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- PDB-4np3: Crystal structure of the murine cd44 hyaluronan binding domain co... -

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Basic information

Entry
Database: PDB / ID: 4np3
TitleCrystal structure of the murine cd44 hyaluronan binding domain complex with a small molecule
ComponentsCD44 antigen
KeywordsCell adhesion/inhibitor / Link module / Cell surface receptor / Hyaluronan / non-glycosylated / Cell surface / Cell adhesion-inhibitor complex
Function / homology
Function and homology information


Hyaluronan uptake and degradation / hyaluronic acid binding / macrophage fusion / macrophage migration inhibitory factor receptor complex / Degradation of the extracellular matrix / negative regulation of regulatory T cell differentiation / regulation of lamellipodium morphogenesis / Integrin cell surface interactions / Cell surface interactions at the vascular wall / hyaluronan catabolic process ...Hyaluronan uptake and degradation / hyaluronic acid binding / macrophage fusion / macrophage migration inhibitory factor receptor complex / Degradation of the extracellular matrix / negative regulation of regulatory T cell differentiation / regulation of lamellipodium morphogenesis / Integrin cell surface interactions / Cell surface interactions at the vascular wall / hyaluronan catabolic process / wound healing involved in inflammatory response / positive regulation of adaptive immune response / positive regulation of neutrophil apoptotic process / branching involved in prostate gland morphogenesis / type II transforming growth factor beta receptor binding / negative regulation of mature B cell apoptotic process / negative regulation of CD4-positive, alpha-beta T cell proliferation / channel regulator activity / cargo receptor activity / wound healing, spreading of cells / cytokine receptor activity / branching involved in ureteric bud morphogenesis / epidermal growth factor receptor binding / 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 / lamellipodium membrane / microvillus / Neutrophil degranulation / receptor-mediated endocytosis / cell projection / regulation of cell growth / phosphoprotein binding / Wnt signaling pathway / negative regulation of inflammatory response / transmembrane signaling receptor activity / neuron projection development / positive regulation of peptidyl-tyrosine phosphorylation / cell migration / positive regulation of peptidyl-serine phosphorylation / basolateral plasma membrane / positive regulation of ERK1 and ERK2 cascade / cell adhesion / inflammatory response / membrane raft / apical plasma membrane / external side of plasma membrane / positive regulation of gene expression / protein kinase binding / cell surface / protein-containing complex / extracellular region / plasma membrane
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
Chem-2L2 / CD44 antigen
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.61 Å
AuthorsLiu, L.K. / Finzel, B.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Fragment-Based Identification of an Inducible Binding Site on Cell Surface Receptor CD44 for the Design of Protein-Carbohydrate Interaction Inhibitors.
Authors: Liu, L.K. / Finzel, B.C.
History
DepositionNov 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release

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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)17,5287
Polymers16,7251
Non-polymers8046
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.000, 82.000, 32.000
Angle α, β, γ (deg.)90.000, 118.000, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#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: 16724.604 Da / Num. of mol.: 1 / Fragment: HYALURONAN BINDING DOMAIN, RESIDUES 23-174
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd44, Cd44 Ly-24, Ly-24 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P15379

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Non-polymers , 5 types, 122 molecules

#2: Chemical ChemComp-2L2 / 2-[(4-methyl-1H-imidazol-5-yl)methyl]-1,2,3,4-tetrahydroisoquinolin-8-amine


Mass: 242.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H18N4
#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: 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
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.15 Å3/Da / Density % sol: 42.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG MME 5000, MES, (NH4)2SO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jul 10, 2013 / 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: 1.61→41 Å / Num. all: 68726 / Num. obs: 18267 / % possible obs: 99.7 % / Redundancy: 3.76 % / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.081 / Χ2: 1.16 / Net I/σ(I): 11.2 / Scaling rejects: 520
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.61-1.673.660.2694.3658117901.47100
1.67-1.733.710.2644.3688318471.4399.9
1.73-1.813.740.2324.9689218351.3499.9
1.81-1.913.740.195.9681218071.2799.9
1.91-2.033.770.1497.4692718251.2199.7
2.03-2.193.770.129.3696418271.0799.7
2.19-2.43.80.09611.6693918030.9799.3
2.4-2.753.810.08713.7709918460.9899.6
2.75-3.473.820.0522705518260.9299.6
3.47-40.923.790.04627.4709418610.9999.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 35.25 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å41 Å
Translation2.5 Å41 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.9.9.4Ldata scaling
d*TREK9.9.9.4Ldata reduction
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.61→41 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.2423 / WRfactor Rwork: 0.1952 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8417 / SU B: 1.841 / SU ML: 0.065 / SU R Cruickshank DPI: 0.1012 / SU Rfree: 0.1053 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2246 927 5.1 %RANDOM
Rwork0.1771 ---
obs0.1795 18127 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 52.63 Å2 / Biso mean: 13.2889 Å2 / Biso min: 5.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å2-0.1 Å2
2--0.16 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.61→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1171 0 49 116 1336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211322
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.9751816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1065166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.68924.35562
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.44915201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.678158
X-RAY DIFFRACTIONr_chiral_restr0.0970.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211032
X-RAY DIFFRACTIONr_mcbond_it0.741.5801
X-RAY DIFFRACTIONr_mcangle_it1.25821318
X-RAY DIFFRACTIONr_scbond_it2.1613521
X-RAY DIFFRACTIONr_scangle_it3.4514.5498
LS refinement shellResolution: 1.61→1.652 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 57 -
Rwork0.217 1206 -
all-1263 -
obs--98.9 %

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