[English] 日本語
Yorodumi
- PDB-3wsr: Crystal structure of CLEC-2 in complex with O-glycosylated podoplanin -

+
Open data


ID or keywords:

Loading...

-
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


regulation of myofibroblast contraction / lymphatic endothelial cell fate commitment / actin-mediated cell contraction / leading edge of lamellipodium / regulation of substrate adhesion-dependent cell spreading / chemokine binding / Specification of primordial germ cells / positive regulation of extracellular matrix disassembly / lymphangiogenesis / regulation of lamellipodium morphogenesis ...regulation of myofibroblast contraction / lymphatic endothelial cell fate commitment / actin-mediated cell contraction / leading edge of lamellipodium / regulation of substrate adhesion-dependent cell spreading / chemokine binding / Specification of primordial germ cells / positive regulation of extracellular matrix disassembly / lymphangiogenesis / regulation of lamellipodium morphogenesis / tetraspanin-enriched microdomain / positive regulation of platelet aggregation / filopodium membrane / wound healing, spreading of cells / platelet formation / anchoring junction / microvillus membrane / lamellipodium membrane / lymph node development / positive regulation of epithelial to mesenchymal transition / GPVI-mediated activation cascade / Rho protein signal transduction / ruffle / lung development / cell projection / filopodium / Heme signaling / defense response / platelet activation / ruffle membrane / cell junction / transmembrane signaling receptor activity / cell migration / regulation of cell shape / lamellipodium / protein-folding chaperone binding / carbohydrate binding / cytoplasmic vesicle / basolateral plasma membrane / cell surface receptor signaling pathway / cell adhesion / positive regulation of cell migration / apical plasma membrane / membrane raft / signaling receptor binding / negative regulation of cell population proliferation / 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) ...: / : / 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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more