[English] 日本語
Yorodumi
- PDB-1uuh: Hyaluronan binding domain of human CD44 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1uuh
TitleHyaluronan binding domain of human CD44
ComponentsCD44 ANTIGEN
KeywordsLECTIN / HYALURONAN / EXTRACELLULAR MATRIX / RECEPTOR / LINK-DOMAIN / C- TYPE LECTIN / SUGAR-BINDING
Function / homology
Function and homology information


positive regulation of monocyte aggregation / Hyaluronan degradation / monocyte aggregation / hyaluronic acid binding / macrophage migration inhibitory factor receptor complex / regulation of lamellipodium morphogenesis / hyaluronan catabolic process / positive regulation of heterotypic cell-cell adhesion / wound healing, spreading of cells / cartilage development ...positive regulation of monocyte aggregation / Hyaluronan degradation / monocyte aggregation / hyaluronic acid binding / macrophage migration inhibitory factor receptor complex / regulation of lamellipodium morphogenesis / hyaluronan catabolic process / positive regulation of heterotypic cell-cell adhesion / wound healing, spreading of cells / cartilage development / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / negative regulation of DNA damage response, signal transduction by p53 class mediator / microvillus / lamellipodium membrane / cellular response to fibroblast growth factor stimulus / Integrin cell surface interactions / collagen binding / Degradation of the extracellular matrix / T cell activation / secretory granule membrane / cell-matrix adhesion / cell projection / Cell surface interactions at the vascular wall / cytokine-mediated signaling pathway / cell-cell adhesion / Interferon gamma signaling / transmembrane signaling receptor activity / cell migration / basolateral plasma membrane / positive regulation of ERK1 and ERK2 cascade / cell adhesion / apical plasma membrane / inflammatory response / focal adhesion / Neutrophil degranulation / negative regulation of apoptotic process / cell surface / Golgi apparatus / extracellular exosome / plasma membrane / cytosol
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 speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.2 Å
AuthorsTeriete, P. / Banerji, S. / Noble, M. / Blundell, C. / Wright, A. / Pickford, A. / Lowe, E. / Mahoney, D. / Tammi, M. / Kahmann, J. ...Teriete, P. / Banerji, S. / Noble, M. / Blundell, C. / Wright, A. / Pickford, A. / Lowe, E. / Mahoney, D. / Tammi, M. / Kahmann, J. / Campbell, I. / Day, A. / Jackson, D.
CitationJournal: Mol.Cell / Year: 2004
Title: Structure of the Regulatory Hyaluronan-Binding Domain in the Inflammatory Leukocyte Homing Receptor Cd44
Authors: Teriete, P. / Banerji, S. / Noble, M. / Blundell, C. / Wright, A. / Pickford, A. / Lowe, E. / Mahoney, D. / Tammi, M. / Kahmann, J. / Campbell, I. / Day, A. / Jackson, D.
History
DepositionDec 19, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 29, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
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 / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CD44 ANTIGEN
B: CD44 ANTIGEN


Theoretical massNumber of molelcules
Total (without water)35,3912
Polymers35,3912
Non-polymers00
Water4,720262
1
A: CD44 ANTIGEN


Theoretical massNumber of molelcules
Total (without water)17,6951
Polymers17,6951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CD44 ANTIGEN


Theoretical massNumber of molelcules
Total (without water)17,6951
Polymers17,6951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)48.881, 77.266, 87.668
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.74746, -0.61772, -0.24439), (0.43944, -0.73566, 0.51545), (0.4982, -0.27789, -0.82133)
Vector: -13.39, -13.608, -23.469)

-
Components

#1: Protein CD44 ANTIGEN / PHAGOCYTIC GLYCOPROTEIN I / PGP-1 / HUTCH-I / EXTRACELLULAR MATRIX RECEPTOR-III / ECMR-III / GP90 ...PHAGOCYTIC GLYCOPROTEIN I / PGP-1 / HUTCH-I / EXTRACELLULAR MATRIX RECEPTOR-III / ECMR-III / GP90 LYMPHOCYTE HOMING/ADHESION RECEPTOR / HERMES ANTIGEN / HYALURONATE RECEPTOR / HEPARAN SULFATE PROTEOGLYCAN / EPICAN / CDW44


Mass: 17695.275 Da / Num. of mol.: 2 / Fragment: HYALURONAN BINDING DOMAIN, RESIDUES 20-178
Source method: isolated from a genetically manipulated source
Details: FIRST RESIDUE IS IN FACT THE LAST RESIDUE OF THE SIGNAL PEPTIDE, AND WOULD NORMALLY BE CLEAVED
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET19B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 PLYSS / References: UniProt: P16070
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsHYALURONAN BINDING DOMAIN ONLY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 40 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.5
Details: HANGING-DROP PROTEIN 13 MG/ML; WELL BUFFER 12% PEG 3350, 50MM NACL, 10% GLYCEROL, pH 5.50
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 %PEG33501reservoir
250 mM1reservoirNaCl
310 %glycerol1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: May 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→23.31 Å / Num. obs: 17476 / % possible obs: 99.8 % / Redundancy: 3.82 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 7.2989
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.53 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 3.16 / % possible all: 99.6
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 23.31 Å / % possible obs: 99.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
% possible obs: 98.2 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.181 / Mean I/σ(I) obs: 3.1

-
Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
SOLVE/RESOLVEphasing
RefinementMethod to determine structure: OTHER / Resolution: 2.2→57.73 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.878 / SU B: 5.483 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.261 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.249 881 5.13 %RANDOM
Rwork0.186 ---
obs-16553 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 17.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20 Å2
2--0.47 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.2→57.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2334 0 0 262 2596
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0212390
X-RAY DIFFRACTIONr_bond_other_d0.0020.022068
X-RAY DIFFRACTIONr_angle_refined_deg1.9561.9373258
X-RAY DIFFRACTIONr_angle_other_deg1.00434818
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4155298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1380.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022700
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02492
X-RAY DIFFRACTIONr_nbd_refined0.240.2462
X-RAY DIFFRACTIONr_nbd_other0.2630.22531
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0980.21416
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.2120
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2730.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9821.51496
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.76922436
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8543894
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4854.5822
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: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.239 52
Rwork0.19 1200
Refinement
*PLUS
Lowest resolution: 23.31 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.011
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.309
LS refinement shell
*PLUS
Lowest resolution: 2.28 Å / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.19

+
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