PDB-8yor: Complex of HARSWHEP and a-HARSWHEP Fab

ID or keywords:

Entry

Database: PDB / ID: 8yor

Title

Complex of HARSWHEP and a-HARSWHEP Fab

Components

Histidine--tRNA ligase, cytoplasmic
a-HARSWHEP Fab-heavy chain
a-HARSWHEP Fab-light chain

Keywords

SPLICING/IMMUNE SYSTEM / NRP2 / Lung Inflammation / His-tRNA Synthetase Splice Variant / SPLICING / SPLICING-IMMUNE SYSTEM complex

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 ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Zhai, L.

Funding support

1items

Citation

Journal: 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. / ...

History

Deposition	Mar 13, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Feb 12, 2025	Provider: repository / Type: Initial release
Revision 1.1	Apr 2, 2025	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8yor.cif.gz	395.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8yor.ent.gz	324.4 KB	Display	PDB format
PDBx/mmJSON format	8yor.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/yo/8yor ftp://data.pdbj.org/pub/pdb/validation_reports/yo/8yor	HTTPS FTP

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Related structure data

Related structure data	8yp1C 4cmhS 5tl5S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1) #16 - Apr 2001 Aminoacyl-tRNA Synthetases similarity (6)

Deposited unit

A: a-HARSWHEP Fab-light chain

B: a-HARSWHEP Fab-heavy chain

E: Histidine--tRNA ligase, cytoplasmic

C: a-HARSWHEP Fab-light chain

F: Histidine--tRNA ligase, cytoplasmic

D: a-HARSWHEP Fab-heavy chain

113 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: a-HARSWHEP Fab-light chain

B: a-HARSWHEP Fab-heavy chain

E: Histidine--tRNA ligase, cytoplasmic

defined by author&software
Evidence: gel filtration
56.4 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: a-HARSWHEP Fab-light chain

F: Histidine--tRNA ligase, cytoplasmic

D: a-HARSWHEP Fab-heavy chain

defined by author&software
56.4 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	86.750, 113.560, 149.499
Angle α, β, γ (deg.)	90.00, 106.60, 90.00
Int Tables number	5
Space group name H-M	I121

Components on special symmetry positions

ID	Model	Components
1	1	B-302- HOH
2	1	D-304- HOH

#1: Antibody	a-HARSWHEP Fab-light chain Mass: 23886.451 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody	a-HARSWHEP Fab-heavy chain Mass: 24961.738 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein	Histidine--tRNA ligase, cytoplasmic / Histidyl-tRNA synthetase / HisRS / HARSWHEP Mass: 7585.847 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HARS1, HARS, HRS / Production host: Escherichia coli (E. coli) / References: UniProt: P12081, histidine-tRNA ligase
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 573 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.13 Å³/Da / Density % sol: 60.65 %
Crystal grow	Temperature: 289.15 K / Method: vapor diffusion, sitting drop Details: 20% w/v PEG 3350, 0.2 M potassium sodium tartrate tetrahydrate pH7.4

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97891 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 23, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97891 Å / Relative weight: 1
Reflection	Resolution: 2.3→88.995 Å / Num. obs: 59732 / % possible obs: 96.85 % / Redundancy: 1.9 % / CC_1/2: 0.985 / Net I/σ(I): 6.64
Reflection shell	Resolution: 2.3→2.382 Å / Num. unique obs: 5993 / CC_1/2: 0.635

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5TL5,4CMH

5tl5

4cmh

Resolution: 2.3→88.995 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 27.64 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2728	2974	4.98 %
R_work	0.2269	-	-
obs	0.2292	59716	96.85 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.3→88.995 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7351	0	0	573	7924

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	7516
X-RAY DIFFRACTION	f_angle_d	0.641	10193
X-RAY DIFFRACTION	f_dihedral_angle_d	11.105	2725
X-RAY DIFFRACTION	f_chiral_restr	0.023	1154
X-RAY DIFFRACTION	f_plane_restr	0.004	1308

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.3-2.3377	0.3201	159	0.2767	2690	X-RAY DIFFRACTION	98
2.3377-2.378	0.3827	137	0.2954	2716	X-RAY DIFFRACTION	98
2.378-2.4213	0.338	161	0.2865	2708	X-RAY DIFFRACTION	97
2.4213-2.4679	0.3023	127	0.2776	2727	X-RAY DIFFRACTION	98
2.4679-2.5182	0.3066	152	0.2684	2688	X-RAY DIFFRACTION	98
2.5182-2.573	0.3259	142	0.2646	2697	X-RAY DIFFRACTION	97
2.573-2.6329	0.302	132	0.2619	2721	X-RAY DIFFRACTION	97
2.6329-2.6987	0.3136	124	0.2539	2731	X-RAY DIFFRACTION	97
2.6987-2.7717	0.3256	130	0.2514	2569	X-RAY DIFFRACTION	92
2.7717-2.8532	0.3311	152	0.2644	2529	X-RAY DIFFRACTION	92
2.8532-2.9453	0.3112	161	0.2522	2727	X-RAY DIFFRACTION	98
2.9453-3.0506	0.2888	137	0.2471	2759	X-RAY DIFFRACTION	99
3.0506-3.1728	0.2836	157	0.2379	2732	X-RAY DIFFRACTION	99
3.1728-3.3172	0.278	149	0.2278	2744	X-RAY DIFFRACTION	98
3.3172-3.492	0.2754	170	0.2137	2703	X-RAY DIFFRACTION	98
3.492-3.7108	0.2702	148	0.2073	2711	X-RAY DIFFRACTION	98
3.7108-3.9974	0.2319	113	0.2023	2703	X-RAY DIFFRACTION	95
3.9974-4.3996	0.2342	113	0.1797	2594	X-RAY DIFFRACTION	92
4.3996-5.0362	0.2095	146	0.1769	2766	X-RAY DIFFRACTION	99
5.0362-6.3448	0.229	133	0.2114	2785	X-RAY DIFFRACTION	98
6.3448-10	0.246	131	0.2413	2742	X-RAY DIFFRACTION	95

Refinement TLS params.

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

ID	L11 (°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)
1	6.2026	1.5953	0.0556	1.6652	0.6576	2.1822	-0.0473	-0.7513	0.0735	0.3335	0.016	0.1909	-0.0481	-0.19	-0.071	0.431	-0.0259	0.0763	0.4376	0.068	0.2316	-19.2068	-12.0388	-31.9561
2	1.7729	0.2677	0.0438	1.5668	0.1048	1.247	0.0855	-0.3352	-0.0936	0.3679	-0.0475	0.0267	0.1296	-0.1994	-0.0376	0.3694	-0.0461	0.026	0.3679	0.0657	0.2145	-18.7174	-20.3236	-38.4382
3	4.6046	5.3429	-0.0484	6.583	-0.0744	0.0017	0.1275	-0.5551	-0.0705	0.1234	-0.2322	-0.2251	-0.482	-0.0617	0.1031	0.3856	-0.0689	-0.0006	0.2866	-0.0419	0.1915	-7.7622	0.1121	-35.1738
4	2.0852	-0.0278	1.1739	3.3521	-1.2451	2.3359	-0.0958	-0.2364	0.5201	0.0609	-0.0413	0.0844	-0.3623	-0.3351	0.1167	0.402	0.0379	-0.0746	0.2411	-0.1368	0.4018	-9.2828	16.9983	-49.7026
5	1.862	0.6313	-0.0439	0.3014	0.158	2.2066	-0.182	-0.2001	0.6262	0.2605	-0.0311	0.0996	-0.5321	-0.2029	0.2112	0.4789	0.0492	-0.0929	0.331	-0.1697	0.4456	-12.1522	17.9326	-48.0384
6	3.9473	-1.0348	3.3471	5.6582	-2.8176	6.9091	-0.2804	0.15	1.0408	0.0294	-0.6229	0.088	-0.92	0.6423	0.8479	0.5783	-0.027	-0.1454	0.3293	-0.1089	0.6106	-3.7676	22.8278	-43.9327
7	0.4219	-1.0451	-0.1162	5.318	-0.333	0.7442	0.129	0.2481	0.0261	-0.2811	-0.1805	-0.0781	-0.0138	-0.0382	0.0586	0.1936	-0.0164	-0.0156	0.2644	0.0468	0.176	-23.6557	-18.9733	-60.5925
8	2.4502	-0.2841	0.0808	3.3347	1.6892	3.2351	-0.1659	-0.1367	0.0871	0.2188	0.1394	0.4072	0.1124	-0.4513	0.0351	0.2125	-0.0288	0.0218	0.341	0.1095	0.2973	-32.9588	-19.8183	-54.1206
9	2.2072	-1.1503	-0.0491	5.6227	0.1059	1.1293	-0.2232	-0.145	-0.1389	0.0613	0.1288	0.6033	-0.106	-0.1481	0.108	0.2032	-0.0488	0.0297	0.3146	0.0397	0.219	-28.2754	-15.613	-59.6111
10	0.7273	0.0485	0.1205	0.7918	0.4747	0.4303	-0.1117	-0.0196	0.0327	0.0936	0.2039	0.1354	-0.0132	-0.1632	-0.0971	0.2597	0.0073	0.0494	0.2847	0.0534	0.2646	-20.9779	-11.5803	-56.5374
11	0.5792	-0.8326	-0.7936	3.901	-1.2537	3.1721	-0.5571	-0.2621	1.7101	0.0721	-0.0148	-0.298	-0.7256	0.5933	0.6247	0.3273	0.006	-0.0415	0.2995	-0.1206	0.4804	-1.9616	14.8628	-55.2387
12	4.7291	-0.2512	1.1072	0.3032	-0.7141	1.5692	-0.025	-0.0352	0.0921	-0.0689	0.106	-0.0522	-0.0536	0.06	-0.0717	0.3223	-0.0128	-0.0093	0.2179	-0.0597	0.2602	-6.9151	6.1239	-59.0062
13	5.1738	-1.1909	1.7931	1.8569	1.2512	4.6697	-0.2187	0.7379	0.9769	-0.599	0.181	-0.6531	-0.8216	0.4546	-0.0786	0.4635	-0.0581	-0.072	0.3684	0.0732	0.4107	-3.2261	11.7847	-66.6419
14	7.0017	-5.2176	0.6014	9.5321	0.2136	3.1788	0.6191	0.9828	-0.7753	-1.1565	-0.662	0.7567	0.8772	-0.1484	-0.0183	0.7407	-0.1823	-0.135	0.5912	0.1061	0.4291	-30.1164	-45.5206	-52.5608
15	3.3516	-1.6504	-0.1738	3.7279	0.4112	2.96	-0.0294	-0.6544	-0.4163	-0.1075	0.2773	0.5742	0.2474	0.0555	-0.1222	0.5658	-0.1757	-0.0028	0.4388	0.1366	0.4125	-28.6206	-42.1271	-43.8822
16	2.4903	0.1796	0.413	1.503	-0.48	0.7465	0.3001	-0.8311	-0.0448	0.614	-0.2435	-0.2671	-0.547	0.5513	-0.1006	0.4812	-0.1724	-0.0755	0.554	-0.0166	0.3168	19.4286	-6.9023	-36.5324
17	1.4681	0.6866	0.318	1.111	0.3592	0.1769	0.2462	-0.593	-0.0234	0.6253	-0.179	-0.1152	-0.3569	0.5161	-0.0361	0.5731	-0.1739	-0.0379	0.5855	-0.023	0.278	13.5748	-5.3178	-36.419
18	1.9026	0.0382	0.3284	0.8869	0.8183	1.9551	0.3844	-0.9802	-0.0137	0.5474	-0.4063	-0.0047	-0.1672	0.4051	0.034	0.4048	-0.0632	-0.0815	0.5315	0.0498	0.2166	18.2322	-13.8541	-38.3188
19	4.5088	-0.5696	-2.156	1.505	-0.0017	3.9491	0.0814	0.4167	-1.0802	-0.0424	-0.1898	-0.3457	0.7281	-0.0216	0.2048	0.5796	-0.0429	0.1229	0.2798	0.0744	1.0299	7.2184	-45.1204	-57.8034
20	1.835	-0.852	0.2659	2.4145	2.0167	3.0014	0.0389	-0.8034	-1.1686	0.0314	-0.0733	-0.7043	0.3776	0.4762	0.0085	0.5043	0.0368	0.047	0.4658	0.2916	0.7691	9.7396	-39.1991	-43.8085
21	0.001	0.1345	0.0247	3.0699	-0.1277	0.2579	0.221	-0.4091	-1.5881	0.4878	0.028	-0.8002	0.7461	0.1567	0.055	0.6585	0.1184	-0.1195	0.6647	0.3999	1.1648	16.2336	-45.5445	-45.9123
22	1.6016	-0.5658	-0.0271	3.8682	1.7661	3.8157	-0.0419	-0.2644	-0.7662	0.5388	0.0818	-0.4279	0.9852	0.1701	-0.0249	0.4821	0.0277	0.0392	0.3956	0.1936	0.7313	9.9212	-41.1019	-47.7255
23	2.7462	0.3464	-0.6812	3.9329	1.7791	2.8863	-0.1611	0.0633	-1.3964	0.1782	0.061	-0.2977	1.1072	-0.2012	0.2383	0.8673	-0.1254	0.1031	0.4134	0.3886	1.1352	3.1595	-48.2019	-44.0016
24	0.4007	0.2461	0.4018	0.2263	0.3042	0.4507	-0.533	0.0233	0.2285	-0.0074	-0.2189	0.2553	-1.1393	-0.9867	0.5482	1.3066	-0.249	0.0862	0.7529	-0.1645	0.7891	26.4219	28.057	-54.5824
25	0.3745	-0.6957	0.4637	1.2886	-0.9574	1.4056	-0.3157	0.2137	0.1922	-1.0131	-0.2268	-0.6443	-0.6155	0.215	0.3419	1.2066	-0.3727	0.2167	0.3098	-0.1962	0.9843	30.7721	21.1601	-53.2673
26	1.363	1.1502	-0.6233	4.9585	-3.8599	3.071	-0.2134	-0.3379	0.3272	-0.1539	-0.2213	-0.9861	0.3543	-0.1653	0.2049	0.5099	-0.5846	0.1718	0.7443	-0.3599	0.8471	34.3847	14.6706	-50.6411
27	0.5096	0.6368	1.0377	4.3512	0.9497	2.1272	-0.0091	-0.4374	0.259	0.6965	-0.3205	-0.7223	-0.4729	0.4521	-0.4727	0.8697	-0.5565	0.0248	0.6751	-0.3396	0.6763	32.7986	12.0155	-43.4163
28	3.2219	-0.0985	-1.3416	9.2978	-1.9718	1.6179	-0.349	-0.0525	1.2861	0.4281	0.1668	1.5394	-0.9193	-0.1033	0.3675	0.8487	-0.3288	0.2254	0.3929	-0.4295	1.272	22.8546	23.5716	-46.0798
29	1.266	0.084	-0.8093	3.4819	-0.0544	2.0677	-0.027	-0.006	-0.068	0.101	-0.1721	-0.4352	-0.0678	0.2458	0.1871	0.1928	-0.0556	0.0332	0.3351	-0.0229	0.316	27.3081	-4.8861	-58.4603
30	1.6411	0.4591	0.2153	2.949	0.1798	0.9232	-0.0291	-0.1242	-0.1738	0.1812	-0.0611	-0.3643	-0.0439	0.1831	0.0716	0.2438	-0.027	0.0128	0.3191	0.0076	0.2871	22.8483	-13.2181	-56.4112
31	0.5935	-0.8708	0.7834	3.487	0.8366	2.8322	-0.3952	-0.2974	-1.5147	0.253	0.0689	-0.1445	0.7914	-0.0865	0.3498	0.3757	0.0351	0.0448	0.2902	0.1228	0.6044	1.3718	-39.4928	-54.9712
32	2.9198	-0.5317	-0.4587	0.8825	0.0156	1.6867	-0.0318	-0.1728	-0.1008	-0.0964	0.075	-0.1121	0.0975	0.006	-0.0502	0.3243	-0.0125	0.0852	0.3029	0.0545	0.4229	6.3709	-30.7951	-58.8084
33	6.0946	0.952	-0.3651	1.2141	0.8306	3.6959	-0.3162	0.8769	-0.5672	-0.4783	0.2433	0.2724	1.0299	-0.2159	0.037	0.3956	-0.0342	0.1227	0.3694	-0.0722	0.5331	2.1764	-37.7179	-65.9601

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 24 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 25 through 104 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 105 through 116 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 117 through 153 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 154 through 200 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 201 through 217 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1 through 39 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 40 through 73 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 74 through 98 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 99 through 133 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 134 through 154 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 155 through 212 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 213 through 224 )
14	X-RAY DIFFRACTION	14	chain 'E' and (resid 11 through 30 )
15	X-RAY DIFFRACTION	15	chain 'E' and (resid 31 through 52 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 1 through 51 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 52 through 93 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 94 through 116 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 117 through 131 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 132 through 153 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 154 through 166 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 167 through 201 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 202 through 217 )
24	X-RAY DIFFRACTION	24	chain 'F' and (resid 12 through 18 )
25	X-RAY DIFFRACTION	25	chain 'F' and (resid 19 through 23 )
26	X-RAY DIFFRACTION	26	chain 'F' and (resid 24 through 28 )
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 29 through 43 )
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 44 through 51 )
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 1 through 83 )
30	X-RAY DIFFRACTION	30	chain 'D' and (resid 84 through 133 )
31	X-RAY DIFFRACTION	31	chain 'D' and (resid 134 through 154 )
32	X-RAY DIFFRACTION	32	chain 'D' and (resid 155 through 212 )
33	X-RAY DIFFRACTION	33	chain 'D' and (resid 213 through 225 )

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