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- PDB-3q5t: V beta/V beta homodimerization-based pre-TCR model suggested by T... -

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Basic information

Entry
Database: PDB / ID: 3q5t
TitleV beta/V beta homodimerization-based pre-TCR model suggested by TCR beta crystal structures
ComponentsTCR N30 beta
KeywordsIMMUNE SYSTEM / IG / T cell receptor / antigen peptide/MHC / membrane
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.005 Å
AuthorsChen, Q. / Zhang, H. / Wang, J.-H.
CitationJournal: Front Immunol / Year: 2011
Title: A conserved hydrophobic patch on V beta domains revealed by TCR beta chain crystal structures: Implications for pre-TCR dimerization.
Authors: Zhou, B. / Chen, Q. / Mallis, R.J. / Zhang, H. / Liu, J.H. / Reinherz, E.L. / Wang, J.H.
History
DepositionDec 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 15, 2014Group: Structure summary
Revision 1.3Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TCR N30 beta


Theoretical massNumber of molelcules
Total (without water)26,9821
Polymers26,9821
Non-polymers00
Water59433
1
A: TCR N30 beta

A: TCR N30 beta


Theoretical massNumber of molelcules
Total (without water)53,9642
Polymers53,9642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Unit cell
Length a, b, c (Å)53.290, 69.829, 126.953
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-270-

HOH

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Components

#1: Protein TCR N30 beta


Mass: 26981.932 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
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: 2.19 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20 % PEG 4000, 100 mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 16208 / Num. obs: 16199 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Rsym value: 0.06 / Net I/σ(I): 19.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.005→19.047 Å / SU ML: 0.35 / σ(F): 0 / Phase error: 32.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2898 813 5.02 %
Rwork0.2351 --
obs0.2375 16199 99.7 %
all-16247 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.651 Å2 / ksol: 0.344 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--11.5227 Å20 Å2-0 Å2
2--23.685 Å2-0 Å2
3----12.1623 Å2
Refinement stepCycle: LAST / Resolution: 2.005→19.047 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1881 0 0 33 1914
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071938
X-RAY DIFFRACTIONf_angle_d1.0972632
X-RAY DIFFRACTIONf_dihedral_angle_d24.8561174
X-RAY DIFFRACTIONf_chiral_restr0.072277
X-RAY DIFFRACTIONf_plane_restr0.006347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0049-2.13030.41791520.33272484X-RAY DIFFRACTION99
2.1303-2.29460.33731160.29342547X-RAY DIFFRACTION100
2.2946-2.5250.33481620.28312514X-RAY DIFFRACTION100
2.525-2.88930.37061370.2682548X-RAY DIFFRACTION100
2.8893-3.63610.34031190.24142610X-RAY DIFFRACTION100
3.6361-19.04830.20831270.1982683X-RAY DIFFRACTION99
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)
10.16331.3088-1.05230.5468-1.2721.91720.3617-0.23760.23310.0968-0.05160.1858-0.17770.201-0.18650.2430.01810.08590.36990.05580.3483-6.615323.638880.3759
22.1742-0.5472-3.21113.03173.28796.95330.61640.5943-0.1594-0.079-0.45580.0668-0.0033-1.4925-0.07230.2862-0.0945-0.00710.46220.0440.2856-14.041714.6785.7898
31.60550.767-3.74962.1273-1.14414.63930.6141-0.22070.03280.14360.01740.3707-0.1193-0.0597-0.40420.1463-0.02380.06120.36980.08370.2604-10.393418.26285.7745
42.34650.8431-1.38521.2268-1.3841.9229-0.08370.174-0.1785-0.36710.0115-0.07540.58740.29860.15540.37870.10350.03730.2623-0.16020.30474.57321.612256.3593
51.148-0.7817-0.030.7561-2.0174.186-0.2457-0.037-0.1391-0.20950.10630.11620.47670.23980.11530.30880.00750.0160.17330.01450.24493.847526.221759.9382
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1resid 3:35
2X-RAY DIFFRACTION2resid 36:58
3X-RAY DIFFRACTION3resid 59:109
4X-RAY DIFFRACTION4resid 110:147
5X-RAY DIFFRACTION5resid 148:240

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