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- PDB-4gkz: HA1.7, a MHC class II restricted TCR specific for haemagglutinin -

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Basic information

Entry
Database: PDB / ID: 4gkz
TitleHA1.7, a MHC class II restricted TCR specific for haemagglutinin
Components
  • Alpha chain of Class II TCR
  • Beta Chain of Class II TCR
KeywordsIMMUNE SYSTEM / Major histocompatibility complex class II (pMHC-II) / T-cell / T-cell receptor (TCR) / influenza / HA1.7
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.39 Å
AuthorsHolland, C.J. / Rizkallah, P.J. / Cole, D.K. / Sewell, A.K. / Godkin, A.J.
CitationJournal: Sci Rep / Year: 2012
Title: Minimal conformational plasticity enables TCR cross-reactivity to different MHC class II heterodimers.
Authors: Holland, C.J. / Rizkallah, P.J. / Vollers, S. / Calvo-Calle, J.M. / Madura, F. / Fuller, A. / Sewell, A.K. / Stern, L.J. / Godkin, A. / Cole, D.K.
History
DepositionAug 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha chain of Class II TCR
B: Beta Chain of Class II TCR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,62611
Polymers49,8982
Non-polymers7289
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-24 kcal/mol
Surface area21150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.240, 49.660, 72.610
Angle α, β, γ (deg.)90.000, 94.330, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Alpha chain of Class II TCR


Mass: 22362.955 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Protein Beta Chain of Class II TCR


Mass: 27534.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

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Non-polymers , 4 types, 58 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-TAM / TRIS(HYDROXYETHYL)AMINOMETHANE / Tris


Mass: 163.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.49 Å3/Da / Density % sol: 50.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM Bis-Tris Propane, 200mM Sodium Bromide, 20% PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 9, 2011 / Details: Si(111)
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.39→26.364 Å / Num. all: 19445 / Num. obs: 19445 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2.3 / Redundancy: 3.8 % / Rsym value: 0.04 / Net I/σ(I): 18.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.39-2.453.90.5761.30.576199.6
2.45-2.523.90.4571.70.457199.3
2.52-2.593.90.37720.377199.4
2.59-2.673.90.3082.50.308198.7
2.67-2.763.90.2513.10.251198.9
2.76-2.863.90.1834.20.183198.2
2.86-2.963.80.1345.80.134198.1
2.96-3.093.70.098.60.09198.2
3.09-3.223.50.07410.40.074197.6
3.22-3.383.30.04915.10.049196.3
3.38-3.563.90.03919.20.039198.4
3.56-3.783.80.03321.90.033198.9
3.78-4.043.70.027250.027198.9
4.04-4.363.80.02229.60.022199.2
4.36-4.783.70.0233.60.02198.9
4.78-5.343.60.01935.20.019198.1
5.34-6.173.50.01933.30.019196
6.17-7.563.50.01738.20.017196.9
7.56-10.693.90.01540.90.015199.5
10.69-26.3643.60.01441.10.014193.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASERphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.11data extraction
GDAdata collection
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FYT

1fyt


Resolution: 2.39→26.36 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.899 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 22.666 / SU ML: 0.247 / Cross valid method: THROUGHOUT / ESU R: 0.533 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29812 994 5.1 %RANDOM
Rwork0.24855 ---
obs0.25127 18443 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.179 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å2-0.07 Å2
2--2.67 Å20 Å2
3----3.4 Å2
Refinement stepCycle: LAST / Resolution: 2.39→26.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3505 0 45 49 3599
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223627
X-RAY DIFFRACTIONr_bond_other_d0.0010.022454
X-RAY DIFFRACTIONr_angle_refined_deg1.7451.9424927
X-RAY DIFFRACTIONr_angle_other_deg0.9835977
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.015447
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57624.235170
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.19415603
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6591519
X-RAY DIFFRACTIONr_chiral_restr0.1080.2534
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214055
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02756
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_it0.7551.52227
X-RAY DIFFRACTIONr_mcbond_other0.1411.5890
X-RAY DIFFRACTIONr_mcangle_it1.39323611
X-RAY DIFFRACTIONr_scbond_it1.81131400
X-RAY DIFFRACTIONr_scangle_it2.7774.51315
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.39→2.452 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.51 66 -
Rwork0.341 1373 -
obs--100 %
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)
11.134-0.2298-0.17871.86160.5933.6922-0.0823-0.0055-0.01230.0734-0.04760.0548-0.147-0.06310.12990.0519-0.0065-0.00540.00460.00960.1712-1.83525.418235.3727
22.9577-0.4737-0.10431.58770.06111.0583-0.04950.0672-0.1488-0.09120.0068-0.14990.10.06960.04270.2852-0.01960.00940.22670.00630.164718.42333.096.4938
32.0475-0.6523-0.7931.22450.61790.8802-0.0928-0.04730.04310.08490.0804-0.1444-0.08810.31330.01240.1755-0.0295-0.03910.19540.03060.123818.23739.36847.0945
40.9834-0.02110.73520.3487-0.00051.1372-0.0358-0.07320.0469-0.0956-0.0109-0.122-0.03840.06120.04660.2221-0.04790.01770.2735-0.01530.168925.971613.33117.2257
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 117
2X-RAY DIFFRACTION2A118 - 201
3X-RAY DIFFRACTION3B2 - 117
4X-RAY DIFFRACTION4B118 - 242

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