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- PDB-1fm5: CRYSTAL STRUCTURE OF HUMAN CD69 -

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Basic information

Entry
Database: PDB / ID: 1fm5
TitleCRYSTAL STRUCTURE OF HUMAN CD69
ComponentsEARLY ACTIVATION ANTIGEN CD69
KeywordsIMMUNE SYSTEM / C-type Lectin-Like Domain / Natural Killer cell receptor / lectin / C-type Lectin
Function / homology
Function and homology information


transmembrane signaling receptor activity / cellular response to xenobiotic stimulus / carbohydrate binding / external side of plasma membrane / protein-containing complex / identical protein binding / 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
Early activation antigen CD69
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.27 Å
AuthorsNatarajan, K. / Sawicki, M.W. / Margulies, D.H. / Mariuzza, R.A.
CitationJournal: Biochemistry / Year: 2000
Title: Crystal structure of human CD69: a C-type lectin-like activation marker of hematopoietic cells.
Authors: Natarajan, K. / Sawicki, M.W. / Margulies, D.H. / Mariuzza, R.A.
History
DepositionAug 16, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 21, 2016Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EARLY ACTIVATION ANTIGEN CD69


Theoretical massNumber of molelcules
Total (without water)16,0981
Polymers16,0981
Non-polymers00
Water2,306128
1
A: EARLY ACTIVATION ANTIGEN CD69

A: EARLY ACTIVATION ANTIGEN CD69


Theoretical massNumber of molelcules
Total (without water)32,1962
Polymers32,1962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_665-x+1,-x+y+1,-z+1/31
Unit cell
Length a, b, c (Å)48.2, 48.2, 117.9
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121
DetailsThe biological assembly is a disulfide linked homodimer

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Components

#1: Protein EARLY ACTIVATION ANTIGEN CD69 / EARLY T-CELL ACTIVATION ANTIGEN P6 / GP32/28 / LEU-23 / MLR-3 / EA1 / BL-AC/P26 / ACTIVATION ...EARLY T-CELL ACTIVATION ANTIGEN P6 / GP32/28 / LEU-23 / MLR-3 / EA1 / BL-AC/P26 / ACTIVATION INDUCER MOLECULE / AIM


Mass: 16098.035 Da / Num. of mol.: 1 / Fragment: C-TYPE LECTIN-LIKE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET21A / Production host: Escherichia coli (E. coli) / References: UniProt: Q07108
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.46 Å3/Da / Density % sol: 49.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Sodium Acetate, pH 4.5, 0.2M Zinc Acetate, 20% PEG 1000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Temperature: 4 ℃
Details: drop was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17 mg/mlprotein1drop
210 mMHEPES1drop
3100 mM1dropNaCl
40.1 Msodium acetate1reservoir
50.2 Mzinc acetate1reservoir
620 %PEG10001reservoir

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.08
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Mar 18, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / % possible obs: 96.3 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.062 / Net I/σ(I): 17.3
Reflection shellResolution: 2.27→2.35 Å / Rmerge(I) obs: 0.306 / % possible all: 86.5
Reflection
*PLUS
Num. obs: 13674 / Num. measured all: 36807
Reflection shell
*PLUS
% possible obs: 86.5 % / Mean I/σ(I) obs: 2.3

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementResolution: 2.27→15 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.299 354 5.4 %Random
Rwork0.243 ---
all-7836 --
obs-6598 --
Refinement stepCycle: LAST / Resolution: 2.27→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms962 0 0 128 1090
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.38
X-RAY DIFFRACTIONc_bond_d0.0069
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d0.76
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76
LS refinement shell
*PLUS
Highest resolution: 2.27 Å / Lowest resolution: 2.35 Å / Rfactor Rfree: 0.309 / Rfactor Rwork: 0.288

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