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- PDB-3wsr: Crystal structure of CLEC-2 in complex with O-glycosylated podoplanin -

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Basic information

Entry
Database: PDB / ID: 3wsr
TitleCrystal structure of CLEC-2 in complex with O-glycosylated podoplanin
Components
  • C-type lectin domain family 1 member B
  • Peptide from Podoplanin
KeywordsSUGAR BINDING PROTEIN / C-type lectin fold / Cell surface receptor / Podoplanin / O-glycosylated / Extracellular region
Function / homology
Function and homology information


lymphatic endothelial cell fate commitment / regulation of myofibroblast contraction / actin-mediated cell contraction / leading edge of lamellipodium / lymphangiogenesis / regulation of substrate adhesion-dependent cell spreading / positive regulation of extracellular matrix disassembly / chemokine binding / Specification of primordial germ cells / regulation of lamellipodium morphogenesis ...lymphatic endothelial cell fate commitment / regulation of myofibroblast contraction / actin-mediated cell contraction / leading edge of lamellipodium / lymphangiogenesis / regulation of substrate adhesion-dependent cell spreading / positive regulation of extracellular matrix disassembly / chemokine binding / Specification of primordial germ cells / regulation of lamellipodium morphogenesis / tetraspanin-enriched microdomain / positive regulation of platelet aggregation / filopodium membrane / anchoring junction / wound healing, spreading of cells / platelet formation / microvillus membrane / lamellipodium membrane / Rho protein signal transduction / response to hyperoxia / positive regulation of epithelial to mesenchymal transition / lymph node development / ruffle / GPVI-mediated activation cascade / filopodium / cell projection / lung development / Heme signaling / defense response / cell-cell adhesion / ruffle membrane / platelet activation / cell migration / transmembrane signaling receptor activity / lamellipodium / cell junction / regulation of cell shape / protein-folding chaperone binding / cytoplasmic vesicle / carbohydrate binding / basolateral plasma membrane / cell surface receptor signaling pathway / positive regulation of cell migration / membrane raft / apical plasma membrane / negative regulation of cell population proliferation / signaling receptor binding / negative regulation of apoptotic process / cell surface / signal transduction / mitochondrion / membrane / plasma membrane / cytosol
Similarity search - Function
Podoplanin / 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 ...Podoplanin / 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
Podoplanin / C-type lectin domain family 1 member B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 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
DepositionMar 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: C-type lectin domain family 1 member B
B: C-type lectin domain family 1 member B
C: Peptide from Podoplanin
D: Peptide from Podoplanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0716
Polymers33,7224
Non-polymers1,3492
Water64936
1
A: C-type lectin domain family 1 member B
C: Peptide from Podoplanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5363
Polymers16,8612
Non-polymers6751
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint11 kcal/mol
Surface area7550 Å2
MethodPISA
2
B: C-type lectin domain family 1 member B
D: Peptide from Podoplanin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5363
Polymers16,8612
Non-polymers6751
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint10 kcal/mol
Surface area7440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.369, 51.194, 54.099
Angle α, β, γ (deg.)90.00, 112.77, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 15157.050 Da / Num. of mol.: 2 / Fragment: CLEC-2, UNP residues 96-221 / Mutation: C99S
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): Rosetta 2 / References: UniProt: Q9P126
#2: Protein/peptide Peptide from Podoplanin /


Mass: 1703.846 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q86YL7
#3: Polysaccharide beta-D-galactopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)]2-acetamido-2-deoxy-alpha-D-galactopyranose


Type: oligosaccharide / Mass: 674.604 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3[DNeup5Aca2-6]DGalpNAca1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2112h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a3-b1_a6-c2WURCSPDB2Glycan 1.1.0
[]{[(3+1)][a-D-GalpNAc]{[(3+1)][b-D-Galp]{}[(6+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.06 Å3/Da / Density % sol: 40.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris-HCl (pH 8.5), 25% (w/v) polyethylene glycol (PEG) 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 4, 2014 / Details: Monochrometer
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→100 Å / Num. obs: 21375 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rsym value: 0.072 / Net I/σ(I): 24.3
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 1048 / Rsym value: 0.495 / % possible all: 100

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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: PDB code 2C6U

2c6u


Resolution: 1.91→50.13 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.908 / SU B: 4.343 / SU ML: 0.127 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25877 1022 4.8 %RANDOM
Rwork0.21737 ---
obs0.21936 20339 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å20 Å20.09 Å2
2---0.14 Å2-0 Å2
3---0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.91→50.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2166 0 90 36 2292
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192327
X-RAY DIFFRACTIONr_bond_other_d0.0010.022043
X-RAY DIFFRACTIONr_angle_refined_deg1.3681.9513141
X-RAY DIFFRACTIONr_angle_other_deg0.82534701
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0485257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.98924.032124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.71215380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8641514
X-RAY DIFFRACTIONr_chiral_restr0.0880.2322
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022577
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02583
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_it1.9052.6721040
X-RAY DIFFRACTIONr_mcbond_other1.9052.6721039
X-RAY DIFFRACTIONr_mcangle_it3.0993.9891293
X-RAY DIFFRACTIONr_mcangle_other3.0983.9891294
X-RAY DIFFRACTIONr_scbond_it2.0542.8721287
X-RAY DIFFRACTIONr_scbond_other2.0542.8721287
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3864.2021849
X-RAY DIFFRACTIONr_long_range_B_refined5.09221.2012598
X-RAY DIFFRACTIONr_long_range_B_other5.09521.2062593
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.909→1.958 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 56 -
Rwork0.257 1405 -
obs--91.71 %

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