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- PDB-5sbm: CD44 PanDDA analysis group deposition -- The hyaluronan-binding d... -

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Basic information

Entry
Database: PDB / ID: 5sbm
TitleCD44 PanDDA analysis group deposition -- The hyaluronan-binding domain of CD44 in complex with Z1267885772
ComponentsCD44 antigen
KeywordsPROTEIN BINDING / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer / antigen
Function / homology
Function and homology information


Hyaluronan uptake and degradation / macrophage fusion / hyaluronic acid binding / macrophage migration inhibitory factor receptor complex / negative regulation of regulatory T cell differentiation / branching involved in prostate gland morphogenesis / Degradation of the extracellular matrix / regulation of lamellipodium morphogenesis / Integrin cell surface interactions / Cell surface interactions at the vascular wall ...Hyaluronan uptake and degradation / macrophage fusion / hyaluronic acid binding / macrophage migration inhibitory factor receptor complex / negative regulation of regulatory T cell differentiation / branching involved in prostate gland morphogenesis / Degradation of the extracellular matrix / 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 / 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 / cargo receptor activity / wound healing, spreading of cells / epidermal growth factor receptor binding / branching involved in ureteric bud morphogenesis / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / channel regulator activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / microvillus / lamellipodium membrane / Neutrophil degranulation / receptor-mediated endocytosis / cell projection / regulation of cell growth / phosphoprotein binding / cytokine-mediated signaling pathway / Wnt signaling pathway / negative regulation of inflammatory response / positive regulation of peptidyl-tyrosine phosphorylation / neuron projection development / 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 / 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 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
(3S)-3-methyl-1-(6-methylpyridin-2-yl)piperazine / CD44 antigen
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.14 Å
AuthorsBradshaw, W.J. / Katis, V.L. / Bezerra, G.A. / Koekemoer, L. / von Delft, F. / Bountra, C. / Brennan, P.E. / Gileadi, O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Aging (NIH/NIA)1RF1AG057443 United States
CitationJournal: To Be Published
Title: CD44 PanDDA analysis group deposition
Authors: Bradshaw, W.J. / Katis, V.L. / Bezerra, G.A. / Koekemoer, L. / von Delft, F. / Bountra, C. / Brennan, P.E. / Gileadi, O.
History
DepositionSep 14, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: 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)17,5998
Polymers16,9711
Non-polymers6287
Water4,828268
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.810, 81.460, 31.970
Angle α, β, γ (deg.)90.000, 117.900, 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: 16970.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cd44, Ly-24 / Production host: Escherichia coli (E. coli) / References: UniProt: P15379
#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-8AB / (3S)-3-methyl-1-(6-methylpyridin-2-yl)piperazine


Mass: 191.273 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H17N3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.09 Å3/Da / Density % sol: 41.13 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 200mM ammonium sulphate, 100mM MES, 24% PEG 5,000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91199 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91199 Å / Relative weight: 1
ReflectionResolution: 1.14→40.73 Å / Num. obs: 37100 / % possible obs: 73.3 % / Redundancy: 2.7 % / Biso Wilson estimate: 8.48 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.044 / Rrim(I) all: 0.08 / Net I/σ(I): 10 / Num. measured all: 98718 / Scaling rejects: 0
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.14-1.1710.1963153100.930.1960.2781.48.4
5.1-40.733.20.0418655820.9950.0270.04825.699

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.4 (20-APR-2021)refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2JCP

2jcp


Resolution: 1.14→40.73 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.962 / SU R Cruickshank DPI: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.05 / SU Rfree Blow DPI: 0.053 / SU Rfree Cruickshank DPI: 0.049
RfactorNum. reflection% reflectionSelection details
Rfree0.1884 1857 5.01 %RANDOM
Rwork0.1599 ---
obs0.1613 37072 73.2 %-
Displacement parametersBiso max: 93.98 Å2 / Biso mean: 13.19 Å2 / Biso min: 6.71 Å2
Baniso -1Baniso -2Baniso -3
1--1.1003 Å20 Å21.0455 Å2
2---0.5095 Å20 Å2
3---1.6098 Å2
Refine analyzeLuzzati coordinate error obs: 0.13 Å
Refinement stepCycle: final / Resolution: 1.14→40.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1171 0 42 275 1488
Biso mean--15.97 24.23 -
Num. residues----150
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d479SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes241HARMONIC5
X-RAY DIFFRACTIONt_it1290HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion180SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1845SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1326HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1812HARMONIC21.17
X-RAY DIFFRACTIONt_omega_torsion5.95
X-RAY DIFFRACTIONt_other_torsion14.34
LS refinement shellResolution: 1.14→1.19 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2608 32 4.31 %
Rwork0.2531 710 -
all-742 -
obs--12.42 %

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