PDB-4ms8: 42F3 TCR pCPB9/H-2Ld Complex

ID or keywords:

Entry

Database: PDB / ID: 4ms8

Title

42F3 TCR pCPB9/H-2Ld Complex

Components

42F3 alpha
42F3 beta
H-2 class I histocompatibility antigen, L-D alpha chain
pCPB9

Keywords

IMMUNE SYSTEM / Ig / TCR MHC

Function / homology

Function and homology information

antigen processing and presentation of peptide antigen via MHC class I / lumenal side of endoplasmic reticulum membrane / defense response / MHC class I protein complex / phagocytic vesicle membrane / immune response
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.922 Å

Authors

Birnbaum, M.E. / Adams, J.J. / Garcia, K.C.

Citation

Journal: Nat. Immunol. / Year: 2016
Title: Structural interplay between germline interactions and adaptive recognition determines the bandwidth of TCR-peptide-MHC cross-reactivity.
Authors: Adams, J.J. / Narayanan, S. / Birnbaum, M.E. / Sidhu, S.S. / Blevins, S.J. / Gee, M.H. / Sibener, L.V. / Baker, B.M. / Kranz, D.M. / Garcia, K.C.

History

Deposition	Sep 18, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 24, 2014	Provider: repository / Type: Initial release
Revision 1.1	Sep 26, 2018	Group: Data collection / 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 9, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4ms8.cif.gz	269.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4ms8.ent.gz	216.5 KB	Display	PDB format
PDBx/mmJSON format	4ms8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4ms8_validation.pdf.gz	449.8 KB	Display	wwPDB validaton report
Full document	4ms8_full_validation.pdf.gz	457.1 KB	Display
Data in XML	4ms8_validation.xml.gz	33.2 KB	Display
Data in CIF	4ms8_validation.cif.gz	46 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ms/4ms8 ftp://data.pdbj.org/pub/pdb/validation_reports/ms/4ms8	HTTPS FTP

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Related structure data

Related structure data	4mvbC 4mxqC 4n0cC 4n5eC 3tf7 3tfk 3tjh 3tpu C: citing same article (ref.)
Similar structure data	4mvb-d 4mxq-d 4n5e-d 5y79-d 5iob-4 3tpu-1 4n0c-2 3c2y-1 3tjh-d 6yry-1 Search similar-shape structures by Omokage search (details) 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

C: 42F3 alpha

D: 42F3 beta

A: H-2 class I histocompatibility antigen, L-D alpha chain

B: pCPB9

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	175.260, 60.620, 70.100
Angle α, β, γ (deg.)	90.00, 96.06, 90.00
Int Tables number	5
Space group name H-M	C121

#1: Antibody	42F3 alpha Mass: 23383.928 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Protein	42F3 beta Mass: 27248.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Protein	H-2 class I histocompatibility antigen, L-D alpha chain Mass: 21115.303 Da / Num. of mol.: 1 / Mutation: F8Y, V12T, P15R, I23T, N30D, A49V, K131R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-L / Production host: Escherichia coli (E. coli) / References: UniProt: P01897
#4: Protein/peptide	pCPB9 Mass: 938.035 Da / Num. of mol.: 1 / Source method: obtained synthetically
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 456 / 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: 2.55 Å³/Da / Density % sol: 51.71 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 20% PEG 4000, 100mM TRIS pH8, 200mM sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 102 K
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.0332 Å
Detector	Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 6, 2010
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0332 Å / Relative weight: 1
Reflection	Resolution: 1.92→69.71 Å / Num. all: 55671 / Num. obs: 52108 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / R_merge(I) obs: 0.043
Reflection shell	Resolution: 1.92→2.03 Å / % possible all: 93.6

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Processing

Software

Name	Version	Classification
Blu-Ice		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.8.1_1168)	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.922→34.854 Å / SU ML: 0.21 / σ(F): 0 / Phase error: 22.76 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2189	2657	5.1 %
R_work	0.1805	-	-
obs	0.1825	52067	93.07 %
all	-	55944	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.922→34.854 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4813	0	0	456	5269

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.016	4952
X-RAY DIFFRACTION	f_angle_d	1.575	6716
X-RAY DIFFRACTION	f_dihedral_angle_d	16.074	1761
X-RAY DIFFRACTION	f_chiral_restr	0.126	703
X-RAY DIFFRACTION	f_plane_restr	0.007	873

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 (%)
1.922-1.9569	0.2822	129	0.2456	2699	X-RAY DIFFRACTION	96
1.9569-1.9946	0.3066	149	0.2328	2633	X-RAY DIFFRACTION	95
1.9946-2.0353	0.2653	139	0.2191	2625	X-RAY DIFFRACTION	95
2.0353-2.0795	0.245	145	0.2128	2604	X-RAY DIFFRACTION	95
2.0795-2.1279	0.2203	147	0.1999	2604	X-RAY DIFFRACTION	93
2.1279-2.1811	0.2316	135	0.1925	2426	X-RAY DIFFRACTION	88
2.1811-2.2401	0.2543	147	0.1967	2669	X-RAY DIFFRACTION	96
2.2401-2.306	0.2543	122	0.1967	2713	X-RAY DIFFRACTION	97
2.306-2.3804	0.2425	140	0.2001	2683	X-RAY DIFFRACTION	96
2.3804-2.4654	0.2473	135	0.2007	2578	X-RAY DIFFRACTION	93
2.4654-2.5641	0.2332	126	0.1965	2553	X-RAY DIFFRACTION	91
2.5641-2.6808	0.2441	143	0.1997	2442	X-RAY DIFFRACTION	88
2.6808-2.8221	0.2745	142	0.2116	2723	X-RAY DIFFRACTION	97
2.8221-2.9988	0.2686	135	0.1954	2649	X-RAY DIFFRACTION	94
2.9988-3.2302	0.2143	143	0.1829	2571	X-RAY DIFFRACTION	92
3.2302-3.5549	0.2159	129	0.1733	2516	X-RAY DIFFRACTION	89
3.5549-4.0687	0.1948	146	0.1552	2660	X-RAY DIFFRACTION	95
4.0687-5.1235	0.169	154	0.137	2426	X-RAY DIFFRACTION	86
5.1235-34.8599	0.2001	151	0.1777	2636	X-RAY DIFFRACTION	91

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	3.7884	-0.1005	-1.4963	3.7638	-0.0134	3.5718	-0.0556	0.1616	-0.0228	0.0345	0.1626	0.0756	0.1915	-0.0205	-0.1184	0.2473	-0.0045	-0.0126	0.1921	-0.0146	0.1748	47.5896	-18.8534	11.6575
2	5.1924	0.9523	-3.0303	2.4559	-0.198	4.0892	-0.0907	-0.1717	-0.3598	0.08	-0.0413	-0.0923	0.2958	0.1287	0.0551	0.2902	0.0229	-0.0129	0.224	0.0079	0.2031	40.0519	-15.6561	16.062
3	4.7043	-1.3874	-0.0595	9.0845	-0.0945	4.3926	-0.0097	0.4852	0.0652	0.1514	-0.1897	0.4244	0.5006	-0.6303	0.1382	0.367	-0.1224	0.0583	0.4289	-0.0027	0.2761	20.612	-9.9305	28.5964
4	5.6631	1.4247	-2.8781	5.0918	-0.7713	5.8804	-0.2835	0.7091	-0.3195	0.0935	0.1391	1.2508	0.4319	-1.4162	0.2018	0.4475	-0.1345	0.0657	0.8682	-0.0662	0.7335	11.073	-9.8553	25.7767
5	3.969	-1.9261	-0.3413	3.9071	0.936	1.9113	-0.0503	0.0504	0.4751	0.1364	0.1768	-0.6889	-0.1676	0.255	-0.0696	0.2707	-0.0497	-0.0031	0.2125	-0.028	0.2957	52.9055	5.0455	13.3315
6	2.2562	-0.5818	-2.492	1.9085	1.5108	3.1585	-0.1532	0.1225	0.3358	0.2967	0.2705	-0.0333	-0.3536	-0.2468	-0.0584	0.323	-0.0085	0.0129	0.1879	0.0293	0.1835	41.1331	6.4352	17.7977
7	2.0728	0.4191	0.1721	1.6374	0.8935	3.1301	0.0558	0.0452	0.0985	0.238	0.0118	0.1461	-0.1337	-0.3484	-0.0965	0.337	0.0337	0.0592	0.1974	0.0204	0.2337	27.667	1.9433	32.6485
8	6.446	1.4193	2.1637	8.5297	2.9932	7.6893	-0.2469	0.1315	1.0641	-0.2756	0.2352	-0.2152	-0.0172	0.5616	0.1532	0.1652	0.0354	-0.0158	0.4472	0.0556	0.4415	81.0079	-14.4984	-2.0019
9	6.0592	1.5706	3.0389	1.4497	0.962	5.4733	-0.5299	-0.5434	2.162	0.3605	0.1869	-0.2006	-0.4978	0.5248	0.3617	0.3169	0.0896	-0.1692	0.5999	-0.0775	1.0447	82.8072	-4.2483	2.5481
10	1.552	-0.4315	-1.2362	4.1182	0.1594	4.7999	-0.1884	0.2865	2.0425	0.0412	-0.0117	0.1057	-0.5327	0.4082	0.0054	0.3733	-0.0576	-0.1032	0.5671	0.2898	1.3085	81.761	-2.6928	-4.8023
11	4.9321	-2.5734	0.2642	1.5945	-0.551	0.6901	-0.091	0.6962	1.0928	-0.2687	-0.2107	-0.1029	-0.354	0.24	0.2724	0.527	-0.059	-0.2193	1.1518	0.5848	1.1565	76.6119	-5.765	-15.3361
12	1.9971	-0.4825	-0.5748	0.6569	0.1351	0.2444	-0.28	-0.3809	1.6594	0.1191	0.0939	-0.2265	-0.4788	0.0871	0.91	0.3852	0.15	-0.3958	0.6031	-0.285	1.4778	73.4626	-1.7421	5.9439
13	2.1268	0.1429	1.0618	1.0647	-0.7844	4.0661	-0.179	-0.726	0.3958	0.2102	0.0509	-0.2659	0.1809	0.4471	0.1095	0.2052	0.0814	-0.0232	0.6514	-0.1412	0.4731	79.7326	-17.127	6.5753
14	0.8464	-0.2703	1.3757	2.8974	-0.4471	2.9412	-0.1216	-1.2692	-0.0246	0.5043	0.1533	0.0612	0.3084	0.6513	0.0717	0.307	0.0932	0.062	0.8383	-0.0575	0.3243	72.0245	-20.1143	13.7447
15	0.4329	1.2786	-1.0015	8.085	-1.51	2.8409	-0.3535	1.3067	1.3458	-0.741	0.0543	0.5729	-0.175	0.0519	0.2254	0.2455	-0.0508	-0.089	0.7401	0.1769	0.4391	72.5288	-15.346	-10.1221
16	1.9061	-0.37	-0.9887	0.5838	0.23	1.6608	-0.0497	-0.8064	1.0797	0.1195	-0.1024	0.0667	-0.2366	-0.0302	0.0334	0.192	0.1332	-0.1065	0.5972	-0.3449	0.7666	70.4439	-9.1831	8.4869

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'C' and (resid 2 through 93 )
2	X-RAY DIFFRACTION	2	chain 'C' and (resid 94 through 120 )
3	X-RAY DIFFRACTION	3	chain 'C' and (resid 121 through 177 )
4	X-RAY DIFFRACTION	4	chain 'C' and (resid 178 through 200 )
5	X-RAY DIFFRACTION	5	chain 'D' and (resid 3 through 96 )
6	X-RAY DIFFRACTION	6	chain 'D' and (resid 97 through 120 )
7	X-RAY DIFFRACTION	7	chain 'D' and (resid 121 through 241 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 0 through 12 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 13 through 28 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 29 through 49 )
11	X-RAY DIFFRACTION	11	chain 'A' and (resid 50 through 56 )
12	X-RAY DIFFRACTION	12	chain 'A' and (resid 57 through 83 )
13	X-RAY DIFFRACTION	13	chain 'A' and (resid 84 through 126 )
14	X-RAY DIFFRACTION	14	chain 'A' and (resid 127 through 162 )
15	X-RAY DIFFRACTION	15	chain 'A' and (resid 163 through 175 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 1 through 9 )

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