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- PDB-3cck: Human CD69 -

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Basic information

Entry
Database: PDB / ID: 3cck
TitleHuman CD69
ComponentsEarly activation antigen CD69
KeywordsIMMUNE SYSTEM / leukocyte activation / C-type lectin / refolding / stability / ligand binding / tumor therapies / Glycoprotein / Membrane / Phosphoprotein / Signal-anchor / Transmembrane
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBrynda, J. / Vanek, O. / Rezacova, P.
CitationJournal: Febs J. / Year: 2008
Title: Soluble recombinant CD69 receptors optimized to have an exceptional physical and chemical stability display prolonged circulation and remain intact in the blood of mice
Authors: Vanek, O. / Nalezkova, M. / Kavan, D. / Borovickova, I. / Pompach, P. / Novak, P. / Kumar, V. / Vannucci, L. / Hudecek, J. / Hofbauerova, K. / Kopecky, V. / Brynda, J. / Kolenko, P. / ...Authors: Vanek, O. / Nalezkova, M. / Kavan, D. / Borovickova, I. / Pompach, P. / Novak, P. / Kumar, V. / Vannucci, L. / Hudecek, J. / Hofbauerova, K. / Kopecky, V. / Brynda, J. / Kolenko, P. / Dohnalek, J. / Kaderavek, P. / Chmelik, J. / Gorcik, L. / Zidek, L. / Sklenar, V. / Bezouska, K.
History
DepositionFeb 26, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Early activation antigen CD69
B: Early activation antigen CD69
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7195
Polymers27,6132
Non-polymers1063
Water1,802100
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.693, 85.693, 61.881
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 6 / Auth seq-ID: 83 - 197 / Label seq-ID: 2 - 116

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Early activation antigen CD69 / Early T-cell activation antigen p60 / GP32/28 / Leu-23 / MLR-3 / EA1 / BL-AC/P26 / Activation ...Early T-cell activation antigen p60 / GP32/28 / Leu-23 / MLR-3 / EA1 / BL-AC/P26 / Activation inducer molecule / AIM


Mass: 13806.557 Da / Num. of mol.: 2 / Fragment: UNP residues 82-199
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD69 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: Q07108
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.38 Å3/Da / Density % sol: 48.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG 3400, 0.1M Arginine.HCl, 10mM CaCl2, 1mM NaN3, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 23, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.8→74.54 Å / Num. all: 22724 / Num. obs: 22276 / % possible obs: 98.03 % / Redundancy: 7.1 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.045 / Net I/σ(I): 29.5
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.575 / Mean I/σ(I) obs: 2.6 / Num. unique all: 929 / Rsym value: 0.575 / % possible all: 76.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E8i

1e8i


Resolution: 1.8→28.05 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.26 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22285 1208 5.1 %RANDOM
Rwork0.19069 ---
obs0.19239 22276 98.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.009 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20.11 Å20 Å2
2--0.22 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1921 0 3 100 2024
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212009
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.92719
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8785235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.13824.3100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80315341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.939158
X-RAY DIFFRACTIONr_chiral_restr0.1190.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021550
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.2892
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21364
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.289
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2460.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9871.51203
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.58921886
X-RAY DIFFRACTIONr_scbond_it2.5833978
X-RAY DIFFRACTIONr_scangle_it4.0534.5833
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 909 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.485
loose thermal1.3510
LS refinement shellResolution: 1.803→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 73 -
Rwork0.234 1396 -
obs--82.85 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.18360.1991-1.48431.72040.71322.7669-0.1187-0.0721-0.15780.1996-0.07330.09070.2217-0.00830.192-0.05080.00270.0363-0.06060.0233-0.05166.48830.5886.41
21.21290.29090.55632.57-0.41993.0988-0.06690.11320.02760.1439-0.04010.0318-0.26640.06820.1071-0.05260.0002-0.0079-0.060.0175-0.060619.97552.039-3.551
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA83 - 1992 - 118
2X-RAY DIFFRACTION2BB82 - 1991 - 118

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