PDB-6xqq: Structure of human D462-E4 TCR

ID or keywords:

Entry

Database: PDB / ID: 6xqq

Title

Structure of human D462-E4 TCR

Components

TRAV12-2 alpha chain
TRBV29-1

Keywords

IMMUNE SYSTEM / MAIT / MR1 / Metabolite presentation

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.68 Å

Authors

Awad, W. / Rossjohn, J.

Funding support

Australia, 1items

Citation

Journal: J.Biol.Chem. / Year: 2020
Title: Atypical TRAV1-2 - T cell receptor recognition of the antigen-presenting molecule MR1.
Authors: Awad, W. / Meermeier, E.W. / Sandoval-Romero, M.L. / Le Nours, J. / Worley, A.H. / Null, M.D. / Liu, L. / McCluskey, J. / Fairlie, D.P. / Lewinsohn, D.M. / Rossjohn, J.

History

Deposition	Jul 10, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 19, 2020	Provider: repository / Type: Initial release
Revision 1.1	Sep 2, 2020	Group: Database references / Category: citation / citation_author Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Oct 28, 2020	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3	Oct 18, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6xqq.cif.gz	421.3 KB	Display	PDBx/mmCIF format
PDB format	pdb6xqq.ent.gz	287.8 KB	Display	PDB format
PDBx/mmJSON format	6xqq.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	6xqq_validation.pdf.gz	459.3 KB	Display	wwPDB validaton report
Full document	6xqq_full_validation.pdf.gz	466.1 KB	Display
Data in XML	6xqq_validation.xml.gz	32.1 KB	Display
Data in CIF	6xqq_validation.cif.gz	44.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xq/6xqq ftp://data.pdbj.org/pub/pdb/validation_reports/xq/6xqq	HTTPS FTP

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Related structure data

Related structure data	6xqpC 4l4tS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6fur-2 3rev-d 3skn-4 6vth-1 5iw1-2 5iw1-1 6dfq-3 4nqd-4 4g8f-d 3vxq-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details)

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: TRAV12-2 alpha chain

B: TRBV29-1

C: TRAV12-2 alpha chain

D: TRBV29-1

hetero molecules

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

1

A: TRAV12-2 alpha chain

B: TRBV29-1

hetero molecules

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

2

C: TRAV12-2 alpha chain

D: TRBV29-1

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

Unit cell

Length a, b, c (Å)	115.222, 115.222, 183.992
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	95
Space group name H-M	P4₃22
Space group name Hall	P4cw2c
Symmetry operation	#1: x,y,z #2: -y,x,z+3/4 #3: y,-x,z+1/4 #4: x,-y,-z+1/2 #5: -x,y,-z #6: -x,-y,z+1/2 #7: y,x,-z+1/4 #8: -y,-x,-z+3/4

#1: Protein	TRAV12-2 alpha chain Mass: 22740.104 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: Protein	TRBV29-1 Mass: 27694.844 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: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.03 Å³/Da / Density % sol: 59.37 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion Details: 16-24% PEG3350, 100 mM Bis Tris Propane, 200 mM Sodium Fluoride

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 9, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9537 Å / Relative weight: 1
Reflection	Resolution: 2.68→41.99 Å / Num. obs: 35384 / % possible obs: 99.56 % / Redundancy: 2 % / B_iso Wilson estimate: 45.04 Å² / CC_1/2: 0.999 / Net I/σ(I): 26.62
Reflection shell	Resolution: 2.68→2.78 Å / Num. unique obs: 3444 / CC_1/2: 0.799

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Processing

Software

Name	Version	Classification
PHENIX	1.18.2_3874	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4L4T

4l4t

Resolution: 2.68→41.99 Å / SU ML: 0.2802 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 19.4474
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2233	1782	5.04 %
R_work	0.1936	33601	-
obs	0.1951	35383	99.6 %

Solvent computation

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

Displacement parameters

B_iso mean: 49.6 Å²

Refinement step

Cycle: LAST / Resolution: 2.68→41.99 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6724	0	6	152	6882

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0017	6936
X-RAY DIFFRACTION	f_angle_d	0.4618	9454
X-RAY DIFFRACTION	f_chiral_restr	0.0412	1044
X-RAY DIFFRACTION	f_plane_restr	0.0034	1247
X-RAY DIFFRACTION	f_dihedral_angle_d	18.7298	2468

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 (%)
2.68-2.75	0.2969	143	0.2604	2505	X-RAY DIFFRACTION	99.14
2.75-2.83	0.279	140	0.2554	2512	X-RAY DIFFRACTION	99.29
2.83-2.92	0.2735	145	0.2313	2524	X-RAY DIFFRACTION	99.37
2.93-3.03	0.2821	121	0.2243	2553	X-RAY DIFFRACTION	99.52
3.03-3.15	0.2392	125	0.2188	2555	X-RAY DIFFRACTION	99.55
3.15-3.29	0.2617	133	0.212	2560	X-RAY DIFFRACTION	99.41
3.29-3.47	0.2598	136	0.2003	2560	X-RAY DIFFRACTION	99.67
3.47-3.68	0.2253	144	0.1967	2562	X-RAY DIFFRACTION	99.67
3.69-3.97	0.2129	137	0.1778	2576	X-RAY DIFFRACTION	99.74
3.97-4.37	0.1918	131	0.1584	2589	X-RAY DIFFRACTION	99.89
4.37-5	0.1671	134	0.1464	2638	X-RAY DIFFRACTION	99.93
5-6.29	0.1909	155	0.1838	2643	X-RAY DIFFRACTION	99.93
6.3-41.99	0.2295	138	0.2108	2824	X-RAY DIFFRACTION	99.76

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	0.45346628334	-0.385490230105	0.195929557891	0.229217895566	0.0943829474877	0.202777311264	-0.104762285552	-0.49938848717	-0.213217771292	-0.3534166973	-0.108809352214	-0.317280640969	0.0978325633986	-0.160057825434	0.0174791965039	0.346832132753	-0.0673277021009	0.179662943272	0.283819824024	-0.124697515717	0.48151706889	27.6144169421	25.3356949218	82.1520769898
2	0.126279230515	-0.169675070084	0.282350481308	0.516311037906	-0.293453935264	0.307313863308	0.13721822716	-0.510825262584	-0.731126364835	-0.38418554676	0.835665725046	0.422501817307	0.407847344793	-0.392573600236	0.185868494315	0.147719936164	0.327767841327	0.593720134419	-0.0650633947322	-0.464382049272	0.0667237319394	35.1886200225	21.7983980541	88.1626743117
3	0.0932150060379	-0.319625993674	-0.0857245001541	0.529677598023	0.0920302418269	0.048640144553	-0.446208642576	0.454482195005	-0.0953301030511	0.13491383556	-0.286459195118	-0.857884712109	0.34034830467	-0.221024770178	-0.640040732705	-0.149490820694	0.525666315815	1.03736387213	-0.249420473971	-0.74016514807	-0.337155255666	32.1580833167	23.1370518839	82.6203329195
4	0.434539662786	0.22823751974	-0.0112264465066	0.672319641041	-0.0804191320911	0.30283813035	0.208022818115	0.314595720173	0.461626786354	0.090068621645	-0.0306277094202	-0.0869860666535	0.0105676928467	-0.180926717724	0.0167051432563	0.318238688893	0.0431166111163	0.147467993495	0.437345155171	0.0331335969479	0.380674998268	49.8588611152	38.79805604	59.8931914977
5	1.18925123222	-0.380403223973	-0.434313840421	1.41906496021	0.127795618607	0.553320920543	-0.0116524135174	-0.0670686815442	0.00903683841165	0.0791762096019	0.0756399058902	0.348839757096	-0.149913913536	-0.032768473254	0.13306356585	0.324316632009	-0.0071305563674	0.134036630746	0.253286919731	-0.0766807441621	0.235546556382	39.8322170631	2.89969028833	73.8748351015
6	0.483581096546	-0.59346821612	-0.284769606617	1.27609835328	-0.535309157333	0.508338009086	0.130393342233	0.11328323249	0.1246851773	-0.0451969204514	-0.152272630514	-0.115381733978	0.116651985179	-0.0892038437727	-5.78365249975E-5	0.262190845964	-0.0351692706728	0.0788799341906	0.284218758445	-0.0398235679711	0.24098761335	58.5876989785	24.3750698065	62.4872470298
7	0.140300725781	-0.31256419089	-0.107306936658	0.255678707172	0.0431229295731	0.198454682912	-0.198315160245	0.0577175751161	-0.33912032595	-0.0112862036329	0.170440042237	0.0719799064432	0.193742502773	0.0360287668304	0.00616521737033	0.205195636279	-0.0230687483496	-0.0749884161142	0.328985735785	0.162400929908	0.41297834129	72.2007264672	-30.3986225507	59.6223407958
8	0.788079947997	-0.434285683583	-0.0192812431301	0.246876283603	0.148961291819	0.552892730774	0.0844429142379	0.118369523776	-0.0163266271325	0.0353107783275	-0.108000701385	0.115495622019	-0.026425137535	0.0896588673112	6.89424934956E-5	0.262358354366	0.0107417292471	-0.0615207972304	0.252326933798	0.0455010099344	0.319351355657	67.076327318	-26.1402354723	55.1391464714
9	0.0405795813111	0.0344914865501	0.0675979316139	0.127721188135	0.185157991682	0.0761014082679	-0.131716917151	-0.179343957676	0.438526532835	-0.373020933536	-0.0277203675989	-0.0687768087166	0.530821901741	-0.0821751202206	-0.00889709116993	0.326548368692	-0.096846967148	-0.0428297123073	0.33670772692	0.161468858503	0.450512300227	88.3544658835	-14.1623063443	58.0487628633
10	0.403022922602	0.0290295795225	-0.241516371759	0.424772934421	-0.32901533651	0.688347408726	-0.164285937505	-0.290248381075	-0.0424127216752	0.0521837097074	-0.599365622682	-0.71191598665	0.581667601852	0.594984910366	-0.211727437379	0.325671556273	-0.0732969953692	-0.149691134854	0.66571759582	0.335564150939	0.545844593296	92.1105485682	-2.46167842362	67.2999364591
11	0.83610550552	-0.780782286134	-0.393862083249	0.67540825128	0.65016509257	0.436792413497	-0.00449130399132	-0.115455145103	-0.419794251348	0.114905840012	-0.111486005274	-0.0222338847532	-0.0561755120591	0.00148875179713	-0.00132788157522	0.366083196223	-0.0434832254579	0.0512418582963	0.309793592318	-0.00322497334906	0.347782121052	52.395995695	-15.0768952147	69.1849770994
12	0.410159873219	-0.13175699141	-0.149418084085	0.585246883643	0.446083934893	0.462326971739	-0.05787843059	-0.276481831792	0.24662812878	0.0498457042647	-0.138323610972	-0.0996328214875	0.0427308597051	0.0446603871314	-0.0248098023094	0.30162251446	-0.0788492249082	0.0415424439031	0.438637621064	0.0319617570274	0.294504005281	76.7240212253	5.45376407995	67.2964702218

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 5 through 32 )	A	A	5 - 32	1 - 28
2	2	chain 'A' and (resid 33 through 67 )	A	A	33 - 67	29 - 63
3	3	chain 'A' and (resid 68 through 110 )	A	A	68 - 110	64 - 106
4	4	chain 'A' and (resid 111 through 201 )	A	A	111 - 201	107 - 197
5	5	chain 'B' and (resid 2 through 127 )	B	C	2 - 127	1 - 128
6	6	chain 'B' and (resid 128 through 247 )	B	C	128 - 247	129 - 249
7	7	chain 'C' and (resid 5 through 32 )	C	D	5 - 32	1 - 28
8	8	chain 'C' and (resid 33 through 104 )	C	D	33 - 104	29 - 101
9	9	chain 'C' and (resid 105 through 118 )	C	D	105 - 118	102 - 115
10	10	chain 'C' and (resid 119 through 200 )	C	D	119 - 200	116 - 193
11	11	chain 'D' and (resid 2 through 112 )	D	E	2 - 112	1 - 113
12	12	chain 'D' and (resid 113 through 247 )	D	E	113 - 247	114 - 250

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