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- PDB-1m1u: AN ISOLEUCINE-BASED ALLOSTERIC SWITCH CONTROLS AFFINITY AND SHAPE... -

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Basic information

Entry
Database: PDB / ID: 1m1u
TitleAN ISOLEUCINE-BASED ALLOSTERIC SWITCH CONTROLS AFFINITY AND SHAPE SHIFTING IN INTEGRIN CD11B A-DOMAIN
ComponentsIntegrin alpha-M
KeywordsCELL ADHESION / INTEGRIN / CELL ADHESION PROTEIN / GLYCOPROTEIN / A-domain / CD11b
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 / vertebrate eye-specific patterning / complement component C3b binding / Toll Like Receptor 4 (TLR4) Cascade ...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 / vertebrate eye-specific patterning / complement component C3b binding / Toll Like Receptor 4 (TLR4) Cascade / complement-mediated synapse pruning / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsXiong, J.-P. / Li, R. / Essafi, M. / Stehle, T. / Arnaout, M.A.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: An isoleucine-based allosteric switch controls affinity and shape shifting in integrin CD11b A-domain.
Authors: Xiong, J.P. / Li, R. / Essafi, M. / Stehle, T. / Arnaout, M.A.
History
DepositionJun 20, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)22,3012
Polymers22,2611
Non-polymers401
Water70339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.7, 45.7, 94.8
Angle α, β, γ (deg.)90, 90, 90
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Integrin alpha-M / CD11b


Mass: 22261.314 Da / Num. of mol.: 1 / Fragment: CD11b A-domain, Residues 123-315 / Mutation: C128S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: P11215
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 2.22 Å3/Da / Density % sol: 44.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 15% PEG8K, 0.1M Tris-HCl 8.2, 5mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
215 %PEG80001reservoir
30.1 MTris-HCl1reservoirpH8.2
45 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 15, 1999 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→8 Å / Num. obs: 7963 / % possible obs: 91.1 % / Observed criterion σ(I): -2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088
Reflection
*PLUS
Num. obs: 7955 / Redundancy: 2.3 % / Rmerge(I) obs: 0.088
Reflection shell
*PLUS
% possible obs: 80.8 % / Rmerge(I) obs: 0.28

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1IDO

1ido


Resolution: 2.3→8 Å / Cross valid method: througthout / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.248 315 random
Rwork0.188 --
obs-7759 -
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1490 0 1 39 1530
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.3
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.248 / Rfactor Rwork: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS

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