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- PDB-2z35: Crystal structure of immune receptor -

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Basic information

Entry
Database: PDB / ID: 2z35
TitleCrystal structure of immune receptor
Components
  • T-cell receptor alpha-chain
  • T-cell receptor beta-chain
KeywordsIMMUNE SYSTEM / immune receptor
Function / homology
Function and homology information


T cell receptor complex / adaptive immune response
Similarity search - Function
: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily ...: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Beta-chain / TRAV6D-7
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFeng, D. / Bond, C.J. / Ely, L.K. / Garcia, K.C.
CitationJournal: Nat.Immunol. / Year: 2007
Title: Structural evidence for a germline-encoded T cell receptor-major histocompatibility complex interaction 'codon'
Authors: Feng, D. / Bond, C.J. / Ely, L.K. / Maynard, J. / Garcia, K.C.
History
DepositionJun 1, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 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
Remark 999SEQUENCE The sequnce database for chain A and B does not currently exist in UNP.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T-cell receptor alpha-chain
B: T-cell receptor beta-chain


Theoretical massNumber of molelcules
Total (without water)24,4762
Polymers24,4762
Non-polymers00
Water45025
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.994, 73.802, 115.374
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein T-cell receptor alpha-chain


Mass: 12396.562 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) / References: UniProt: Q5R1F5
#2: Protein T-cell receptor beta-chain


Mass: 12079.190 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) / References: UniProt: A2NTY6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 2.96 Å3/Da / Density % sol: 58.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.8M mono-sodium dihydrogen phosphate, 0.8M mono-potassium dihydrogen phosphate and 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 13532 / Num. obs: 13532 / % possible obs: 96.1 % / Redundancy: 6 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 22.2
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 5.6 / Num. unique all: 13532 / Rsym value: 0.372 / % possible all: 99.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→50 Å
RfactorNum. reflection% reflection
Rfree0.285 --
Rwork0.263 --
all0.263 13532 -
obs-13532 96.1 %
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1726 0 0 25 1751

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