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- PDB-6fur: F11 T-Cell Receptor Recognising PKYVKQNTLKLAT Peptide Presented b... -

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Basic information

Entry
Database: PDB / ID: 6fur
TitleF11 T-Cell Receptor Recognising PKYVKQNTLKLAT Peptide Presented by HLA-DR*0101
Components(Human F11 T-Cell ...) x 2
KeywordsIMMUNE SYSTEM / T Cell Receptor / Human Leukocyte Antigen / Influenza Epitope / Haemagglutinin / 3D Structure
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsRizkallah, P.J. / Cole, D.K.
CitationJournal: Front Immunol / Year: 2018
Title: In Silicoand Structural Analyses Demonstrate That Intrinsic Protein Motions Guide T Cell Receptor Complementarity Determining Region Loop Flexibility.
Authors: Holland, C.J. / MacLachlan, B.J. / Bianchi, V. / Hesketh, S.J. / Morgan, R. / Vickery, O. / Bulek, A.M. / Fuller, A. / Godkin, A. / Sewell, A.K. / Rizkallah, P.J. / Wells, S. / Cole, D.K.
History
DepositionFeb 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1May 9, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _citation.journal_volume ..._chem_comp.name / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2Jan 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 F11 T-Cell Receptor alpha chain
B: Human F11 T-Cell Receptor
C: Human F11 T-Cell Receptor alpha chain
D: Human F11 T-Cell Receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,13340
Polymers99,2934
Non-polymers2,84136
Water11,476637
1
A: Human F11 T-Cell Receptor alpha chain
B: Human F11 T-Cell Receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,73915
Polymers49,6462
Non-polymers1,09313
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-67 kcal/mol
Surface area21250 Å2
MethodPISA
2
C: Human F11 T-Cell Receptor alpha chain
D: Human F11 T-Cell Receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,39425
Polymers49,6462
Non-polymers1,74823
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9010 Å2
ΔGint-86 kcal/mol
Surface area21320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.650, 114.860, 85.330
Angle α, β, γ (deg.)90.00, 91.01, 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: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERAA1 - 2021 - 202
21SERSERCC1 - 2021 - 202
12ASPASPBB1 - 2401 - 240
22ASPASPDD1 - 2401 - 240

NCS ensembles :
ID
1
2

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Components

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Human F11 T-Cell ... , 2 types, 4 molecules ACBD

#1: Protein Human F11 T-Cell Receptor alpha chain


Mass: 22438.043 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 F11 T-Cell Receptor


Mass: 27208.246 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)

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Non-polymers , 4 types, 673 molecules

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


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 637 / 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: 2.5 Å3/Da / Density % sol: 50.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M NH4 SO4, 0.1 M MES, 25% PEG 4K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.73→46.34 Å / Num. obs: 96229 / % possible obs: 94.8 % / Redundancy: 3.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.088 / Net I/σ(I): 11.1
Reflection shellResolution: 1.73→1.77 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.656 / Mean I/σ(I) obs: 2 / Num. unique obs: 7382 / CC1/2: 0.663 / Rrim(I) all: 0.777 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
xia2data reduction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EH6

6eh6


Resolution: 1.73→46.34 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.772 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.119 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22563 4819 5 %RANDOM
Rwork0.18921 ---
obs0.19101 91379 94.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.356 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å2-0 Å2-0.27 Å2
2---0.5 Å2-0 Å2
3---0.96 Å2
Refinement stepCycle: 1 / Resolution: 1.73→46.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6990 0 173 637 7800
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0197444
X-RAY DIFFRACTIONr_bond_other_d0.0020.026541
X-RAY DIFFRACTIONr_angle_refined_deg1.9011.95310100
X-RAY DIFFRACTIONr_angle_other_deg1.059315272
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5595917
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.18324.499349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.581151192
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8851538
X-RAY DIFFRACTIONr_chiral_restr0.1240.21098
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218262
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021524
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_it1.1251.593605
X-RAY DIFFRACTIONr_mcbond_other1.1251.5893604
X-RAY DIFFRACTIONr_mcangle_it1.8462.3764522
X-RAY DIFFRACTIONr_mcangle_other1.8472.3774523
X-RAY DIFFRACTIONr_scbond_it1.5411.8863839
X-RAY DIFFRACTIONr_scbond_other1.5341.8873839
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3282.7185572
X-RAY DIFFRACTIONr_long_range_B_refined6.77820.0277987
X-RAY DIFFRACTIONr_long_range_B_other6.77920.0327988
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)
11A117280.11
12C117280.11
21B153600.09
22D153600.09
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 369 -
Rwork0.265 7003 -
obs--98.57 %
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)
11.2224-0.50341.13791.2422-0.06495.65850.03730.10280.1048-0.1859-0.0487-0.08010.04730.06830.01140.03220.00690.01060.01510.01430.015321.80544.6656-3.3788
22.68010.11790.08113.9883-1.15582.2702-0.0629-0.17020.12690.30550.14510.2982-0.0064-0.1808-0.08220.04810.02070.00910.0482-0.00540.033814.892210.934429.5748
32.53170.2008-1.86920.9637-0.42494.08290.00750.06540.1297-0.1698-0.05140.07480.0601-0.01090.04390.03090.0086-0.01050.02480.00280.02080.832415.2864-8.5179
45.2584-0.42341.67541.39280.01461.2873-0.0456-0.04460.22610.0932-0.0109-0.16750.0222-0.06420.05650.0091-0.0008-0.00970.0050.00130.02846.912523.363121.1212
51.2320.369-1.06941.12880.11715.60780.0225-0.1006-0.07930.1589-0.0389-0.0402-0.10140.13890.01630.028-0.0038-0.0020.03620.01750.010620.9309-6.023346.7803
63.65990.17680.01113.9295-1.05022.50770.01010.1807-0.1647-0.17030.16060.32160.0139-0.1765-0.17070.0147-0.0153-0.00880.04140.00180.041515.3952-12.528213.4908
72.0926-0.32431.83920.9054-0.91864.39180.0178-0.0405-0.12890.1326-0.0460.10490.0313-0.04720.02830.0282-0.00750.02340.0218-0.00340.0353-0.1326-17.017351.3743
84.77780.1689-1.42821.3352-0.05441.1866-0.0246-0.0667-0.237-0.0015-0.0024-0.0578-0.0094-0.02550.0270.0126-0.0035-0.00360.00770.0070.01957.3227-25.101521.3203
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 113
2X-RAY DIFFRACTION2A114 - 215
3X-RAY DIFFRACTION3B0 - 114
4X-RAY DIFFRACTION4B115 - 250
5X-RAY DIFFRACTION5C0 - 113
6X-RAY DIFFRACTION6C114 - 215
7X-RAY DIFFRACTION7D0 - 114
8X-RAY DIFFRACTION8D115 - 250

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