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- PDB-5bzk: Crystal structure of the murine cd44 hyaluronan binding domain co... -

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Basic information

Entry
Database: PDB / ID: 5bzk
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 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
Chem-4WP / CD44 antigen
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 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 20, 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 / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CD44 antigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2454
Polymers16,8561
Non-polymers3903
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.804, 81.745, 32.279
Angle α, β, γ (deg.)90.000, 118.140, 90.000
Int Tables number4
Space group name H-MP1211

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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: 16855.803 Da / Num. of mol.: 1
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-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-4WP / methyl 3-(3,4-dihydroisoquinolin-2(1H)-yl)propanoate


Mass: 219.280 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H17NO2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O
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: 2.14 Å3/Da / Density % sol: 42.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: EG MME 5000, MES, (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→81.745 Å / Num. obs: 26772 / % possible obs: 96.7 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 11.9 / Num. measured all: 88448
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique all% possible all
1.4-1.4053.30.43381224692.8
6.497-81.7453.10.03884227395.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→40.87 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.208 / WRfactor Rwork: 0.1891 / FOM work R set: 0.8717 / SU B: 1.144 / SU ML: 0.046 / SU R Cruickshank DPI: 0.0705 / SU Rfree: 0.0695 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2086 1327 5 %RANDOM
Rwork0.1875 ---
obs0.1885 25382 96.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 42.65 Å2 / Biso mean: 14.002 Å2 / Biso min: 3.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å2-0 Å2-0.39 Å2
2--0.07 Å20 Å2
3----0.13 Å2
Refinement stepCycle: final / Resolution: 1.4→40.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1171 0 26 71 1268
Biso mean--25.9 21.29 -
Num. residues----150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211325
X-RAY DIFFRACTIONr_angle_refined_deg1.5031.9541816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8435170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0482465
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.52415207
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3061510
X-RAY DIFFRACTIONr_chiral_restr0.1030.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211054
X-RAY DIFFRACTIONr_mcbond_it0.9771.5813
X-RAY DIFFRACTIONr_mcangle_it1.76821339
X-RAY DIFFRACTIONr_scbond_it2.7793512
X-RAY DIFFRACTIONr_scangle_it4.4674.5477
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 91 -
Rwork0.34 1798 -
all-1889 -
obs--96.33 %

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