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- PDB-4pz4: High-resolution crystal structure of the human CD44 hyaluronan bi... -

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Basic information

Entry
Database: PDB / ID: 4pz4
TitleHigh-resolution crystal structure of the human CD44 hyaluronan binding domain in new space group
ComponentsCD44 antigen
KeywordsCELL ADHESION / Link module / Binding protein / Hyaluronan / Ectodomain
Function / homology
Function and homology information


Hyaluronan uptake and degradation / positive regulation of monocyte aggregation / hyaluronic acid binding / macrophage migration inhibitory factor receptor complex / regulation of lamellipodium morphogenesis / hyaluronan catabolic process / monocyte aggregation / cellular response to fibroblast growth factor stimulus / cartilage development / positive regulation of heterotypic cell-cell adhesion ...Hyaluronan uptake and degradation / positive regulation of monocyte aggregation / hyaluronic acid binding / macrophage migration inhibitory factor receptor complex / regulation of lamellipodium morphogenesis / hyaluronan catabolic process / monocyte aggregation / cellular response to fibroblast growth factor stimulus / cartilage development / positive regulation of heterotypic cell-cell adhesion / 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 / T cell activation / cell-matrix adhesion / secretory granule membrane / cell projection / Cell surface interactions at the vascular wall / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / cell-cell adhesion / cytokine-mediated signaling pathway / Interferon gamma signaling / positive regulation of peptidyl-tyrosine phosphorylation / cell migration / transmembrane signaling receptor activity / 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 / Extracellular link domain / Link domain signature. / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,51318
Polymers34,0942
Non-polymers1,41916
Water3,585199
1
A: CD44 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7649
Polymers17,0471
Non-polymers7178
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CD44 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7509
Polymers17,0471
Non-polymers7038
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.271, 70.271, 286.458
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 1 types, 2 molecules AB

#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: 17047.043 Da / Num. of mol.: 2 / Fragment: HYALURONAN BINDING DOMAIN, RESIDUES 18-171 / 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

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Non-polymers , 6 types, 215 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


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


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O

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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: 2.99 Å3/Da / Density % sol: 58.92 %
Crystal growTemperature: 277 K / Method: hanging drop / pH: 7
Details: 25% PEG 3350, 100 mM NACl, 100 mM HEPES, (5% DMSO), pH 7.0, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 5, 2011
Details: K-B pair of biomorph mirrors for vertical and horizontal focusing
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.598→286.458 Å / Num. all: 56358 / Num. obs: 56356 / % possible obs: 99.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 12.8 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 26.4
Reflection shellResolution: 1.598→1.604 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 5.3 / Num. unique all: 455 / Rsym value: 0.516 / % possible all: 80.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 35.09 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å47.74 Å
Translation2.5 Å47.74 Å

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASER2.1.4phasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.14data extraction
Blu-Icedata collection
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→60.86 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.23 / WRfactor Rwork: 0.1981 / FOM work R set: 0.8664 / SU B: 1.391 / SU ML: 0.05 / SU R Cruickshank DPI: 0.0824 / SU Rfree: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2289 2864 5.1 %RANDOM
Rwork0.1974 ---
obs0.1989 56286 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 78.4 Å2 / Biso mean: 18.407 Å2 / Biso min: 8.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20.25 Å2-0 Å2
2--0.5 Å2-0 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 1.6→60.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2373 0 84 199 2656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0222627
X-RAY DIFFRACTIONr_angle_refined_deg1.4061.9653576
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7235330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.39623.984123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38315402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3971519
X-RAY DIFFRACTIONr_chiral_restr0.0940.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212021
X-RAY DIFFRACTIONr_mcbond_it0.8691.51611
X-RAY DIFFRACTIONr_mcangle_it1.59322640
X-RAY DIFFRACTIONr_scbond_it2.46631016
X-RAY DIFFRACTIONr_scangle_it3.8054.5936
LS refinement shellResolution: 1.598→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 180 -
Rwork0.26 3738 -
all-3918 -
obs--96.08 %

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