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- PDB-4pz3: High-resolution crystal structure of the human CD44 hyaluronan bi... -

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Basic information

Entry
Database: PDB / ID: 4pz3
TitleHigh-resolution crystal structure of the human CD44 hyaluronan binding domain complex with undefined peptides
Components
  • CD44 antigen
  • Undefined peptides modeled as AAAV
KeywordsCELL ADHESION / Link module / Binding protein / Hyaluronan / Ectodomain
Function / homology
Function and homology information


positive regulation of monocyte aggregation / Hyaluronan uptake and degradation / hyaluronic acid binding / monocyte aggregation / macrophage migration inhibitory factor receptor complex / regulation of lamellipodium morphogenesis / hyaluronan catabolic process / cellular response to fibroblast growth factor stimulus / positive regulation of heterotypic cell-cell adhesion / cartilage development ...positive regulation of monocyte aggregation / Hyaluronan uptake and degradation / hyaluronic acid binding / monocyte aggregation / macrophage migration inhibitory factor receptor complex / regulation of lamellipodium morphogenesis / hyaluronan catabolic process / cellular response to fibroblast growth factor stimulus / positive regulation of heterotypic cell-cell adhesion / cartilage development / wound healing, spreading of cells / 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 / Integrin cell surface interactions / collagen binding / Degradation of the extracellular matrix / cell-matrix adhesion / : / T cell activation / secretory granule membrane / cell projection / Cell surface interactions at the vascular wall / cytokine-mediated signaling pathway / cell-cell adhesion / positive regulation of peptidyl-tyrosine phosphorylation / Interferon gamma signaling / transmembrane signaling receptor activity / cell migration / positive regulation of peptidyl-serine phosphorylation / basolateral plasma membrane / positive regulation of ERK1 and ERK2 cascade / cell adhesion / inflammatory response / apical plasma membrane / focal adhesion / Neutrophil degranulation / negative regulation of apoptotic process / Golgi apparatus / cell surface / 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
DI(HYDROXYETHYL)ETHER / CD44 antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.083 Å
AuthorsLiu, L.K. / Finzel, B.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2014
Title: High-resolution crystal structures of alternate forms of the human CD44 hyaluronan-binding domain reveal a site for protein interaction.
Authors: Liu, L.K. / Finzel, B.
History
DepositionMar 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2014Group: Database references
Revision 1.2Oct 16, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CD44 antigen
B: CD44 antigen
C: Undefined peptides modeled as AAAV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6767
Polymers34,2503
Non-polymers4254
Water6,702372
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.498, 60.288, 75.134
Angle α, β, γ (deg.)90.000, 113.400, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein / Protein/peptide , 2 types, 3 molecules ABC

#1: Protein CD44 antigen / CDw44 / Epican / Extracellular matrix receptor III / ECMR-III / GP90 lymphocyte homing/adhesion ...CDw44 / Epican / Extracellular matrix receptor III / ECMR-III / GP90 lymphocyte homing/adhesion receptor / HUTCH-I / Heparan sulfate proteoglycan / Hermes antigen / Hyaluronate receptor / Phagocytic glycoprotein 1 / PGP-1 / Phagocytic glycoprotein I / PGP-I


Mass: 16959.965 Da / Num. of mol.: 2 / Fragment: HYALURONAN BINDING DOMAIN, RESIDUES 18-170 / Mutation: S18A, L19M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD44, Cd44 Ly-24, LHR, MDU2, MDU3, MIC4 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P16070
#2: Protein/peptide Undefined peptides modeled as AAAV


Mass: 330.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Undefined peptides from the expression system co-purified with the target protein
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: Undefined / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)

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Non-polymers , 4 types, 376 molecules

#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.09 %
Crystal growTemperature: 277 K / Method: hanging drop / pH: 6.5
Details: 30% PEG MME 5000, 100 mM MES, 200 mM (NH4)2SO4, 5%DMSO, pH 6.5, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2012 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.083→44.676 Å / Num. all: 123233 / Num. obs: 122395 / % possible obs: 97.1 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 21.2
Reflection shellResolution: 1.083→1.086 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.154 / Mean I/σ(I) obs: 5.4 / Num. unique all: 834 / Rsym value: 0.284 / % possible all: 69.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 24.86 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å44.68 Å
Translation2.5 Å44.68 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASER2.1.4phasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.14data extraction
JDirectordata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.083→44.67 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.967 / WRfactor Rfree: 0.1864 / WRfactor Rwork: 0.174 / FOM work R set: 0.9109 / SU B: 0.374 / SU ML: 0.019 / SU R Cruickshank DPI: 0.0311 / SU Rfree: 0.0315 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.031 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1774 6171 5 %RANDOM
Rwork0.1662 ---
obs0.1668 122393 97.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 36.94 Å2 / Biso mean: 11.604 Å2 / Biso min: 4.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å2-0 Å20.04 Å2
2---0.24 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.083→44.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2364 0 27 372 2763
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222660
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.9513655
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1415349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.43824.113124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.25215408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7421518
X-RAY DIFFRACTIONr_chiral_restr0.2120.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212112
X-RAY DIFFRACTIONr_mcbond_it0.8871.51669
X-RAY DIFFRACTIONr_mcangle_it1.51922749
X-RAY DIFFRACTIONr_scbond_it2.0133991
X-RAY DIFFRACTIONr_scangle_it3.1334.5906
LS refinement shellResolution: 1.083→1.111 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.19 339 -
Rwork0.187 6803 -
all-7142 -
obs--77.47 %

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