[English] 日本語
Yorodumi
- PDB-5bzc: Crystal structure of the murine CD44 hyaluronan binding domain co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5bzc
TitleCrystal structure of the murine CD44 hyaluronan binding domain complex with a small molecule
ComponentsCD44 antigen
KeywordsPROTEIN BINDING / Link module
Function / homology
Function and homology information


Hyaluronan uptake and 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 / positive regulation of adaptive immune response / wound healing involved in inflammatory response ...Hyaluronan uptake and 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 / positive regulation of adaptive immune response / wound healing involved in inflammatory response / hyaluronan catabolic process / branching involved in prostate gland morphogenesis / type II transforming growth factor beta receptor binding / channel regulator activity / negative regulation of mature B cell apoptotic process / 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 / negative regulation of DNA damage response, signal transduction by p53 class mediator / microvillus / lamellipodium membrane / Neutrophil degranulation / receptor-mediated endocytosis / cell projection / cytokine-mediated signaling pathway / negative regulation of inflammatory response / Wnt 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
4,4-dimethyl-1,2,3,4-tetrahydroisoquinoline / CD44 antigen
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsLiu, L.K. / Finzel, B.C.
CitationJournal: To Be Published
Title: Crystal structure of the murine cd44 hyaluronan binding domain complex with a small molecule
Authors: Liu, L.K. / Finzel, B.C.
History
DepositionJun 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CD44 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0793
Polymers16,8401
Non-polymers2392
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.970, 81.940, 32.060
Angle α, β, γ (deg.)90.000, 117.910, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein CD44 antigen / Extracellular matrix receptor III / ECMR-III / GP90 lymphocyte homing/adhesion receptor / HUTCH-I / ...Extracellular matrix receptor III / ECMR-III / GP90 lymphocyte homing/adhesion receptor / HUTCH-I / Hermes antigen / Hyaluronate receptor / Lymphocyte antigen 24 / Ly-24 / Phagocytic glycoprotein 1 / PGP-1 / Phagocytic glycoprotein I / PGP-I


Mass: 16839.693 Da / Num. of mol.: 1 / Fragment: HYALURONAN BINDING DOMAIN, unp RESIDUES 21-171
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd44, Ly-24 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P15379
#2: Chemical ChemComp-4WT / 4,4-dimethyl-1,2,3,4-tetrahydroisoquinoline


Mass: 161.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H15N
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.15 Å3/Da / Density % sol: 42.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG MME 5000, MES, (NH4)2SO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Dec 16, 2012
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→40.97 Å / Num. obs: 10233 / % possible obs: 97 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.864 Å2 / Rmerge F obs: 0.996 / Rmerge(I) obs: 0.098 / Rrim(I) all: 0.114 / Χ2: 0.948 / Net I/σ(I): 14.37 / Num. measured all: 39128
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.94-1.990.8780.3823.4323187636730.44888.2
1.99-2.050.9050.3514.3628697677430.40796.9
2.05-2.10.9340.2915.1727127227020.33897.2
2.1-2.170.950.2336.3227407337080.2796.6
2.17-2.240.9620.2147.0325476756540.24896.9
2.24-2.320.9680.1848.2625896806690.21498.4
2.32-2.410.9740.178.8824116396200.19897
2.41-2.50.9780.1689.123706316140.19597.3
2.5-2.620.9810.13310.9722585945810.15597.8
2.62-2.740.9850.12611.7421985755690.14799
2.74-2.890.9920.09714.4320675455330.11297.8
2.89-3.070.9960.06918.3319095024950.0898.6
3.07-3.280.9960.05822.2318594974850.06797.6
3.28-3.540.9970.04626.6217584634560.05498.5
3.54-3.880.9980.03931.0815484154050.04597.6
3.88-4.340.9990.03335.5214163733720.03999.7
4.34-5.010.9990.03137.2812233293230.03698.2
5.01-6.140.9980.03632.1410972942910.04199
6.14-8.680.9990.03432.468092212180.0498.6
8.680.9990.02441.974301271220.02996.1

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 31.8 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.66 Å
Translation2.5 Å19.66 Å

-
Processing

Software
NameVersionClassification
REFMACrefinement
XSCALEdata scaling
PHASER2.1.4phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→40.97 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.877 / WRfactor Rfree: 0.2021 / WRfactor Rwork: 0.1641 / FOM work R set: 0.8629 / SU B: 3.613 / SU ML: 0.106 / SU R Cruickshank DPI: 0.1881 / SU Rfree: 0.1665 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2317 530 5.2 %RANDOM
Rwork0.1816 ---
obs0.1841 9618 97.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 37.19 Å2 / Biso mean: 11.037 Å2 / Biso min: 2.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å2-0.33 Å2
2--0.57 Å20 Å2
3----0.7 Å2
Refinement stepCycle: final / Resolution: 1.95→40.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1171 0 16 54 1241
Biso mean--12.23 13.18 -
Num. residues----150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221222
X-RAY DIFFRACTIONr_angle_refined_deg1.4661.951666
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8115151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14424.06859
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.77915189
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.027158
X-RAY DIFFRACTIONr_chiral_restr0.1010.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021944
X-RAY DIFFRACTIONr_mcbond_it0.721.5754
X-RAY DIFFRACTIONr_mcangle_it1.25921229
X-RAY DIFFRACTIONr_scbond_it2.1853468
X-RAY DIFFRACTIONr_scangle_it3.5284.5437
LS refinement shellResolution: 1.946→1.997 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 35 -
Rwork0.206 658 -
all-693 -
obs--92.52 %

+
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