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- PDB-3of6: Human pre-T cell receptor crystal structure -

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Basic information

Entry
Database: PDB / ID: 3of6
TitleHuman pre-T cell receptor crystal structure
Components
  • Pre T-cell antigen receptor alpha
  • T cell receptor beta chain
KeywordsIMMUNE SYSTEM / Ig fold
Function / homology
Function and homology information


negative regulation of thymocyte apoptotic process / NOTCH3 Intracellular Domain Regulates Transcription / membrane => GO:0016020
Similarity search - Function
Pre-T-cell antigen receptor / Pre-T-cell antigen receptor / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Pre T-cell antigen receptor alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPang, S.S.
CitationJournal: Nature / Year: 2010
Title: The structural basis for autonomous dimerization of the pre-T-cell antigen receptor
Authors: Pang, S.S. / Berry, R. / Chen, Z. / Kjer-Nielsen, L. / Perugini, M.A. / King, G.F. / Wang, C. / Chew, S.H. / La Gruta, N.L. / Williams, N.K. / Beddoe, T. / Tiganis, T. / Cowieson, N.P. / ...Authors: Pang, S.S. / Berry, R. / Chen, Z. / Kjer-Nielsen, L. / Perugini, M.A. / King, G.F. / Wang, C. / Chew, S.H. / La Gruta, N.L. / Williams, N.K. / Beddoe, T. / Tiganis, T. / Cowieson, N.P. / Godfrey, D.I. / Purcell, A.W. / Wilce, M.C.J. / McCluskey, J. / Rossjohn, J.
History
DepositionAug 13, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T cell receptor beta chain
B: T cell receptor beta chain
C: T cell receptor beta chain
D: Pre T-cell antigen receptor alpha
E: Pre T-cell antigen receptor alpha
F: Pre T-cell antigen receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,87110
Polymers125,9866
Non-polymers8854
Water1,964109
1
A: T cell receptor beta chain
D: Pre T-cell antigen receptor alpha
hetero molecules

A: T cell receptor beta chain
D: Pre T-cell antigen receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,4336
Polymers83,9914
Non-polymers4422
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_435x-y-1,-y-2,-z+1/31
Buried area6650 Å2
ΔGint-49 kcal/mol
Surface area30430 Å2
MethodPISA
2
B: T cell receptor beta chain
C: T cell receptor beta chain
E: Pre T-cell antigen receptor alpha
F: Pre T-cell antigen receptor alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,6557
Polymers83,9914
Non-polymers6643
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6750 Å2
ΔGint-47 kcal/mol
Surface area31370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.902, 114.902, 183.101
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein T cell receptor beta chain


Mass: 28607.553 Da / Num. of mol.: 3 / Fragment: ectodomain / Mutation: C192A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HiFIVE insect cells / Production host: Trichoplusia ni (cabbage looper)
#2: Protein Pre T-cell antigen receptor alpha / pre-T alpha chain / pT-alpha / pTa / pT-alpha-TCR


Mass: 13387.915 Da / Num. of mol.: 3 / Fragment: ectodomain, UNP residues 17-135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HiFIVE insect cells / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6ISU1
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE NUMBERING OF THE PROTEIN IS BASED THAT OF A T CELL RECEPTOR AND THERE IS A GAP IN THE NUMBERING ...THE NUMBERING OF THE PROTEIN IS BASED THAT OF A T CELL RECEPTOR AND THERE IS A GAP IN THE NUMBERING IN THE CDR3 LOOP REGION (101-104). FOR CHAINS A,B,C, THE UNICODE IS DEFINE AS P01850. THE N-TERMINAL HALF OF THE PROTEIN (RESIDUE 3-117) IS A VARIABLE REGION OF A T CELL RECEPTOR. THE FIRST FOUR RESIDUES AGSH AND LAST 9 RESIDUES CTSGDDDDK ARE EXPRESSION TAG REGIONS.

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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: 2.77 Å3/Da / Density % sol: 55.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M sodium cacodylate, pH 7.0, 0.1M calcium acetate, 13-16% PEG 1500, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.979461 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 3, 2009
RadiationMonochromator: Si Vortex-ES / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979461 Å / Relative weight: 1
Reflection twinOperator: -k,h+k,l / Fraction: 0.515
ReflectionResolution: 2.8→67.4 Å / Num. all: 35135 / Num. obs: 35135 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shell
Resolution (Å)% possible all
2.8-2.95100
8.85-67.4299.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASESphasing
PHENIX(phenix.refine: 1.4_4)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KGC; E chain

1kgc


Resolution: 2.8→67.374 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8277 / σ(F): 1.38 / Phase error: 24.02 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2402 1809 5.16 %Random
Rwork0.1753 33245 --
obs0.1787 35090 99.99 %-
all-35135 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.974 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso max: 244.66 Å2 / Biso mean: 86.0365 Å2 / Biso min: 16.62 Å2
Baniso -1Baniso -2Baniso -3
1-4.9259 Å20 Å2-0 Å2
2--4.9259 Å20 Å2
3----18.4947 Å2
Refinement stepCycle: LAST / Resolution: 2.8→67.374 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7895 0 56 109 8060
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028196
X-RAY DIFFRACTIONf_angle_d0.37811205
X-RAY DIFFRACTIONf_dihedral_angle_d10.3752870
X-RAY DIFFRACTIONf_chiral_restr0.0211226
X-RAY DIFFRACTIONf_plane_restr0.0031472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8009-2.87660.28471400.26042531X-RAY DIFFRACTION95
2.8766-2.96120.30011360.25282515X-RAY DIFFRACTION95
2.9612-3.05680.25211320.24072489X-RAY DIFFRACTION95
3.0568-3.1660.26441340.22552544X-RAY DIFFRACTION95
3.166-3.29270.29061380.22192529X-RAY DIFFRACTION95
3.2927-3.44260.33771370.20542536X-RAY DIFFRACTION95
3.4426-3.6240.20021400.19052537X-RAY DIFFRACTION95
3.624-3.8510.21451380.17762536X-RAY DIFFRACTION95
3.851-4.14820.25451410.15782551X-RAY DIFFRACTION95
4.1482-4.56530.20281410.13742561X-RAY DIFFRACTION95
4.5653-5.22530.19941400.12332593X-RAY DIFFRACTION95
5.2253-6.58070.27391400.17472601X-RAY DIFFRACTION95
6.5807-48.67010.22821520.17232722X-RAY DIFFRACTION95

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