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- PDB-2c6u: Crystal structure of human CLEC-2 (CLEC1B) -

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Basic information

Entry
Database: PDB / ID: 2c6u
TitleCrystal structure of human CLEC-2 (CLEC1B)
ComponentsCLEC1B PROTEIN
KeywordsLECTIN / CLEC-2 / RHODOCYTIN / AGGRETIN / C-TYPE LECTIN-LIKE / PLATELETS / THROMBOSIS / CLEC1B
Function / homology
Function and homology information


platelet formation / GPVI-mediated activation cascade / Heme signaling / defense response / transmembrane signaling receptor activity / carbohydrate binding / cell surface receptor signaling pathway / cell surface / signal transduction / 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
C-type lectin domain family 1 member B
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWatson, A.A. / Brown, J. / O'Callaghan, C.A.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: The Crystal Structure and Mutational Binding Analysis of the Extracellular Domain of the Platelet-Activating Receptor Clec-2.
Authors: Watson, A.A. / Brown, J. / Harlos, K. / Eble, J.A. / Walter, T.S. / O'Callaghan, C.A.
History
DepositionNov 11, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CLEC1B PROTEIN


Theoretical massNumber of molelcules
Total (without water)14,6011
Polymers14,6011
Non-polymers00
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)35.064, 55.065, 56.165
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CLEC1B PROTEIN / CLEC-2 / C-TYPE LECTIN-LIKE RECEPTOR-2


Mass: 14601.466 Da / Num. of mol.: 1 / Fragment: C-TYPE LECTIN-LIKE DOMAIN, RESIDUES 100-221
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: PERIPHERAL BLOOD MONONUCLEAR CELLS / Plasmid: PGMT7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q9P126
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 246 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsMODELLED AS GLY, PROVEN BY DNA SEQUENCING AND MASS SPECTROSCOPY TO BE SER UNIPROT REFERENCE Q8NHR6_ ...MODELLED AS GLY, PROVEN BY DNA SEQUENCING AND MASS SPECTROSCOPY TO BE SER UNIPROT REFERENCE Q8NHR6_HUMAN REPRESENTS A SPLICE VARIANT OF THE FULL LENGTH CLEC-2 PROTEIN IN WHICH THE TRANSMEMBRANE DOMAIN IS ABSENT. A SINGLE NUCLEOTIDE POLYMORPHISM RS612593 IS PRESENT AT RESIDUE 115

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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: 1.81 Å3/Da / Density % sol: 31.99 %
Description: A COMPOSITE MODEL WAS CONSTRUCTED USING THE CASPR WEBSERVER FROM THE FOLLOWING PDB ENTRIES 1MPU, 1K9I, 1P4L, 1QO3, 1XPH AND 1YPQ.
Crystal growpH: 6.5
Details: 20% W/V POLYETHYLENE GLYCOL MONOMETHYL ETHER 5000 0.1M BIS-TRIS PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 28, 2005 / Details: MIRRORS
RadiationMonochromator: ASYMMETRIC CUT SI (111) CRYTALS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.44→50 Å / Num. obs: 20396 / % possible obs: 88 % / Observed criterion σ(I): -3 / Redundancy: 11.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 49.02
Reflection shellResolution: 1.44→1.49 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 10.13 / % possible all: 24.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
CaspRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: COMPOSITE MODEL - SEE REMARKS

Resolution: 1.6→39.31 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.593 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.198 762 5.1 %RANDOM
Rwork0.159 ---
obs0.161 14114 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.02 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20 Å2
2---0.43 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.6→39.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1021 0 0 246 1267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0211119
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1871.9091516
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1635131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.26424.26568
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.22215202
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.92158
X-RAY DIFFRACTIONr_chiral_restr0.0890.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02890
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.2537
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.2763
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2171
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.258
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7791.5647
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.19121020
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1683555
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1314.5495
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.298 45
Rwork0.203 999

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