PDB-8d5p: Mouse TCR TG6

ID or keywords:

Entry

Database: PDB / ID: 8d5p

Title

Mouse TCR TG6

Components

TCR-alpha
TCR-beta

Keywords

IMMUNE SYSTEM / MHCI / CD8 T cell

Function / homology

Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta

Function and homology information

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.75 Å

Authors

Wang, Y. / Dai, S.

Funding support

United States, 1items

Citation

Journal: Front Immunol / Year: 2022
Title: Peptide Centric V beta Specific Germline Contacts Shape a Specialist T Cell Response.
Authors: Wang, Y. / Tsitsiklis, A. / Devoe, S. / Gao, W. / Chu, H.H. / Zhang, Y. / Li, W. / Wong, W.K. / Deane, C.M. / Neau, D. / Slansky, J.E. / Thomas, P.G. / Robey, E.A. / Dai, S.

History

Deposition	Jun 5, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 14, 2022	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8d5p.cif.gz	336.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8d5p.ent.gz	269.1 KB	Display	PDB format
PDBx/mmJSON format	8d5p.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d5/8d5p ftp://data.pdbj.org/pub/pdb/validation_reports/d5/8d5p	HTTPS FTP

-
Related structure data

Related structure data	8d5nC 8d5qC 3to4S 6x2t PDB Unreleased entry S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: TCR-alpha

B: TCR-beta

C: TCR-alpha

D: TCR-beta

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

1

A: TCR-alpha

B: TCR-beta

defined by author&software
Evidence: gel filtration
51.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: TCR-alpha

D: TCR-beta

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

Unit cell

Length a, b, c (Å)	86.160, 196.331, 63.112
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P2₁2₁2

#1: Protein	TCR-alpha Mass: 23161.312 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Variant: Transgenic mouse line TG6 / Production host: Escherichia coli (E. coli)
#2: Protein	TCR-beta Mass: 27929.439 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Variant: Transgenic mouse line TG6 / Production host: Escherichia coli (E. coli)
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.63 Å³/Da / Density % sol: 53.31 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 20% w/v PEG10K, 0.1M Sodium citrate tribasic dihydrate pH 5.5, 1M Lithium sulfate monohydrate

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.982 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 21, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.982 Å / Relative weight: 1
Reflection	Resolution: 2.75→98 Å / Num. obs: 28636 / % possible obs: 98.5 % / Redundancy: 1.2 % / R_pim(I) all: 0.01 / Net I/σ(I): 16
Reflection shell	Resolution: 2.75→2.91 Å / Num. unique obs: 28062 / R_pim(I) all: 0.1

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3TO4

3to4

Resolution: 2.75→45.238 Å / Cor.coef. F_o:F_c: 0.905 / Cor.coef. F_o:F_c free: 0.83 / SU B: 38.234 / SU ML: 0.339 / Cross valid method: FREE R-VALUE / ESU R Free: 0.439
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.3006	1426	5.082 %
R_work	0.2243	26636	-
all	0.228	-	-
obs	-	28062	97.917 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 34.662 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.258 Å²	-0 Å²	-0 Å²
2-	-	-0.759 Å²	0 Å²
3-	-	-	0.5 Å²

Refinement step

Cycle: LAST / Resolution: 2.75→45.238 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7138	0	0	14	7152

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.013	7333
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.017	6374
X-RAY DIFFRACTION	r_angle_refined_deg	2.011	1.648	9980
X-RAY DIFFRACTION	r_angle_other_deg	1.326	1.574	14858
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	10.361	5	893
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.863	22.723	415
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	22.666	15	1162
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.879	15	46
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	926
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	8339
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1603
X-RAY DIFFRACTION	r_nbd_refined	0.227	0.2	1140
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.217	0.2	5897
X-RAY DIFFRACTION	r_nbtor_refined	0.181	0.2	3242
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.091	0.2	3736
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.189	0.2	127
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.113	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.178	0.2	27
X-RAY DIFFRACTION	r_nbd_other	0.236	0.2	86
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.198	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	1.815	2.308	3587
X-RAY DIFFRACTION	r_mcbond_other	1.815	2.307	3586
X-RAY DIFFRACTION	r_mcangle_it	3.265	3.45	4475
X-RAY DIFFRACTION	r_mcangle_other	3.265	3.452	4476
X-RAY DIFFRACTION	r_scbond_it	1.548	2.428	3745
X-RAY DIFFRACTION	r_scbond_other	1.547	2.425	3742
X-RAY DIFFRACTION	r_scangle_it	2.714	3.567	5505
X-RAY DIFFRACTION	r_scangle_other	2.715	3.566	5504
X-RAY DIFFRACTION	r_lrange_it	5.313	25.382	7405
X-RAY DIFFRACTION	r_lrange_other	5.313	25.389	7406

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 (%)
2.75-2.821	0.448	108	0.297	1678	X-RAY DIFFRACTION	87.207
2.821-2.898	0.374	109	0.282	1830	X-RAY DIFFRACTION	95.0024
2.898-2.982	0.391	96	0.301	1844	X-RAY DIFFRACTION	97.9303
2.982-3.073	0.463	113	0.356	1749	X-RAY DIFFRACTION	97.8455
3.073-3.173	0.336	91	0.265	1751	X-RAY DIFFRACTION	99.1922
3.173-3.284	0.287	97	0.219	1694	X-RAY DIFFRACTION	99.3896
3.284-3.408	0.296	74	0.252	1661	X-RAY DIFFRACTION	99.37
3.408-3.546	0.38	82	0.256	1584	X-RAY DIFFRACTION	98.9899
3.546-3.703	0.305	67	0.239	1538	X-RAY DIFFRACTION	98.9519
3.703-3.883	0.262	74	0.22	1431	X-RAY DIFFRACTION	99.0132
3.883-4.091	0.315	80	0.206	1403	X-RAY DIFFRACTION	98.8008
4.091-4.338	0.244	67	0.169	1315	X-RAY DIFFRACTION	99.6395
4.338-4.634	0.229	64	0.162	1258	X-RAY DIFFRACTION	99.6232
4.634-5.002	0.212	61	0.168	1165	X-RAY DIFFRACTION	99.5938
5.002-5.474	0.232	57	0.169	1094	X-RAY DIFFRACTION	99.8265
5.474-6.111	0.284	49	0.202	1002	X-RAY DIFFRACTION	99.9049
6.111-7.038	0.181	41	0.184	893	X-RAY DIFFRACTION	99.4675
7.038-8.576	0.336	35	0.191	758	X-RAY DIFFRACTION	99.3734
8.576-11.949	0.177	38	0.174	608	X-RAY DIFFRACTION	99.3846
11.949-45.238	0.386	23	0.311	380	X-RAY DIFFRACTION	98.2927

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	0.2861	-0.5842	-0.5051	2.3602	0.6831	1.2114	0.0375	-0.0518	0.0284	-0.1988	-0.1243	-0.0563	0.0741	0.0506	0.0868	0.0556	-0.0214	0.0597	0.1283	-0.0546	0.1081	22.7981	23.2202	1.1538
2	0.442	-0.8318	0.0589	2.6064	0.2863	0.2152	0.0998	-0.2041	-0.1218	-0.2006	0.0283	0.2286	0.0257	-0.1419	-0.1281	0.0339	-0.0648	-0.0321	0.2049	0.0354	0.1801	10.5001	12.1144	11.5981
3	0.9763	0.5011	0.5383	0.428	0.4098	0.6127	-0.15	0.0578	-0.008	0.0039	0.1584	0.0139	0.0729	0.1002	-0.0084	0.1073	0.0111	0.0311	0.1927	-0.0716	0.0963	-19.4863	20.5779	-30.1412
4	1.8701	0.71	0.2624	0.419	0.3098	0.4812	0.0282	0.0709	0.1151	0.0392	0.0689	0.0265	-0.0697	0.0031	-0.0971	0.1281	0.0243	0.0809	0.071	-0.0009	0.1404	-31.4281	32.6637	-19.8059

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	A	1 - 208
2	X-RAY DIFFRACTION	2	ALL	B	1 - 243
3	X-RAY DIFFRACTION	3	ALL	C	1 - 208
4	X-RAY DIFFRACTION	4	ALL	D	1 - 243

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi