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- PDB-3wwk: Crystal structure of CLEC-2 in complex with rhodocytin -

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Basic information

Entry
Database: PDB / ID: 3wwk
TitleCrystal structure of CLEC-2 in complex with rhodocytin
Components
  • C-type lectin domain family 1 member B
  • Snaclec rhodocytin subunit alpha
  • Snaclec rhodocytin subunit beta
KeywordsSUGAR BINDING PROTEIN / C-type lectin fold / Carbohydrate binding / Podoplanin / Rhodocytin
Function / homology
Function and homology information


regulation of cytokine activity / platelet formation / GPVI-mediated activation cascade / Heme signaling / defense response / transmembrane signaling receptor activity / signaling receptor activity / toxin activity / carbohydrate binding / cell surface receptor signaling pathway ...regulation of cytokine activity / platelet formation / GPVI-mediated activation cascade / Heme signaling / defense response / transmembrane signaling receptor activity / signaling receptor activity / toxin activity / carbohydrate binding / cell surface receptor signaling pathway / cell surface / signal transduction / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
Natural killer cell receptor-like, C-type lectin-like domain / C-type lectin, conserved site / C-type lectin domain signature. / 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 ...Natural killer cell receptor-like, C-type lectin-like domain / C-type lectin, conserved site / C-type lectin domain signature. / 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
Snaclec rhodocytin subunit beta / Snaclec rhodocytin subunit alpha / C-type lectin domain family 1 member B
Similarity search - Component
Biological speciesHomo sapiens (human)
Calloselasma rhodostoma (Malayan pit viper)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsNagae, M. / Morita-Matsumoto, K. / Kato, M. / Kato-Kaneko, M. / Kato, Y. / Yamaguchi, Y.
CitationJournal: Structure / Year: 2014
Title: A Platform of C-type Lectin-like Receptor CLEC-2 for Binding O-Glycosylated Podoplanin and Nonglycosylated Rhodocytin
Authors: Nagae, M. / Morita-Matsumoto, K. / Kato, M. / Kato-Kaneko, M. / Kato, Y. / Yamaguchi, Y.
History
DepositionJun 20, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 8, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: C-type lectin domain family 1 member B
A: Snaclec rhodocytin subunit alpha
B: Snaclec rhodocytin subunit beta
D: Snaclec rhodocytin subunit alpha
E: Snaclec rhodocytin subunit beta
I: C-type lectin domain family 1 member B
G: Snaclec rhodocytin subunit alpha
H: Snaclec rhodocytin subunit beta
J: Snaclec rhodocytin subunit alpha
K: Snaclec rhodocytin subunit beta
L: C-type lectin domain family 1 member B
F: C-type lectin domain family 1 member B


Theoretical massNumber of molelcules
Total (without water)191,03812
Polymers191,03812
Non-polymers00
Water00
1
C: C-type lectin domain family 1 member B
A: Snaclec rhodocytin subunit alpha
B: Snaclec rhodocytin subunit beta


Theoretical massNumber of molelcules
Total (without water)47,7603
Polymers47,7603
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Snaclec rhodocytin subunit alpha
E: Snaclec rhodocytin subunit beta
F: C-type lectin domain family 1 member B


Theoretical massNumber of molelcules
Total (without water)47,7603
Polymers47,7603
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
I: C-type lectin domain family 1 member B
G: Snaclec rhodocytin subunit alpha
H: Snaclec rhodocytin subunit beta


Theoretical massNumber of molelcules
Total (without water)47,7603
Polymers47,7603
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: Snaclec rhodocytin subunit alpha
K: Snaclec rhodocytin subunit beta
L: C-type lectin domain family 1 member B


Theoretical massNumber of molelcules
Total (without water)47,7603
Polymers47,7603
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.851, 117.072, 152.238
Angle α, β, γ (deg.)90.00, 115.78, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
C-type lectin domain family 1 member B / CLEC-2 lectin / C-type lectin-like receptor 2 / CLEC-2


Mass: 15157.050 Da / Num. of mol.: 4 / Fragment: CLEC-2, UNP residues 96-221 / Mutation: C96S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLEC1B, CLEC2, UNQ721/PRO1384 / Plasmid: pCold / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: Q9P126
#2: Protein
Snaclec rhodocytin subunit alpha / Rhodocytin alpha subunit / Aggretin alpha chain / Rhodoaggretin subunit alpha


Mass: 15812.376 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Calloselasma rhodostoma (Malayan pit viper)
References: UniProt: Q9I841
#3: Protein
Snaclec rhodocytin subunit beta / Rhodocytin beta subunit / Aggretin beta chain / Rhodoaggretin subunit beta


Mass: 16790.094 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Calloselasma rhodostoma (Malayan pit viper)
References: UniProt: Q9I840

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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: 2.75 Å3/Da / Density % sol: 55.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 0.1M Hepes (pH 7.6), 0.2M L-proline, 10% (w/v) PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 4, 2014
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.649
11-H, -K, H+L20.351
ReflectionResolution: 2.98→100 Å / Num. all: 41633 / Num. obs: 41508 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 44.3 Å2 / Rsym value: 0.099 / Net I/σ(I): 16.9
Reflection shellResolution: 2.983→3.05 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 2103 / Rsym value: 0.458 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SERGUIdata collection
MOLREPphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C6U and 2VRP

2c6u

2vrp


Resolution: 2.98→37.56 Å / Cor.coef. Fo:Fc: 0.853 / Cor.coef. Fo:Fc free: 0.79 / SU B: 32.825 / SU ML: 0.593 / Cross valid method: THROUGHOUT / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.32492 2089 5 %RANDOM
Rwork0.28192 ---
obs0.28407 39290 98.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.923 Å2
Baniso -1Baniso -2Baniso -3
1-19.22 Å20 Å2-0.7 Å2
2--21.86 Å20 Å2
3----41.08 Å2
Refinement stepCycle: LAST / Resolution: 2.98→37.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12453 0 0 0 12453
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01912864
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.90217405
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.52751489
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.36124.375704
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.214152140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.8191560
X-RAY DIFFRACTIONr_chiral_restr0.1290.21673
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0210076
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4176.0696007
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.7859.1017479
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.2146.16857
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined3.00460.25257143
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: 2.983→3.06 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.443 120 -
Rwork0.404 2246 -
obs--76.74 %

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