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- PDB-1b6e: HUMAN CD94 -

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Basic information

Entry
Database: PDB / ID: 1b6e
TitleHUMAN CD94
ComponentsCD94
KeywordsNK CELL / RECEPTOR / C-TYPE LECTIN / C-TYPE LECTIN-LIKE / NKD
Function / homology
Function and homology information


natural killer cell mediated immunity / MHC class Ib protein binding, via antigen binding groove / HLA-E specific inhibitory MHC class Ib receptor activity / MHC class I protein complex binding / regulation of natural killer cell activation / negative regulation of T cell mediated cytotoxicity / protein antigen binding / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of natural killer cell mediated cytotoxicity / stimulatory C-type lectin receptor signaling pathway ...natural killer cell mediated immunity / MHC class Ib protein binding, via antigen binding groove / HLA-E specific inhibitory MHC class Ib receptor activity / MHC class I protein complex binding / regulation of natural killer cell activation / negative regulation of T cell mediated cytotoxicity / protein antigen binding / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of natural killer cell mediated cytotoxicity / stimulatory C-type lectin receptor signaling pathway / DAP12 interactions / transmembrane signaling receptor activity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / DAP12 signaling / carbohydrate binding / adaptive immune response / cell surface receptor signaling pathway / receptor complex / external side of plasma membrane / plasma membrane
Similarity search - Function
Natural killer cell receptor-like, C-type lectin-like domain / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
Natural killer cells antigen CD94
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.6 Å
AuthorsBoyington, J.C. / Riaz, A.N. / Patamawenu, A. / Coligan, J.E. / Brooks, A.G. / Sun, P.D.
CitationJournal: Immunity / Year: 1999
Title: Structure of CD94 reveals a novel C-type lectin fold: implications for the NK cell-associated CD94/NKG2 receptors.
Authors: Boyington, J.C. / Riaz, A.N. / Patamawenu, A. / Coligan, J.E. / Brooks, A.G. / Sun, P.D.
History
DepositionJan 14, 1999Processing site: BNL
Revision 1.0Jun 15, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CD94


Theoretical massNumber of molelcules
Total (without water)15,0051
Polymers15,0051
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.710, 91.710, 84.230
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein CD94


Mass: 15004.530 Da / Num. of mol.: 1 / Fragment: C-TYPE LECTIN DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: NATURAL KILLER CELL / Cellular location: CELL SURFACECell membrane / Plasmid: MODIFIED PET30 / Species (production host): Escherichia coli / Cellular location (production host): INCLUSION BODIES / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q13241
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 3.4 Å3/Da / Density % sol: 63.7 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 %PEG80001reservoir
2100 mM1reservoirCaCl2
350 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9795
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1998
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 6450 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rsym value: 0.063 / Net I/σ(I): 12.5
Reflection shellResolution: 2.6→2.7 Å / Rsym value: 0.301 / % possible all: 91.7
Reflection
*PLUS
Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 91.7 % / Rmerge(I) obs: 0.301

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.6→8 Å / Rfactor Rfree error: 0.019 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT CORRECTION DURING REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.322 279 4.9 %RANDOM
Rwork0.22 ---
obs0.22 5667 86.4 %-
Displacement parametersBiso mean: 40.6 Å2
Baniso -1Baniso -2Baniso -3
1--18.587 Å2-10.633 Å20 Å2
2---18.587 Å20 Å2
3---10.638 Å2
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms997 0 0 39 1036
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.75
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.91.5
X-RAY DIFFRACTIONx_mcangle_it3.22
X-RAY DIFFRACTIONx_scbond_it2.62
X-RAY DIFFRACTIONx_scangle_it3.92.5
LS refinement shellResolution: 2.6→2.7 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rwork0.348 387 -
obs--62.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.75

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