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- PDB-5nmd: 868 TCR Specific for HLA A02 presenting HIV Epitope SLYNTVATL -

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Basic information

Entry
Database: PDB / ID: 5nmd
Title868 TCR Specific for HLA A02 presenting HIV Epitope SLYNTVATL
Components
  • Human T-cell Receptor, beta chain
  • human T-cell Receptor alpha chain
KeywordsIMMUNE SYSTEM / MHC / TCR / CD8+
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsRizkallah, P.J. / Cole, D.K. / Fuller, A. / Sewell, A.K.
CitationJournal: Front Immunol / Year: 2017
Title: Dual Molecular Mechanisms Govern Escape at Immunodominant HLA A2-Restricted HIV Epitope.
Authors: Cole, D.K. / Fuller, A. / Dolton, G. / Zervoudi, E. / Legut, M. / Miles, K. / Blanchfield, L. / Madura, F. / Holland, C.J. / Bulek, A.M. / Bridgeman, J.S. / Miles, J.J. / Schauenburg, A.J.A. ...Authors: Cole, D.K. / Fuller, A. / Dolton, G. / Zervoudi, E. / Legut, M. / Miles, K. / Blanchfield, L. / Madura, F. / Holland, C.J. / Bulek, A.M. / Bridgeman, J.S. / Miles, J.J. / Schauenburg, A.J.A. / Beck, K. / Evavold, B.D. / Rizkallah, P.J. / Sewell, A.K.
History
DepositionApr 5, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Dec 20, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Jan 17, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: human T-cell Receptor alpha chain
B: Human T-cell Receptor, beta chain
C: human T-cell Receptor alpha chain
D: Human T-cell Receptor, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,05813
Polymers99,3304
Non-polymers7299
Water3,729207
1
A: human T-cell Receptor alpha chain
B: Human T-cell Receptor, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0437
Polymers49,6652
Non-polymers3785
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-46 kcal/mol
Surface area20830 Å2
MethodPISA
2
C: human T-cell Receptor alpha chain
D: Human T-cell Receptor, beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0156
Polymers49,6652
Non-polymers3504
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-48 kcal/mol
Surface area20870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.470, 50.620, 114.310
Angle α, β, γ (deg.)90.00, 90.16, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSSERSERAA2 - 2011 - 200
21LYSLYSSERSERCC2 - 2011 - 200
12ASPASPASPASPBB1 - 2421 - 242
22ASPASPASPASPDD1 - 2421 - 242

NCS ensembles :
ID
1
2

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Components

#1: Protein human T-cell Receptor alpha chain


Mass: 22224.604 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 Human T-cell Receptor, beta chain /


Mass: 27440.178 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O

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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: 2.55 Å3/Da / Density % sol: 51.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Sodium Cacodylate, pH 6.5, 20% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 2.07→43.81 Å / Num. obs: 60507 / % possible obs: 98.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 40.7 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.1
Reflection shellResolution: 2.07→2.13 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.723 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4492 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BNU

2bnu


Resolution: 2.07→43.81 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 11.417 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.168 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22319 3051 5 %RANDOM
Rwork0.18857 ---
obs0.19039 57421 98.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 56.984 Å2
Baniso -1Baniso -2Baniso -3
1--1.58 Å20 Å2-1.41 Å2
2--2.81 Å20 Å2
3----1.23 Å2
Refinement stepCycle: 1 / Resolution: 2.07→43.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6998 0 41 207 7246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0197261
X-RAY DIFFRACTIONr_bond_other_d0.0020.026242
X-RAY DIFFRACTIONr_angle_refined_deg1.971.9389872
X-RAY DIFFRACTIONr_angle_other_deg1.125314582
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2675892
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44524.56364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.929151146
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4921540
X-RAY DIFFRACTIONr_chiral_restr0.1430.21047
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218194
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021526
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.253.2523562
X-RAY DIFFRACTIONr_mcbond_other2.2493.2513561
X-RAY DIFFRACTIONr_mcangle_it3.6214.8584456
X-RAY DIFFRACTIONr_mcangle_other3.6214.8594457
X-RAY DIFFRACTIONr_scbond_it2.9123.5843699
X-RAY DIFFRACTIONr_scbond_other2.7833.5553679
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.285.2125387
X-RAY DIFFRACTIONr_long_range_B_refined7.05338.0387725
X-RAY DIFFRACTIONr_long_range_B_other7.01637.9357706
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A118220.1
12C118220.1
21B154860.09
22D154860.09
LS refinement shellResolution: 2.072→2.126 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 240 -
Rwork0.288 4224 -
obs--99.09 %
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)
15.0323-1.76820.2753.4569-2.29415.8678-0.09390.0514-0.2729-0.0461-0.0716-0.2140.35730.46090.16550.0794-0.01080.01560.07790.0070.1448.7464-10.607928.7977
25.1598-0.4058-1.6675.49041.84246.40840.220.21540.74390.027-0.0697-0.5749-0.83840.3747-0.15020.1995-0.0687-0.08160.19440.15430.289732.320116.664618.3434
32.3231-1.1710.48787.23420.77922.5258-0.08250.0429-0.1160.05860.10810.07460.1127-0.1736-0.02570.0282-0.0208-0.01760.02520.00840.031636.0968-10.316748.2205
42.7059-0.39270.63141.45240.19426.1798-0.14190.21450.1270.14340.09090.0164-0.2221-0.3270.0510.0350.0126-0.03390.05490.01640.105121.55238.897428.6888
55.25220.68411.69362.3434-1.47764.8704-0.10320.0235-0.1183-0.11980.0690.0131-0.0778-0.27410.03420.07070.05240.06060.1760.00490.128460.05910.664411.0712
65.20721.2375-0.07887.01440.4644.20780.1438-0.7270.29370.4856-0.03560.2799-0.3235-0.4963-0.10820.19810.02120.02070.70220.08620.262476.06985.121140.9873
74.0330.72471.01623.98810.55925.598-0.19120.40390.0703-0.33730.0904-0.38290.06090.24410.10080.09350.06960.05310.23840.14210.212273.278517.36492.0855
82.7584-0.42840.4014.5148-1.38032.5091-0.0269-0.37640.13920.17180.12050.1955-0.2485-0.3898-0.09360.0341-0.0038-0.01920.35750.04180.207386.72379.543729.0522
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 112
2X-RAY DIFFRACTION2A115 - 200
3X-RAY DIFFRACTION3B0 - 112
4X-RAY DIFFRACTION4B115 - 250
5X-RAY DIFFRACTION5C0 - 112
6X-RAY DIFFRACTION6C115 - 200
7X-RAY DIFFRACTION7D0 - 112
8X-RAY DIFFRACTION8D115 - 250

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