PDB-7l15: Marsupial T cell receptor Spl_118

ID or keywords:

Entry

Database: PDB / ID: 7l15

Title

Marsupial T cell receptor Spl_118

Components

T cell receptor gamma chain
T cell receptor mu chain

Keywords

IMMUNE SYSTEM / T cell receptor / antigen recognition / IgV domain

Biological species

Monodelphis domestica (gray short-tailed opossum)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.25 Å

Authors

Wegrecki, M. / Kannan Sivaraman, K. / Praveena, T. / Le Nours, J. / Rossjohn, J.

Citation

Journal: Science / Year: 2021
Title: The molecular assembly of the marsupial gamma mu T cell receptor defines a third T cell lineage.
Authors: Morrissey, K.A. / Wegrecki, M. / Praveena, T. / Hansen, V.L. / Bu, L. / Sivaraman, K.K. / Darko, S. / Douek, D.C. / Rossjohn, J. / Miller, R.D. / Le Nours, J.

History

Deposition	Dec 14, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 24, 2021	Provider: repository / Type: Initial release
Revision 1.1	Apr 14, 2021	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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	Apr 3, 2024	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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Download

PDBx/mmCIF format	7l15.cif.gz	223.2 KB	Display	PDBx/mmCIF format
PDB format	pdb7l15.ent.gz	147.5 KB	Display	PDB format
PDBx/mmJSON format	7l15.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7l15_validation.pdf.gz	721 KB	Display	wwPDB validaton report
Full document	7l15_full_validation.pdf.gz	723.7 KB	Display
Data in XML	7l15_validation.xml.gz	17.8 KB	Display
Data in CIF	7l15_validation.cif.gz	24.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l1/7l15 ftp://data.pdbj.org/pub/pdb/validation_reports/l1/7l15	HTTPS FTP

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Related structure data

Related structure data	7k0xC 7k0zC C: citing same article (ref.)
Similar structure data	5aa3-3 4jy5-d 6syi-d 6jsz-d 2x6v-d 4fbw-2 1hwo-d 6bmr-2 5obf-d 1z05-d Search similar-shape structures by Omokage search (details)

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: T cell receptor mu chain

B: T cell receptor gamma chain

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	56.396, 82.705, 108.439
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

#1: Protein

T cell receptor mu chain

Mass: 24182.193 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Monodelphis domestica (gray short-tailed opossum)
Production host:

Homo sapiens (human)

#2: Protein

T cell receptor gamma chain

Mass: 26046.412 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Monodelphis domestica (gray short-tailed opossum)
Production host:

Homo sapiens (human)

#3: Polysaccharide

2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1 / Source method: isolated from a natural source

Descriptor	Type	Program
DGlcpNAcb1-4DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}	LINUCS	PDB-CARE

#4: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.52 Å³/Da / Density % sol: 51.14 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.2M LiSO4

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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: 0.95372 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 27, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.95372 Å / Relative weight: 1
Reflection	Resolution: 2.25→45.34 Å / Num. obs: 24810 / % possible obs: 100 % / Redundancy: 6.7 % / B_iso Wilson estimate: 50.41 Å² / R_pim(I) all: 0.03 / Net I/σ(I): 13.8
Reflection shell	Resolution: 2.25→2.32 Å / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2247 / R_pim(I) all: 0.376

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Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
XDS		data reduction
Aimless		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: unpublished

Resolution: 2.25→45.34 Å / SU ML: 0.2722 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.8673
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2265	1235	4.99 %
R_work	0.1808	23517	-
obs	0.1831	24752	99.97 %

Solvent computation

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

Displacement parameters

B_iso mean: 57.34 Å²

Refinement step

Cycle: LAST / Resolution: 2.25→45.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3325	0	42	101	3468

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0072	3454
X-RAY DIFFRACTION	f_angle_d	0.927	4697
X-RAY DIFFRACTION	f_chiral_restr	0.0534	536
X-RAY DIFFRACTION	f_plane_restr	0.0061	604
X-RAY DIFFRACTION	f_dihedral_angle_d	21.2211	1246

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 (%)
2.25-2.34	0.2972	123	0.2469	2576	X-RAY DIFFRACTION	99.96
2.34-2.45	0.3337	158	0.2459	2573	X-RAY DIFFRACTION	100
2.45-2.58	0.2959	153	0.2353	2547	X-RAY DIFFRACTION	99.96
2.58-2.74	0.2714	124	0.2307	2565	X-RAY DIFFRACTION	100
2.74-2.95	0.2793	125	0.2195	2620	X-RAY DIFFRACTION	99.96
2.95-3.24	0.2653	138	0.2062	2586	X-RAY DIFFRACTION	100
3.24-3.71	0.247	136	0.1792	2622	X-RAY DIFFRACTION	100
3.71-4.68	0.1728	143	0.1429	2639	X-RAY DIFFRACTION	99.96
4.68-45.34	0.195	135	0.1631	2789	X-RAY DIFFRACTION	99.86

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	0.154341170364	0.106073083266	-0.0616067920161	0.124893719512	0.0022514632196	0.363551449594	0.238987792019	0.193633875	0.0937746499175	-0.39698211699	-0.222269437949	-0.254242201271	0.136332545426	0.071233393481	-6.98038163938E-5	0.434824166995	0.049136618199	0.0319701108566	0.459742756618	0.0904006822832	0.437661116648	-15.893938113	-7.20364138069	-14.6045223325
2	0.41184982785	-0.0474575125607	-0.331479136693	0.0767278416822	-0.156084773756	0.40398003014	-0.132168399666	0.500087648832	0.484226113321	-0.232377906683	0.0509130827978	-0.65660851766	0.25944356383	-0.42469772323	-0.021067439609	0.39199841955	0.0589230909742	0.0735875172652	0.544274769282	0.20118566492	0.474887531837	-12.5815245108	-5.58612076978	-19.6083430822
3	0.107015321034	-0.236312562847	-0.0716422631049	0.182606872688	0.0530982974681	0.0473084635665	-0.0636323703281	0.245158466199	0.24902615877	0.396803004569	-0.0124072278637	-0.395140767586	-0.212950829808	0.110744053705	-0.000142205552025	0.419139912943	0.0402465169428	0.0434422285533	0.4635823182	0.0790391441145	0.451053788297	-11.4032662787	-7.31671673146	-3.3879157377
4	0.089583325218	-0.164068678665	-0.121756759267	1.04167955041	0.831905575599	1.29636416618	0.19752499758	-0.0241794076952	1.01128619188	0.142668526807	-0.00939164651922	-1.02372379242	-0.0144508896705	0.618383859529	0.178786360625	0.283296434196	-0.0210346615189	0.137110520447	0.50020509208	0.199018738058	0.677989331857	-2.38759763676	-6.674293438	-12.8178799931
5	0.421287242493	-0.00917042604943	-0.00140132110405	0.644426118222	0.151769944427	0.0839577622849	-0.0665502060111	0.186773218638	0.108773519015	-0.119897124744	-0.319728683811	-0.574470557486	-0.405478520244	-0.16240924475	0.00041291350702	0.555093389197	0.0893116432948	0.0691526792903	0.502503727454	0.117239353214	0.463257403719	-6.80515336899	-14.4249174771	-12.8241467287
6	0.385590755295	-0.179294725105	0.328656463386	0.0989727976473	-0.0207905738211	0.301261314308	0.244198142925	0.252748141599	0.297217730385	0.134717186978	-0.291734096376	0.223666132822	-0.0987319134237	0.052742215925	0.00038981146218	0.451918194735	0.000245338630429	0.0649445933619	0.402023775601	0.15948563581	0.597253698666	-12.6573933097	1.65413609458	-9.78465127939
7	0.590178687162	0.137531057574	-0.143478323198	0.230410322916	-0.355842800644	0.278144782495	-0.00453810767555	0.273224951552	-0.0463250764366	0.278328089432	-0.160547220293	-0.0224063073623	-0.0964088159345	0.248799751557	0.000147879992773	0.380748761002	-0.0241649028897	-0.0208490412938	0.303644361854	0.0436940523147	0.356479881649	-11.5839762736	-20.8373179164	-2.38336666638
8	0.255185061314	0.32073470415	0.174658438825	0.336830469172	0.0567771989836	0.125365340355	0.113981847225	-0.307429024241	0.104921641833	0.0587364349878	0.0150050976267	0.211865207969	0.059647720849	-0.251841266985	-0.000351217284646	0.468241637396	-0.00240228259059	0.0198600123265	0.611194572772	0.0348458108826	0.372648611183	-12.5345513587	-31.1909703711	25.1107176134
9	0.508005719694	-0.362558095579	0.40394805789	0.498191815033	-0.608682224937	0.626012578508	0.133885792017	-0.0596329007971	-0.0592388415689	0.0940281518509	-0.0299750613355	0.149175529404	-8.7441045665E-6	-0.0972021201791	-0.000448829615088	0.329811640752	-0.0673325398104	0.00115897370202	0.441552225595	0.0375991726726	0.436843454053	-16.0950500324	-32.5959383334	15.6169303215
10	0.0857128084435	0.305456994817	-0.109466321444	0.352859595947	-0.284718814978	0.24698528724	-0.134627510375	-0.506589310643	-0.715572013887	0.296143313612	-0.180015728092	0.13245557998	0.601890030326	0.0534361065711	-0.000976639826347	0.580284387549	-0.066340785727	-0.0660383015325	0.646711948511	0.140287430026	0.56068433289	-15.5327496893	-40.2228250418	25.0275225185
11	0.232730048213	-0.370847623615	0.666568125915	0.64187562796	-0.697141249706	0.892586087808	-0.229890843391	-0.330119866076	0.456439449333	0.405775205861	0.0322840416054	-0.318461322352	-0.476216265868	-0.104691379487	-0.000499191540463	0.601329060816	0.0294319368755	-0.0670289371291	0.399328622873	-0.039854618678	0.606790139909	-16.53074576	4.22686427154	7.91079477808
12	0.743920388474	-0.156214367198	-0.115388998962	0.572112510183	-0.355856834005	0.811572283075	-0.0436357571254	-0.0876354920305	0.349765013636	0.498954308124	0.00842120798648	-0.466472122477	-0.34209277434	-0.231618304597	0.000120052182247	0.631685936602	0.0502040128127	-0.0617987961482	0.314254704755	-0.0410228391025	0.571979345385	-21.0264525454	9.26548618083	2.20345734068
13	0.748045426566	-0.140869835418	0.378820086152	0.793703040769	-0.536275583013	1.20862408349	-0.113652858087	-0.262722712963	0.230499834135	0.187008616497	0.119888996454	-0.179901298845	-0.273621151174	-0.0554646196569	-0.000179838819776	0.390699704307	-0.00422772294701	0.010135943604	0.371599396191	-0.0388035948574	0.349398390291	-16.262110206	-11.1471000263	13.9661105606
14	0.537138142258	-0.620856495082	-0.565392608477	2.34220148658	-0.358392054813	1.3145659537	-0.0921180442303	-0.219261871881	0.125577347301	0.0040687542595	0.100636680511	-0.180213465154	-0.235079169662	-0.0295413307146	-1.922745682E-5	0.420159040481	-0.0258178496359	-0.057490649335	0.409114391757	-0.00969769609868	0.405635953192	-10.1949147548	-14.5218447555	20.3141561327

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 131 through 154 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 155 through 170 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 171 through 182 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 183 through 205 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 206 through 223 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 224 through 239 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 240 through 261 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 262 through 277 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 278 through 317 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 318 through 343 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 2 through 40 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 41 through 84 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 85 through 150 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 151 through 222 )

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