PDB-7sr3: Single chain trimer HLA-A*02:01 (H98L, Y108C) with HPV.16 E7 pept...

ID or keywords:

Entry

Database: PDB / ID: 7sr3

Title

Single chain trimer HLA-A*02:01 (H98L, Y108C) with HPV.16 E7 peptide YMLDLQPETTDL

Components

Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera
VHH

Keywords

IMMUNE SYSTEM / HLA / VHH / HPV / SCT

Function / homology

Function and homology information

symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host IRF9 activity / symbiont-mediated activation of of host transcription / : / : / antigen processing and presentation of peptide antigen via MHC class I / positive regulation of actin filament polymerization / cadmium ion binding / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / antigen processing and presentation / viral process ...
Similarity search - Function

Biological species

Human papillomavirus type 16

Pongo pygmaeus (Bornean orangutan)

Homo sapiens (human)

Lama glama (llama)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.49 Å

Authors

Finton, K.A.K. / Rupert, P.B.

Funding support

United States, 1items

Citation

Journal: Front Immunol / Year: 2023
Title: Effects of HLA single chain trimer design on peptide presentation and stability.
Authors: Finton, K.A.K. / Rupert, P.B. / Friend, D.J. / Dinca, A. / Lovelace, E.S. / Buerger, M. / Rusnac, D.V. / Foote-McNabb, U. / Chour, W. / Heath, J.R. / Campbell, J.S. / Pierce, R.H. / Strong, R.K.

History

Deposition	Nov 7, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 23, 2022	Provider: repository / Type: Initial release
Revision 1.1	May 31, 2023	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
Revision 1.2	Oct 25, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7sr3.cif.gz	371.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7sr3.ent.gz	299.9 KB	Display	PDB format
PDBx/mmJSON format	7sr3.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/sr/7sr3 ftp://data.pdbj.org/pub/pdb/validation_reports/sr/7sr3	HTTPS FTP

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Related structure data

Related structure data	7sqpSC 7sr0C 7sr4C 7sr5C 7srkC 7sshC 7st3C 7stgC 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) #62 - Feb 2005 Major Histocompatibility Complex similarity (2) #63 - Mar 2005 T-Cell Receptor similarity (2)

Deposited unit

A: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera

B: VHH

C: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera

D: VHH

121 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera

B: VHH

defined by author
Evidence: surface plasmon resonance
60.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera

D: VHH

defined by author
60.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	118.093, 118.093, 262.205
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	Protein E7 peptide,Beta-2-microglobulin,MHC class I antigen chimera Mass: 48001.797 Da / Num. of mol.: 2 / Mutation: H98L, Y108C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human papillomavirus type 16, (gene. exp.) Pongo pygmaeus (Bornean orangutan), (gene. exp.) Homo sapiens (human) Gene: E7, B2M, HLA-A / Production host: Homo sapiens (human) References: UniProt: P03129, UniProt: P16213, UniProt: A0A678ZGP6
#2: Antibody	VHH Mass: 12536.822 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Homo sapiens (human)
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.78 Å³/Da / Density % sol: 67.42 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 200 mM K2SO4, 17% PEG 3350

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Data collection

Diffraction	Mean temperature: 93 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.49→50 Å / Num. obs: 65593 / % possible obs: 99.9 % / Redundancy: 8.1 % / B_iso Wilson estimate: 38.78 Å² / CC_1/2: 0.996 / Net I/σ(I): 19.7
Reflection shell	Resolution: 2.49→2.58 Å / Num. unique obs: 6332 / CC_1/2: 0.847

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Processing

Software

Name: PHENIX / Version: 1.19.1_4122 / Classification: refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 7SQP

7sqp

Resolution: 2.49→48.99 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.1 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2477	3215	4.9 %
R_work	0.2249	62378	-
obs	0.226	65593	99.61 %

Solvent computation

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

Displacement parameters

B_iso max: 136.85 Å² / B_iso mean: 42.6929 Å² / B_iso min: 17.54 Å²

Refinement step

Cycle: final / Resolution: 2.49→48.99 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7120	0	0	135	7255
B_iso mean	-	-	-	34.71	-
Num. residues	-	-	-	-	933

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 23

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.49-2.53	0.3044	125	0.2921	2504	2629	94
2.53-2.57	0.2757	124	0.2755	2715	2839	100
2.57-2.61	0.282	119	0.2509	2687	2806	100
2.61-2.65	0.3102	131	0.2506	2660	2791	100
2.65-2.7	0.3371	119	0.2752	2705	2824	100
2.7-2.75	0.2522	124	0.2545	2707	2831	100
2.75-2.81	0.299	163	0.2481	2653	2816	100
2.81-2.87	0.3012	138	0.2561	2680	2818	100
2.87-2.94	0.2887	159	0.2525	2678	2837	100
2.94-3.01	0.3183	131	0.2544	2691	2822	100
3.01-3.09	0.277	130	0.2591	2711	2841	100
3.09-3.18	0.2753	159	0.2411	2681	2840	100
3.18-3.28	0.2551	140	0.2335	2702	2842	100
3.28-3.4	0.2664	141	0.2293	2698	2839	100
3.4-3.54	0.2419	155	0.2366	2691	2846	100
3.54-3.7	0.265	135	0.2251	2738	2873	100
3.7-3.89	0.2044	143	0.2084	2705	2848	100
3.89-4.14	0.1955	143	0.1972	2722	2865	100
4.14-4.46	0.2057	138	0.1762	2753	2891	100
4.46-4.91	0.1817	149	0.1709	2775	2924	100
4.91-5.61	0.2201	144	0.1998	2773	2917	100
5.62-7.07	0.2632	151	0.2349	2805	2956	100
7.07-48.99	0.2771	154	0.2439	2944	3098	98

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	0.2039	0.1864	-0.0532	0.2761	0.0756	0.0351	0.0192	0.023	0.1269	0.0516	-0.0949	0.2367	0.0962	0.0437	-0.0011	0.3123	-0.0499	0.0031	0.2184	-0.0242	0.2734	-30.8394	11.6412	41.6451
2	0.2867	0.1096	0.0327	0.4098	0.2352	0.3189	-0.1293	-0.0463	0.0098	-0.2201	-0.0471	0.1473	0.0018	0.1256	-0.0379	0.2972	-0.0358	-0.0725	0.2125	-0.013	0.2799	-37.7037	1.4512	25.2234
3	0.0538	-0.0645	0.0544	0.054	-0.1057	0.11	0.1735	-0.1849	0.348	0.0512	-0.1485	0.4459	0.121	-0.1243	0.0138	0.2325	-0.0678	0.471	0.2554	-0.427	0.5048	-47.5615	7.8036	53.0714
4	0.0031	-0.0053	-0.0017	0.0059	-0.0006	0.0015	-0.0057	0.0143	0.026	-0.0055	-0.0223	-0.0617	-0.0293	-0.0173	-0.0001	0.4057	-0.0249	0.0636	0.3132	-0.1058	0.434	-14.1024	37.9073	50.1983
5	0.0004	0.0048	-0.0011	0.0039	0.0043	0.0022	0.0206	0.076	0.0179	-0.0141	-0.0272	-0.0553	0.0025	-0.0059	-0	0.3011	0.0458	0.0561	0.3084	0.0184	0.3279	-5.133	37.7085	29.5933
6	0.0005	0.0031	-0.0011	0.0037	-0.0029	0.0083	0.0474	-0.0509	0.0067	0.103	-0.1314	0.0243	0.0749	0.0339	0.0003	0.3742	-0.0559	0.0422	0.3598	-0.0255	0.3991	-6.664	35.0285	43.6679
7	-0.0001	0.0014	0.0016	0.0112	0.0072	0.0033	0.0092	-0.022	0.0061	0.0345	-0.0062	0.0209	-0.1008	-0.0393	-0	0.4	-0.107	-0.0171	0.3925	0.0159	0.1764	-13.3974	29.5022	57.3454
8	0.0056	0.004	0.0023	0.0031	-0.0009	0.0017	0.0365	-0.0339	0.0597	-0.0115	-0.0203	0.0745	-0.0185	0.0474	0.0001	0.289	-0.0034	0.0436	0.3288	0.0369	0.2395	-15.9357	29.9804	40.847
9	0.0119	0.0159	0.0027	0.014	0.002	0.0011	0.1479	-0.0422	-0.0829	-0.0768	0.0121	0.1157	0.0595	0.0083	-0.0001	0.3057	-0.0002	-0.0006	0.2474	0.0237	0.2665	-14.1548	23.4704	40.7385
10	-0.0021	0.0025	-0.0006	0.0028	-0.0023	0.0018	0.0552	-0.0974	-0.1015	-0.0237	-0.0722	-0.1025	-0.0547	0.0778	0.0001	0.3883	-0.0018	0.0392	0.308	0.0193	0.3013	-6.0717	25.3404	39.3728
11	0.0006	-0.0011	0.0038	-0.0003	0.0015	0.0056	0.0074	-0.0656	0.0012	0.0739	0.0408	0.0203	0.038	0.0418	0.0001	0.342	-0.0106	0.0312	0.3261	-0.0595	0.3071	-5.0522	30.6652	47.091
12	0.0001	-0.0003	-0.0012	0.008	0.0038	0.0026	0.0242	0.0077	-0.0605	-0.0117	0.0214	-0.0245	0.0855	0.051	0.0001	0.3396	0.0011	-0.011	0.3258	0.0321	0.3043	-9.3959	30.879	27.9095
13	0.0019	0.0021	-0.0001	0.0026	-0.0033	0.0057	0.023	0.0173	0.0813	-0.0011	-0.0605	-0.0058	-0.0523	-0.0236	0.0001	0.2169	-0.0048	0.0258	0.2572	-0.0194	0.2449	-16.8317	32.1985	42.445
14	0.021	-0.0167	-0.0012	0.0047	0.0005	0.0085	0.1358	-0.0002	0.2227	0.108	-0.0486	0.1187	0.0677	-0.0486	-0.0001	0.4102	-0.059	0.0667	0.3672	0.0106	0.3347	-20.4759	30.0756	51.8269
15	0.0054	-0.0041	-0.0114	0.0045	0.0031	0.0292	-0.0368	0.0089	0.037	0.0029	-0.0142	0.0234	-0.0079	-0.0437	0	0.3161	0.0029	0.0138	0.2444	0.0159	0.2455	-11.8707	38.671	31.2314
16	0.1034	-0.2331	0.0105	0.2466	-0.0002	0.0174	0.0982	0.0147	0.1442	-0.232	-0.1846	-0.282	0.2218	0.1022	-0.0021	0.4087	0.1001	0.0331	0.2941	0.0207	0.2569	-87.5416	13.3656	24.4414
17	0.0763	-0.1415	0.0533	0.1205	-0.1004	0.0264	0.0642	0.0213	0.0722	-0.1705	-0.063	-0.0534	0.0644	-0.1182	0	0.3126	0.0385	0.021	0.3038	0.023	0.2935	-87.2118	7.1694	30.921
18	0.1437	-0.2145	0.1355	0.3235	-0.2406	0.2068	-0.0375	0.0102	0.0623	0.0799	-0.0249	-0.2236	-0.0239	-0.1388	-0	0.3304	0.0657	-0.0363	0.2389	-0.0079	0.3022	-77.5359	3.9954	43.4782
19	0.0584	-0.0106	0.0185	-0.0073	-0.0073	0.0062	0.0182	0.1778	0.2295	-0.0594	-0.335	-0.4519	0.1673	0.253	-0.2543	0.3373	0.7397	0.2281	0.0944	0.7121	0.6443	-69.9458	9.202	13.8352
20	0.0097	-0.0059	-0.0153	0.0019	0.0083	0.0177	-0.024	-0.0272	0.0109	-0.035	-0.0073	0.0017	-0.0178	0.0288	-0.0001	0.4385	0.0115	0.0792	0.4308	0.0102	0.448	-102.3048	40.1739	14.5783
21	-0	0.0016	-0.001	0.0021	0.0001	0.0016	0.0231	-0.0564	0.0069	0.0043	0.0214	0.0665	0.0248	-0.0736	0	0.3946	0.0026	0.1108	0.281	0.0275	0.3866	-113.7577	40.1132	34.0711
22	0.0017	0.0023	-0.0013	0.0018	-0.0042	0.0123	0.0448	0.0608	-0.0291	-0.0989	0.0241	0.061	0.0149	-0.005	0.0001	0.3923	0.0852	0.0506	0.314	0.064	0.2541	-110.2294	37.4559	20.0509
23	0.0018	0.0025	0.0025	0.0337	0.0146	0.0078	-0.0121	0.008	-0.0227	0.0044	-0.0101	-0.0067	-0.0157	0.0121	0.0001	0.9629	0.0778	0.0365	0.5685	0.1684	0.7215	-102.6204	34.3032	4.7366
24	0.0097	-0.0299	0.0209	0.0249	-0.0154	0.0034	0.1248	-0.0119	-0.0254	-0.0283	-0.0424	0.0081	-0.0368	-0.1257	-0	0.2265	0.0442	0.0081	0.2137	0.0068	0.2019	-100.2048	30.2825	23.6664
25	0.0036	0.0122	-0.0079	0.0155	-0.0041	0.0076	0.1525	0.0695	-0.1214	-0.0313	0.0474	0.1911	0.0737	0.0119	0.0001	0.416	-0.0104	-0.0087	0.3211	-0.0124	0.3261	-108.9805	25.114	23.43
26	0.0004	-0.0057	0.0019	0.0061	-0.0018	0.0001	-0.0461	0.0912	0.0482	0.0119	0.0336	0.1769	-0.0155	0.0092	-0.0001	0.3562	-0.0021	0.0026	0.3135	0.0068	0.3675	-111.9579	33.0906	16.1885
27	0.0128	-0.0008	-0.0023	0.0162	0.0162	0.0018	0.1153	0.0171	-0.0329	0.1028	-0.1767	0.0734	0.0061	0.0196	-0	0.2758	0.0358	0.0317	0.2436	-0.0253	0.2227	-104.9003	33.8975	29.2633
28	0.014	0.0068	-0.0019	0.0044	-0.0027	0.0081	0.1214	0.0585	0.1937	-0.1976	-0.0389	-0.0868	0.0662	0.021	-0	0.4542	0.0816	0.0422	0.4025	0.0123	0.2773	-95.9617	32.2195	13.6317
29	0.0068	0.0037	-0.0081	-0.0003	-0.0026	0.011	0.004	-0.0043	0.0085	0.0363	-0.0072	0.0283	-0.0044	0.0157	-0	0.3476	-0.012	0.0668	0.2517	-0.0308	0.2594	-106.6684	41.0271	33.1752

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 155 )	A	1 - 155
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 156 through 328 )	A	156 - 328
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 329 through 416 )	A	329 - 416
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 3 through 9 )	B	3 - 9
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 10 through 19 )	B	10 - 19
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 20 through 26 )	B	20 - 26
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 27 through 35 )	B	27 - 35
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 36 through 41 )	B	36 - 41
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 45 through 65 )	B	45 - 65
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 66 through 73 )	B	66 - 73
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 74 through 84 )	B	74 - 84
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 85 through 92 )	B	85 - 92
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 93 through 100 )	B	93 - 100
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 101 through 111 )	B	101 - 111
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 112 through 117 )	B	112 - 117
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 1 through 107 )	C	1 - 107
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 108 through 199 )	C	108 - 199
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 200 through 328 )	C	200 - 328
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 329 through 416 )	C	329 - 416
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 3 through 9 )	D	3 - 9
21	X-RAY DIFFRACTION	21	chain 'D' and (resid 10 through 19 )	D	10 - 19
22	X-RAY DIFFRACTION	22	chain 'D' and (resid 20 through 26 )	D	20 - 26
23	X-RAY DIFFRACTION	23	chain 'D' and (resid 27 through 32 )	D	27 - 32
24	X-RAY DIFFRACTION	24	chain 'D' and (resid 33 through 53 )	D	33 - 53
25	X-RAY DIFFRACTION	25	chain 'D' and (resid 54 through 73 )	D	54 - 73
26	X-RAY DIFFRACTION	26	chain 'D' and (resid 74 through 84 )	D	74 - 84
27	X-RAY DIFFRACTION	27	chain 'D' and (resid 85 through 100 )	D	85 - 100
28	X-RAY DIFFRACTION	28	chain 'D' and (resid 101 through 111 )	D	101 - 111
29	X-RAY DIFFRACTION	29	chain 'D' and (resid 112 through 117 )	D	112 - 117

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About Yorodumi

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Yorodumi