[English] 日本語
Yorodumi
- PDB-2wuh: Crystal structure of the DDR2 discoidin domain bound to a triple-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2wuh
TitleCrystal structure of the DDR2 discoidin domain bound to a triple- helical collagen peptide
Components
  • COLLAGEN PEPTIDE
  • DISCOIDIN DOMAIN RECEPTOR 2
KeywordsRECEPTOR/PEPTIDE / RECEPTOR-PEPTIDE COMPLEX / TRANSFERASE / NUCLEOTIDE-BINDING / TYROSINE-PROTEIN KINASE
Function / homology
Function and homology information


positive regulation of hepatic stellate cell proliferation / protein tyrosine kinase collagen receptor activity / biomineral tissue development / chondrocyte proliferation / positive regulation of hepatic stellate cell activation / endochondral bone growth / regulation of extracellular matrix disassembly / positive regulation of extracellular matrix disassembly / negative regulation of hydrogen peroxide-mediated programmed cell death / collagen-activated tyrosine kinase receptor signaling pathway ...positive regulation of hepatic stellate cell proliferation / protein tyrosine kinase collagen receptor activity / biomineral tissue development / chondrocyte proliferation / positive regulation of hepatic stellate cell activation / endochondral bone growth / regulation of extracellular matrix disassembly / positive regulation of extracellular matrix disassembly / negative regulation of hydrogen peroxide-mediated programmed cell death / collagen-activated tyrosine kinase receptor signaling pathway / regulation of bone mineralization / positive regulation of vascular associated smooth muscle cell migration / collagen fibril organization / regulation of tissue remodeling / positive regulation of fibroblast migration / positive regulation of wound healing / positive regulation of protein kinase activity / positive regulation of collagen biosynthetic process / cellular response to angiotensin / Non-integrin membrane-ECM interactions / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of osteoblast differentiation / cellular response to transforming growth factor beta stimulus / positive regulation of DNA-binding transcription factor activity / positive regulation of vascular associated smooth muscle cell proliferation / collagen binding / response to muscle stretch / transmembrane receptor protein tyrosine kinase activity / ossification / cell surface receptor protein tyrosine kinase signaling pathway / peptidyl-tyrosine phosphorylation / receptor protein-tyrosine kinase / positive regulation of neuron projection development / positive regulation of fibroblast proliferation / actin cytoskeleton / protein autophosphorylation / cellular response to hypoxia / positive regulation of ERK1 and ERK2 cascade / receptor complex / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / apical plasma membrane / focal adhesion / negative regulation of apoptotic process / signal transduction / ATP binding / plasma membrane
Similarity search - Function
: / Discoidin domain-containing receptor 1/2, DS-like domain / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. ...: / Discoidin domain-containing receptor 1/2, DS-like domain / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / Galactose-binding domain-like / : / Galactose-binding-like domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Jelly Rolls / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Discoidin domain-containing receptor 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsCarafoli, F. / Bihan, D. / Stathopoulos, S. / Konitsiotis, A.D. / Kvansakul, M. / Farndale, R.W. / Leitinger, B. / Hohenester, E.
Citation
Journal: Structure / Year: 2009
Title: Crystallographic Insight Into Collagen Recognition by Discoidin Domain Receptor 2
Authors: Carafoli, F. / Bihan, D. / Stathopoulos, S. / Konitsiotis, A.D. / Kvansakul, M. / Farndale, R.W. / Leitinger, B. / Hohenester, E.
#1: Journal: Embo J. / Year: 2007
Title: Structural Basis of the Collagen-Binding Mode of Discoidin Domain Receptor 2.
Authors: Ichikawa, O. / Osawa, M. / Nishida, N. / Goshima, N. / Nomura, N. / Shimada, I.
#2: Journal: J.Biol.Chem. / Year: 2008
Title: Characterization of High Affinity Binding Motifs for the Discoidin Domain Receptor Ddr2 in Collagen.
Authors: Konitsiotis, A.D. / Raynal, N. / Bihan, D. / Hohenester, E. / Farndale, R.W. / Leitinger, B.
History
DepositionOct 5, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 29, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 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 / struct_conn
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 / _struct_conn.pdbx_leaving_atom_flag
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.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DISCOIDIN DOMAIN RECEPTOR 2
B: COLLAGEN PEPTIDE
C: COLLAGEN PEPTIDE
D: COLLAGEN PEPTIDE


Theoretical massNumber of molelcules
Total (without water)28,0104
Polymers28,0104
Non-polymers00
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-32.36 kcal/mol
Surface area11810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.397, 40.863, 48.917
Angle α, β, γ (deg.)66.19, 88.90, 76.92
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein DISCOIDIN DOMAIN RECEPTOR 2


Mass: 20108.637 Da / Num. of mol.: 1 / Fragment: DISCOIDIN DOMAIN, RESIDUES 26-190
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): 293-EBNA / Production host: HOMO SAPIENS (human) / References: UniProt: Q16832
#2: Protein/peptide COLLAGEN PEPTIDE


Mass: 2633.847 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: ACETYLATED N-TERMINUS / Source: (synth.) HOMO SAPIENS (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsACETYL GROUP (ACE): ACETYLATED N-TERMINUS OF COLLAGEN PEPTIDE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 40.85 % / Description: NONE
Crystal growpH: 7 / Details: pH 7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98
DetectorDetector: CCD / Date: Dec 16, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 27359 / % possible obs: 90.2 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.8
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.3 / % possible all: 67.4

-
Processing

Software
NameVersionClassification
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2QQJ AND 2V53

2qqj

2v53


Resolution: 1.6→20 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2298 2726 9 %RANDOM
Rwork0.2019 ---
obs0.2019 27359 90.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.2491 Å2 / ksol: 0.45 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.382 Å26.95 Å2-2.351 Å2
2--0.993 Å2-4.021 Å2
3----2.375 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1845 0 0 176 2021
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
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_it2.022
X-RAY DIFFRACTIONc_scbond_it1.962
X-RAY DIFFRACTIONc_scangle_it2.492.5
LS refinement shellResolution: 1.6→1.61 Å / Total num. of bins used: 50 /
RfactorNum. reflection
Rfree0.374 37
Rwork0.281 293
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP-HYP.PARAMA
X-RAY DIFFRACTION2WATER_REP.PARAMA

+
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