA ligase, cytoplasmic


Theoretical massNumber of molelcules
Total (without water)64,6402
Polymers64,6402
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-14 kcal/mol
Surface area27850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.943, 112.984, 110.211
Angle α, β, γ (deg.)90.00, 90.37, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
77
88
99
/ NCS ensembles :
ID
1
2
3
4
5
6
7
8
9

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Components

#1: Protein
Immunoglobulin heavy constant gamma 1,Histidine--tRNA ligase, cytoplasmic / Ig gamma-1 chain C region / Ig gamma-1 chain C region EU / Ig gamma-1 chain C region KOL / Ig gamma- ...Ig gamma-1 chain C region / Ig gamma-1 chain C region EU / Ig gamma-1 chain C region KOL / Ig gamma-1 chain C region NIE / Histidyl-tRNA synthetase / HisRS


Mass: 32319.906 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1, HARS1, HARS, HRS / Production host: Escherichia coli (E. coli)
References: UniProt: P01857, UniProt: P12081, histidine-tRNA ligase
Has protein modificationY

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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: 2.89 Å3/Da / Density % sol: 57.39 %
Crystal growTemperature: 289 K / Method: evaporation / pH: 5.5 / Details: 100mM BIS-TRIS pH 5.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 4, 2019
RadiationMonochromator: Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.79→50 Å / Num. obs: 36360 / % possible obs: 99.9 % / Redundancy: 6 % / CC1/2: 0.99 / CC star: 0.997 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.073 / Rrim(I) all: 0.181 / Χ2: 1.107 / Net I/σ(I): 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.8-2.855.81.78518420.6390.8830.7881.9540.472100
2.85-2.95.91.45917940.7010.9080.6391.5950.474100
2.9-2.9661.23917850.7150.9130.5361.3520.51100
2.96-3.026.21.0318260.8360.9540.4421.1220.502100
3.02-3.086.10.78218020.8860.9690.3380.8530.52899.9
3.08-3.1560.58818360.9330.9830.2590.6430.56999.9
3.15-3.235.70.44918000.9490.9870.2030.4930.632100
3.23-3.325.80.36518210.9550.9880.1640.4010.73199.9
3.32-3.426.20.29317720.980.9950.1260.320.667100
3.42-3.536.30.24418460.9810.9950.1040.2660.74799.9
3.53-3.656.20.22418040.980.9950.0970.2450.87199.9
3.65-3.86.10.18618100.9850.9960.080.2030.92699.9
3.8-3.9760.1518130.9890.9970.0670.1651.1199.9
3.97-4.185.60.1218020.990.9970.0550.1321.39799.7
4.18-4.446.20.10118200.9940.9990.0440.111.527100
4.44-4.796.20.0918230.9940.9980.040.0991.76799.8
4.79-5.2760.08618260.9950.9990.0380.0941.98699.9
5.27-6.035.70.08518520.9940.9990.0390.0941.938100
6.03-7.596.10.08118230.9950.9990.0350.0882.155100
7.59-505.20.05718630.9960.9990.0270.0642.85499.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VH5

5vh5


Resolution: 2.79→49.58 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.899 / SU B: 17.976 / SU ML: 0.323 / Cross valid method: THROUGHOUT / ESU R: 1.253 / ESU R Free: 0.356 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25634 1706 4.8 %RANDOM
Rwork0.21683 ---
obs0.21869 33853 97.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.981 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å20.68 Å2
2--4.73 Å2-0 Å2
3----4.38 Å2
Refinement stepCycle: 1 / Resolution: 2.79→49.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7973 0 0 0 7973
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0138167
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177606
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.65111087
X-RAY DIFFRACTIONr_angle_other_deg1.1551.57817821
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6365996
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.45823.878392
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.948151467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3451534
X-RAY DIFFRACTIONr_chiral_restr0.0590.21033
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028916
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021522
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.3386.9514002
X-RAY DIFFRACTIONr_mcbond_other5.3396.9514001
X-RAY DIFFRACTIONr_mcangle_it8.32210.4254992
X-RAY DIFFRACTIONr_mcangle_other8.32110.4264993
X-RAY DIFFRACTIONr_scbond_it5.9477.5484165
X-RAY DIFFRACTIONr_scbond_other5.9477.5484166
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.708116096
X-RAY DIFFRACTIONr_long_range_B_refined15.303132.26931057
X-RAY DIFFRACTIONr_long_range_B_other15.302132.26831058
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A71900.12
12B71900.12
21A68580.07
22C68580.07
31A3170.18
32C3170.18
41A72030.12
42D72030.12
51B65460.12
52C65460.12
61B3510.19
62C3510.19
71B78170.03
72D78170.03
81C65570.12
82D65570.12
91C3500.18
92D3500.18
LS refinement shellResolution: 2.794→2.866 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 126 -
Rwork0.373 2419 -
obs--93.7 %

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