[English] 日本語
Yorodumi
- PDB-2jcp: The hyaluronan binding domain of murine CD44 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2jcp
TitleThe hyaluronan binding domain of murine CD44
ComponentsCD44 ANTIGEN
KeywordsSUGAR BINDING PROTEIN / SUGAR-BINDING PROTEIN / HYAURONAN / LINK-DOMAIN / PROTEOGLYCAN / POLYMORPHISM / BLOOD GROUP ANTIGEN / ALTERNATIVE SPLICING / LECTIN / ANTIGEN / MEMBRANE / RECEPTOR / SULFATION / GLYCOPROTEIN / C-TYPE LECTIN / CELL ADHESION / EXTRACELLULAR MATRIX / PYRROLIDONE CARBOXYLIC ACID / TRANSMEMBRANE / PHOSPHORYLATION
Function / homology
Function and homology information


Hyaluronan degradation / hyaluronic acid binding / macrophage migration inhibitory factor receptor complex / negative regulation of regulatory T cell differentiation / Degradation of the extracellular matrix / regulation of lamellipodium morphogenesis / Integrin cell surface interactions / Cell surface interactions at the vascular wall / wound healing involved in inflammatory response / hyaluronan catabolic process ...Hyaluronan degradation / hyaluronic acid binding / macrophage migration inhibitory factor receptor complex / negative regulation of regulatory T cell differentiation / Degradation of the extracellular matrix / regulation of lamellipodium morphogenesis / Integrin cell surface interactions / Cell surface interactions at the vascular wall / wound healing involved in inflammatory response / hyaluronan catabolic process / positive regulation of adaptive immune response / branching involved in prostate gland morphogenesis / type II transforming growth factor beta receptor binding / negative regulation of mature B cell apoptotic process / channel regulator activity / negative regulation of CD4-positive, alpha-beta T cell proliferation / wound healing, spreading of cells / cargo receptor activity / branching involved in ureteric bud morphogenesis / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / microvillus / negative regulation of DNA damage response, signal transduction by p53 class mediator / lamellipodium membrane / Neutrophil degranulation / receptor-mediated endocytosis / cell projection / negative regulation of inflammatory response / Wnt signaling pathway / cytokine-mediated signaling pathway / basolateral plasma membrane / positive regulation of ERK1 and ERK2 cascade / cell adhesion / apical plasma membrane / membrane raft / external side of plasma membrane / positive regulation of gene expression / cell surface / extracellular region / plasma membrane
Similarity search - Function
CD44 antigen / CD44 antigen-like / Link domain signature. / Link domain / Extracellular link domain / Link domain profile. / Link (Hyaluronan-binding) / C-type lectin-like/link domain superfamily / C-type lectin fold
Similarity search - Domain/homology
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsBanerji, S. / Wright, A.J. / Noble, M.E.M. / Mahoney, D.J. / Campbell, I.D. / Day, A.J. / Jackson, D.G.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Structures of the Cd44-Hyaluronan Complex Provide Insight Into a Fundamental Carbohydrate-Protein Interaction.
Authors: Banerji, S. / Wright, A.J. / Noble, M.E.M. / Mahoney, D.J. / Campbell, I.D. / Day, A.J. / Jackson, D.G.
History
DepositionJan 3, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.5Feb 7, 2024Group: Structure summary / Category: struct_keywords / Item: _struct_keywords.text
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CD44 ANTIGEN


Theoretical massNumber of molelcules
Total (without water)17,1431
Polymers17,1431
Non-polymers00
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)30.726, 82.097, 32.336
Angle α, β, γ (deg.)90.00, 117.92, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein CD44 ANTIGEN / PHAGOCYTIC GLYCOPROTEIN 1 / PGP-1 / HUTCH-I / EXTRACELLULAR MATRIX RECEPTOR III / GP90 LYMPHOCYTE ...PHAGOCYTIC GLYCOPROTEIN 1 / PGP-1 / HUTCH-I / EXTRACELLULAR MATRIX RECEPTOR III / GP90 LYMPHOCYTE HOMING/ADHESION RECEPTOR / HERMES ANTIGEN / HYALURONATE RECEPTOR / LYMPHOCYTE ANTIGEN LY-24 / CD44


Mass: 17143.072 Da / Num. of mol.: 1 / Fragment: HYALURONAN BINDING DOMAIN, RESIDUES 23-174
Source method: isolated from a genetically manipulated source
Details: ENCODED RESIDUES 25-174, EQUIVALENT TO RESIDUES 1-151 OF THE MATURE PROTEIN, WITH ADDITIONAL RESIDUES M, N ADDED AT THE N-TERMINUS
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET19B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 PLYSS / References: UniProt: P15379
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.12 Å3/Da / Density % sol: 42 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.5
Details: DROPLETS COMPRISING 200NL CD4425-174 (AT A CONCENTRATION OF 0.5MM) MIXED WITH 200NL WELL SOLUTION WERE DISPENSED AS SITTING DROPS AND UNDERWENT VAPOR DIFFUSION WITH A WELL SOLUTION OF 30% ...Details: DROPLETS COMPRISING 200NL CD4425-174 (AT A CONCENTRATION OF 0.5MM) MIXED WITH 200NL WELL SOLUTION WERE DISPENSED AS SITTING DROPS AND UNDERWENT VAPOR DIFFUSION WITH A WELL SOLUTION OF 30% PEG MONOMETHYLETHER 5000, AND 200 MM (NH4)2SO4 IN 100 MM MES BUFFER PH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: May 9, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.3→41.05 Å / Num. obs: 34562 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 6.4
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.2 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UUH

1uuh


Resolution: 1.3→41.17 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.397 / SU ML: 0.028 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUE H23, A MET IN THIS CONSTRUCT, IS MISSING. RESIDUE Q24, AN ASN IN THIS CONSTRUCT, IS POORLY VISIBLE AND IS BUILT AS A Q
RfactorNum. reflection% reflectionSelection details
Rfree0.191 1736 5 %RANDOM
Rwork0.157 ---
obs0.158 32795 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å2-0.1 Å2
2--0.03 Å20 Å2
3----0.038 Å2
Refinement stepCycle: LAST / Resolution: 1.3→41.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1172 0 0 178 1350
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0211284
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2621.9321762
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8185167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0224.28663
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.80215204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.975158
X-RAY DIFFRACTIONr_chiral_restr0.0810.2194
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021020
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1960.2615
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.2919
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2740.2144
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1970.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0860.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.041.5814
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.60321317
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4053517
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3054.5445
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: 1.3→1.33 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.166 137
Rwork0.145 2371

+
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