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- PDB-3rbg: Crystal structure analysis of Class-I MHC restricted T-cell assoc... -

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Basic information

Entry
Database: PDB / ID: 3rbg
TitleCrystal structure analysis of Class-I MHC restricted T-cell associated molecule
ComponentsCytotoxic and regulatory T-cell molecule
KeywordsIMMUNE SYSTEM / IgV / CRTAM / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / Atoms-to-Animals: The Immune Function Network / IFN
Function / homology
Function and homology information


regulation of CD8-positive, alpha-beta T cell activation / detection of stimulus / detection of tumor cell / cell recognition / establishment of T cell polarity / lymphocyte migration into lymphoid organs / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / positive regulation of natural killer cell mediated cytotoxicity / regulation of T cell activation / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules ...regulation of CD8-positive, alpha-beta T cell activation / detection of stimulus / detection of tumor cell / cell recognition / establishment of T cell polarity / lymphocyte migration into lymphoid organs / positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / positive regulation of natural killer cell mediated cytotoxicity / regulation of T cell activation / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / regulation of T cell differentiation / negative regulation of activated T cell proliferation / immunological synapse / positive regulation of cytokine production / positive regulation of type II interferon production / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / adaptive immune response / signaling receptor binding / identical protein binding / plasma membrane
Similarity search - Function
: / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily ...: / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Cytotoxic and regulatory T-cell molecule
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRubinstein, R. / Ramagopal, U.A. / Toro, R. / Nathenson, S.G. / Fiser, A. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC) / Atoms-to-Animals: The Immune Function Network (IFN)
CitationJournal: Structure / Year: 2013
Title: Functional classification of immune regulatory proteins.
Authors: Rubinstein, R. / Ramagopal, U.A. / Nathenson, S.G. / Almo, S.C. / Fiser, A.
History
DepositionMar 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 7, 2013Group: Database references
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Sep 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytotoxic and regulatory T-cell molecule
B: Cytotoxic and regulatory T-cell molecule
C: Cytotoxic and regulatory T-cell molecule
D: Cytotoxic and regulatory T-cell molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3658
Polymers56,9854
Non-polymers3804
Water2,090116
1
A: Cytotoxic and regulatory T-cell molecule
C: Cytotoxic and regulatory T-cell molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6824
Polymers28,4922
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-22 kcal/mol
Surface area10510 Å2
MethodPISA
2
B: Cytotoxic and regulatory T-cell molecule
hetero molecules

B: Cytotoxic and regulatory T-cell molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6824
Polymers28,4922
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area1880 Å2
ΔGint-21 kcal/mol
Surface area10240 Å2
MethodPISA
3
D: Cytotoxic and regulatory T-cell molecule
hetero molecules

D: Cytotoxic and regulatory T-cell molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6824
Polymers28,4922
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area1780 Å2
ΔGint-23 kcal/mol
Surface area10890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.020, 116.291, 79.018
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
DetailsANALYTICAL ULTRA CENTRIFUGATION STUDIES SUGGESTS IT IS DIMER IN SOLUTION.

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Components

#1: Protein
Cytotoxic and regulatory T-cell molecule / Class-I MHC-restricted T-cell-associated molecule


Mass: 14246.207 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRTAM / Plasmid: pET-28a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(AI) / References: UniProt: O95727
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.9
Details: 0.49 M Sodium Phosphate, 0.91M Potasium Phosphate pH 6.9, Vapor diffusion, Sitting drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.551
11K, H, -L20.449
ReflectionResolution: 2.3→40 Å / Num. all: 23676 / Num. obs: 23676 / % possible obs: 98.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 38.2 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.057 / Χ2: 1.369 / Net I/σ(I): 12.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.365.60.46211681.436199.8
2.36-2.45.60.36111771.432199.9
2.4-2.455.60.29711911.443199.9
2.45-2.55.70.27511711.387199.9
2.5-2.555.70.23611831.387199.6
2.55-2.615.70.20211701.386199.9
2.61-2.685.70.19111851.411199.7
2.68-2.755.60.16711711.438199.7
2.75-2.835.60.13611861.385199.6
2.83-2.925.60.12511701.435199.6
2.92-3.035.60.10211811.445199.5
3.03-3.155.60.0911861.52199.6
3.15-3.295.50.08111921.555199
3.29-3.475.40.07211901.561199
3.47-3.685.20.06611651.539198.6
3.68-3.975.10.06111881.475198.3
3.97-4.365.30.05211831.334198
4.36-55.20.04511920.914198.3
5-6.295.40.04512030.973197.3
6.29-405.40.04112240.893194.3

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Z9M

1z9m


Resolution: 2.3→28.47 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.2319 / WRfactor Rwork: 0.1997 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.6938 / SU B: 8.227 / SU ML: 0.184 / SU R Cruickshank DPI: 0.0598 / SU Rfree: 0.0449 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2335 1190 5 %RANDOM
Rwork0.1983 ---
all0.2001 23571 --
obs0.2001 23571 97.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 61.61 Å2 / Biso mean: 30.1721 Å2 / Biso min: 14.29 Å2
Baniso -1Baniso -2Baniso -3
1--13.73 Å20 Å20 Å2
2---10 Å20 Å2
3---23.72 Å2
Refinement stepCycle: LAST / Resolution: 2.3→28.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3146 0 20 116 3282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223270
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.9644473
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6225409
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.05425.68125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.97815579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.554154
X-RAY DIFFRACTIONr_chiral_restr0.0890.2557
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212334
X-RAY DIFFRACTIONr_mcbond_it0.7321.52030
X-RAY DIFFRACTIONr_mcangle_it1.41323347
X-RAY DIFFRACTIONr_scbond_it1.9631240
X-RAY DIFFRACTIONr_scangle_it3.3134.51124
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 85 -
Rwork0.278 1430 -
all-1515 -
obs--87.12 %

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