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- PDB-7k0x: Marsupial T cell receptor Spl_145 -

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Basic information

Entry
Database: PDB / ID: 7k0x
TitleMarsupial T cell receptor Spl_145
Components
  • T cell receptor gamma chain
  • T cell receptor mu chain
KeywordsIMMUNE SYSTEM / T cell receptor / antigen recognition / IgV domain
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMonodelphis domestica (gray short-tailed opossum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsWegrecki, M. / Kannan Sivaraman, K. / Le Nours, J. / Rossjohn, J.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: 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
DepositionSep 6, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 14, 2021Group: 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 1.2Apr 3, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: T cell receptor mu chain
D: T cell receptor gamma chain
A: T cell receptor mu chain
B: T cell receptor gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,88110
Polymers128,1884
Non-polymers1,6936
Water00
1
C: T cell receptor mu chain
D: T cell receptor gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1235
Polymers64,0942
Non-polymers1,0293
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-6 kcal/mol
Surface area25990 Å2
MethodPISA
2
A: T cell receptor mu chain
B: T cell receptor gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7585
Polymers64,0942
Non-polymers6643
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-14 kcal/mol
Surface area26030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.925, 87.112, 214.408
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLYGLYILEILE(chain 'B' and (resid 3 through 41 or (resid 42...BD3 - 1373 - 137
121LYSLYSPHEPHE(chain 'B' and (resid 3 through 41 or (resid 42...BD140 - 217140 - 217
211GLYGLYILEILE(chain 'D' and (resid 3 through 25 or (resid 26...DB3 - 1373 - 137
221LYSLYSPHEPHE(chain 'D' and (resid 3 through 25 or (resid 26...DB140 - 217140 - 217
112VALVALLEULEU(chain 'C' and (resid 9 through 16 or (resid 17...CA9 - 1079 - 107
122ARGARGLEULEU(chain 'C' and (resid 9 through 16 or (resid 17...CA119 - 134119 - 134
212VALVALLEULEU(chain 'A' and ((resid 9 through 12 and (name N...AC9 - 1079 - 107
222ARGARGLEULEU(chain 'A' and ((resid 9 through 12 and (name N...AC119 - 134119 - 134

NCS ensembles :
ID
1
2

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Components

#1: Protein T cell receptor mu chain


Mass: 38105.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monodelphis domestica (gray short-tailed opossum)
Cell line (production host): HEK293S / Production host: Homo sapiens (human)
#2: Protein T cell receptor gamma chain


Mass: 25988.311 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monodelphis domestica (gray short-tailed opossum)
Cell line (production host): HEK293S / Production host: Homo sapiens (human)
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-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.: 5 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20-25% PEG 3350, 0.2M Na Formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.1→49.26 Å / Num. obs: 25260 / % possible obs: 100 % / Redundancy: 6.8 % / Biso Wilson estimate: 60.88 Å2 / CC1/2: 0.789 / Rpim(I) all: 0.123 / Net I/σ(I): 7
Reflection shellResolution: 3.1→3.31 Å / Redundancy: 7.1 % / Mean I/σ(I) obs: 2 / Num. unique obs: 4496 / CC1/2: 0.653 / Rpim(I) all: 0.643 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: unpublished

Resolution: 3.1→45.65 Å / SU ML: 0.4361 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.6104
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2507 1215 4.82 %
Rwork0.2026 23984 -
obs0.2051 25199 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.49 Å2
Refinement stepCycle: LAST / Resolution: 3.1→45.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8119 0 109 0 8228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00298425
X-RAY DIFFRACTIONf_angle_d0.680611486
X-RAY DIFFRACTIONf_chiral_restr0.04741330
X-RAY DIFFRACTIONf_plane_restr0.0041468
X-RAY DIFFRACTIONf_dihedral_angle_d14.4431227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.220.40061110.29712640X-RAY DIFFRACTION100
3.22-3.370.32091540.24642577X-RAY DIFFRACTION99.96
3.37-3.550.26771350.22322621X-RAY DIFFRACTION100
3.55-3.770.2721290.21682649X-RAY DIFFRACTION99.96
3.77-4.060.2691470.19762620X-RAY DIFFRACTION100
4.06-4.470.21431320.16552650X-RAY DIFFRACTION100
4.47-5.120.2061250.15742701X-RAY DIFFRACTION99.96
5.12-6.440.23831290.19272696X-RAY DIFFRACTION100
6.44-45.650.2291530.2172830X-RAY DIFFRACTION99.8
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
14.16656194417-1.813394061691.210875759969.60750803988-3.399794797352.551908918290.572461453009-0.51265122148-0.0763637202677-0.596558218475-0.06247376408280.7412478241890.5566481052720.233844534758-0.4498934649270.9177600860490.0241754453829-0.0002813087288490.636319720749-0.001652186550230.606932874874-10.4137144151-20.539027764230.9983098308
22.513515689951.469265754072.632446272291.810736786041.920179023224.60085274928-0.1271030732330.09802345677210.191438863263-0.367570085876-0.1153621066410.0614698596315-0.3006112739-0.1714394260190.2441836565260.3373548111720.086539713219-0.01420923417620.22070633274-0.001334304533030.247489070421-5.8395524169-15.394234033-20.6779657111
34.605128356663.014080571820.6974908427435.64974434193-0.8318713234951.812003326110.101720873275-0.234248603123-0.2416020058730.0860083225027-0.26053500992-0.2671918144060.09306413998820.2481923530190.1153593515720.2560921034930.0272402475113-0.002850422571770.2115947457750.05164208955140.1870442554135.96478499713-27.5557823575-0.630409211111
42.38965533845-0.1664961060940.5632073413032.55271257749-1.627048769577.237969606960.09786206666040.414039614839-0.00112870571144-0.52107802409-0.194033955585-0.05602971865920.369694276171.070489844360.1094669957010.3606082141310.05857968620740.01337362471430.338548653992-0.02764681321960.304429273981-5.0241463032-35.2756123855-25.237794692
56.177208523843.82551323528-1.868336906267.25801024965-2.614803968383.532853353930.138465669085-0.277667817413-0.1835534636280.140328516738-0.114136539853-0.688270718678-1.205317093331.4542609393-0.001426501881071.04653070366-0.4280437977810.05046394959340.986453660522-0.1180474915280.605706842666-21.947343360811.343703611318.8746217762
62.991408181750.7653949107790.3623962974886.98456868724-1.406190220424.698847531880.07140551689810.2643083205210.3432914313150.02993468295180.10707506053-0.081411663883-0.8482739429170.177429400079-0.121097766440.39577436147-0.0167250891947-0.002036194339320.2634819364110.1169236094060.475379300378-16.03784301922.9686224078-23.5908832066
73.03620641794-0.08344333446435.182754595661.009419600561.208903803448.43641952506-0.06698037398130.144176087675-0.220296471384-0.0929859935629-0.0851819080694-0.008647341558440.1541251599250.1836830292540.04271786220160.664225635902-0.0264568501344-0.08902288859140.5028650056170.1541814278620.370700495859-41.672965153812.3939220312-50.3550334713
84.668162371592.17178816718-0.2715486887471.85073249231-0.405048693353.085716900280.2257713117930.00838000821070.05028091191410.2619946016160.0573843607740.1189662545090.270956733652-0.0326483155933-0.2133026800310.3744087025010.0144906449802-0.1117060653580.2391730170860.1518962903780.350469322543-24.30634585993.93455444749-14.3786615153
91.028116805060.2942774851521.063066525962.96219026444-1.624986590464.747346410960.2808684625670.176995647906-0.2769714799-0.769055676211-0.434049506984-0.2346884637650.9036704103971.155522015670.2107758803940.6835660353820.13778154559-0.09059907146750.7490837593060.2343463270890.482208945352-34.471939536-0.375376658217-40.2048943976
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 9 through 134 )
2X-RAY DIFFRACTION2chain 'C' and (resid 135 through 341 )
3X-RAY DIFFRACTION3chain 'D' and (resid 2 through 116 )
4X-RAY DIFFRACTION4chain 'D' and (resid 117 through 220 )
5X-RAY DIFFRACTION5chain 'A' and (resid 5 through 134 )
6X-RAY DIFFRACTION6chain 'A' and (resid 135 through 243 )
7X-RAY DIFFRACTION7chain 'A' and (resid 244 through 340 )
8X-RAY DIFFRACTION8chain 'B' and (resid 3 through 115 )
9X-RAY DIFFRACTION9chain 'B' and (resid 116 through 219 )

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