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- PDB-1e87: Human CD69 - trigonal form -

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Basic information

Entry
Database: PDB / ID: 1.0E+87
TitleHuman CD69 - trigonal form
ComponentsEARLY ACTIVATION ANTIGEN CD69
KeywordsSUGAR BINDING PROTEIN / HEMATOPOIETIC CELL RECEPTOR / LEUCOCYTE / NKD / KLR
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: 1.5 Å
AuthorsTormo, J.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Crystal Structure of the C-Type Lectin-Like Domain from the Human Hematopoietic Cell Receptor Cd69
Authors: Llera, A.S. / Viedma, F. / Sanchez-Madrid, F. / Tormo, J.
History
DepositionSep 18, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2000Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2011Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9643
Polymers13,8071
Non-polymers1582
Water1,946108
1
A: EARLY ACTIVATION ANTIGEN CD69
hetero molecules

A: EARLY ACTIVATION ANTIGEN CD69
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9286
Polymers27,6132
Non-polymers3154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2150 Å2
ΔGint-1.7 kcal/mol
Surface area13950 Å2
MethodPQS
Unit cell
Length a, b, c (Å)48.424, 48.424, 119.886
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsTHE BIOLOGICALLY FUNTIONAL MOLECULE IS A DIMER WHICH CAN BE BUILT BY APPLYING THE MATRIX GIVEN IN REMARK 350

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Components

#1: Protein EARLY ACTIVATION ANTIGEN CD69 / ACTIVATION INDUCER MOLECULE / AIM / BL-AC/P26 / C-TYPE LECTIN DOMAIN FAMILY 2 MEMBER C / EA1 / ...ACTIVATION INDUCER MOLECULE / AIM / BL-AC/P26 / C-TYPE LECTIN DOMAIN FAMILY 2 MEMBER C / EA1 / EARLY T-CELL ACTIVATION ANTIGEN P60 / GP32/28 / LEUKOCYTE SURFACE ANTIGEN LEU-23 / MLR-3 / CD69 / LEU-23


Mass: 13806.557 Da / Num. of mol.: 1 / Fragment: C-TYPE LECTIN-LIKE DOMAIN, RESIDUES 82-199
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: HEMATOPOIETIC CELL / Cellular location: CELL SURFACE / Cellular location (production host): INCLUSION BODIES / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q07108
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Compound detailsSIGNAL TRANSMITTING RECEPTOR IN LYMPHOCYTES, NATURAL KILLER (NK) CELLS, AND PLATELETS. INVOLVED IN ...SIGNAL TRANSMITTING RECEPTOR IN LYMPHOCYTES, NATURAL KILLER (NK) CELLS, AND PLATELETS. INVOLVED IN LYMPHOCYTE PROLIFERATION

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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: 2.94 Å3/Da / Density % sol: 58 %
Crystal growpH: 5.2 / Details: pH 5.20
Crystal grow
*PLUS
pH: 7.2 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
15 mg/mlprotein1drop
215 mMHEPES1drop
350 mM1dropNaCl
40.1 Msodium acetate1reservoir
5150 mMzinc sulfate1reservoiror sodium sulfate
615 %PEG60001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. obs: 26542 / % possible obs: 98.6 % / Redundancy: 5.7 % / Biso Wilson estimate: 19.5 Å2 / Rsym value: 0.062 / Net I/σ(I): 33.5
Reflection shellResolution: 1.5→1.53 Å / Mean I/σ(I) obs: 15.6 / Rsym value: 0.106 / % possible all: 100
Reflection
*PLUS
Num. measured all: 151066 / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.106

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E8I

1e8i


Resolution: 1.5→19.79 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1961 7.4 %RANDOM
Rwork0.229 ---
obs0.229 26522 98.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.6827 Å2 / ksol: 0.386021 e/Å3
Displacement parametersBiso mean: 20.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20.36 Å20 Å2
2--0.29 Å20 Å2
3----0.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.5→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms963 0 7 108 1078
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it2.12
X-RAY DIFFRACTIONc_scbond_it2.172
X-RAY DIFFRACTIONc_scangle_it3.332.5
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.281 335 7.7 %
Rwork0.235 4015 -
obs--99.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4GOL.PARGOL.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Num. reflection obs: 24561 / % reflection Rfree: 7.3 % / Rfactor Rfree: 0.244
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.57
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.94

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