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- PDB-4xw2: Structural basis for simvastatin competitive antagonism of comple... -

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Basic information

Entry
Database: PDB / ID: 4xw2
TitleStructural basis for simvastatin competitive antagonism of complement receptor 3
ComponentsIntegrin alpha-M
KeywordsIMMUNE SYSTEM / Complement receptor 3 / Rossmann fold / integrin / statin / protein-inhibitor complex / Mac-1 / I domain / vWA
Function / homology
Function and homology information


ectodermal cell differentiation / integrin alphaM-beta2 complex / positive regulation of prostaglandin-E synthase activity / response to curcumin / positive regulation of neutrophil degranulation / response to Gram-positive bacterium / positive regulation of microglial cell mediated cytotoxicity / complement component C3b binding / vertebrate eye-specific patterning / complement-mediated synapse pruning ...ectodermal cell differentiation / integrin alphaM-beta2 complex / positive regulation of prostaglandin-E synthase activity / response to curcumin / positive regulation of neutrophil degranulation / response to Gram-positive bacterium / positive regulation of microglial cell mediated cytotoxicity / complement component C3b binding / vertebrate eye-specific patterning / complement-mediated synapse pruning / Toll Like Receptor 4 (TLR4) Cascade / negative regulation of dopamine metabolic process / cell-cell adhesion via plasma-membrane adhesion molecules / complement receptor mediated signaling pathway / heterotypic cell-cell adhesion / integrin complex / cargo receptor activity / cell adhesion mediated by integrin / phagocytosis, engulfment / amyloid-beta clearance / plasma membrane raft / tertiary granule membrane / positive regulation of protein targeting to membrane / Integrin cell surface interactions / specific granule membrane / response to mechanical stimulus / forebrain development / heat shock protein binding / receptor-mediated endocytosis / cell-matrix adhesion / positive regulation of superoxide anion generation / response to ischemia / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / microglial cell activation / cell-cell adhesion / integrin binding / response to estradiol / amyloid-beta binding / Interleukin-4 and Interleukin-13 signaling / cell adhesion / external side of plasma membrane / innate immune response / Neutrophil degranulation / cell surface / extracellular space / extracellular exosome / metal ion binding / plasma membrane
Similarity search - Function
: / Integrin alpha-X-like, Ig-like domain 3 / Integrin alpha cytoplasmic region / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / von Willebrand factor, type A domain / : / Integrin alpha Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor ...: / Integrin alpha-X-like, Ig-like domain 3 / Integrin alpha cytoplasmic region / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / von Willebrand factor, type A domain / : / Integrin alpha Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin domain superfamily / Integrin alpha, N-terminal / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Simvastatin acid / Integrin alpha-M
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.001 Å
AuthorsBajic, G. / Jensen, M.R. / Vorup-Jensen, T. / Andersen, G.R.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Basis for Simvastatin Competitive Antagonism of Complement Receptor 3.
Authors: Jensen, M.R. / Bajic, G. / Zhang, X. / Laustsen, A.K. / Kolds, H. / Skeby, K.K. / Schitt, B. / Andersen, G.R. / Vorup-Jensen, T.
History
DepositionJan 28, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 6, 2016Group: Database references
Revision 1.2Aug 24, 2016Group: Database references
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Integrin alpha-M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9413
Polymers22,4811
Non-polymers4612
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area510 Å2
ΔGint-14 kcal/mol
Surface area9320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.380, 57.690, 58.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein Integrin alpha-M / CD11 antigen-like family member B / CR-3 alpha chain / Cell surface glycoprotein MAC-1 subunit ...CD11 antigen-like family member B / CR-3 alpha chain / Cell surface glycoprotein MAC-1 subunit alpha / Leukocyte adhesion receptor MO1 / Neutrophil adherence receptor


Mass: 22480.596 Da / Num. of mol.: 1 / Fragment: UNP residues 145-337
Source method: isolated from a genetically manipulated source
Details: The discrepancies come from the expression vector / Source: (gene. exp.) Homo sapiens (human) / Gene: ITGAM, CD11B, CR3A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P11215
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SIM / Simvastatin acid / DIMETHYL-COMPACTIN / Simvastatin


Mass: 436.582 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H40O6 / Comment: medication*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.11 Å3/Da / Density % sol: 41.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M sodium malonate pH 7.0, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 30, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→29.2 Å / Num. obs: 13336 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 9 % / Biso Wilson estimate: 18.15 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.111 / Rrim(I) all: 0.118 / Χ2: 0.937 / Net I/σ(I): 18.96 / Num. measured all: 120240
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2-2.10.9260.5834.1415515177517380.61997.9
2.1-2.20.9580.4215.9413641147514750.445100
2.2-2.30.9750.3267.8511091123312270.34699.5
2.3-2.50.9830.259.9317813192919290.264100
2.5-30.9940.14616.0226287286728670.154100
3-40.9990.0632.620796231623160.064100
4-60.9990.03747.9610648122312230.039100
6-1010.03348.435814364360.035100
10-200.9990.02755.797931101100.029100
20-300.9980.02753.027515150.03100
304

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata reduction
PHASERphasing
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IDO

1ido


Resolution: 2.001→29.2 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 21.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2317 941 7.06 %
Rwork0.1886 12393 -
obs0.1916 13334 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.91 Å2 / Biso mean: 22.7239 Å2 / Biso min: 7.44 Å2
Refinement stepCycle: final / Resolution: 2.001→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1490 0 32 65 1587
Biso mean--37.81 27.3 -
Num. residues----184
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071550
X-RAY DIFFRACTIONf_angle_d1.0522088
X-RAY DIFFRACTIONf_chiral_restr0.052233
X-RAY DIFFRACTIONf_plane_restr0.005271
X-RAY DIFFRACTIONf_dihedral_angle_d12.912639
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0011-2.10660.25861330.20431713184699
2.1066-2.23850.2591340.196117411875100
2.2385-2.41130.28541440.208617271871100
2.4113-2.65380.24691360.199617521888100
2.6538-3.03750.20111190.190817841903100
3.0375-3.82560.2141300.179718001930100
3.8256-29.20310.21531450.175918762021100

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