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- PDB-3q3g: Crystal Structure of A-domain in complex with antibody -

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Basic information

Entry
Database: PDB / ID: 3q3g
TitleCrystal Structure of A-domain in complex with antibody
Components
  • Antibody Heavy chain
  • Antibody Light Chain
  • Integrin alpha-M
KeywordsIMMUNE SYSTEM/CELL ADHESION / IMMUNE SYSTEM-CELL ADHESION COMPLEX
Function / homology
Function and homology information


ectodermal cell differentiation / positive regulation of prostaglandin-E synthase activity / response to curcumin / positive regulation of neutrophil degranulation / integrin alphaM-beta2 complex / 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 / positive regulation of prostaglandin-E synthase activity / response to curcumin / positive regulation of neutrophil degranulation / integrin alphaM-beta2 complex / 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 / cell-matrix adhesion / receptor-mediated endocytosis / 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 / von Willebrand factor, type A domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / : / 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 / von Willebrand factor, type A domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / : / 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 alpha, N-terminal / Integrin domain superfamily / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Integrin alpha-M
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMahalingam, B. / Xiong, J.P. / Arnaout, M.A.
CitationJournal: J.Immunol. / Year: 2011
Title: Stable Coordination of the Inhibitory Ca2+ Ion at the Metal Ion-Dependent Adhesion Site in Integrin CD11b/CD18 by an Antibody-Derived Ligand Aspartate: Implications for Integrin Regulation and ...Title: Stable Coordination of the Inhibitory Ca2+ Ion at the Metal Ion-Dependent Adhesion Site in Integrin CD11b/CD18 by an Antibody-Derived Ligand Aspartate: Implications for Integrin Regulation and Structure-Based Drug Design.
Authors: Mahalingam, B. / Ajroud, K. / Alonso, J.L. / Anand, S. / Adair, B.D. / Horenstein, A.L. / Malavasi, F. / Xiong, J.P. / Arnaout, M.A.
History
DepositionDec 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Antibody Light Chain
D: Antibody Heavy chain
G: Integrin alpha-M
A: Antibody Light Chain
B: Antibody Heavy chain
E: Integrin alpha-M
F: Antibody Light Chain
H: Antibody Heavy chain
I: Integrin alpha-M
J: Antibody Light Chain
K: Antibody Heavy chain
L: Integrin alpha-M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)284,19661
Polymers281,11912
Non-polymers3,07749
Water5,765320
1
C: Antibody Light Chain
D: Antibody Heavy chain
G: Integrin alpha-M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,33519
Polymers70,2803
Non-polymers1,05616
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9610 Å2
ΔGint-19 kcal/mol
Surface area26970 Å2
MethodPISA
2
A: Antibody Light Chain
B: Antibody Heavy chain
E: Integrin alpha-M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,16417
Polymers70,2803
Non-polymers88414
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7830 Å2
ΔGint-44 kcal/mol
Surface area27050 Å2
MethodPISA
3
F: Antibody Light Chain
H: Antibody Heavy chain
I: Integrin alpha-M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5348
Polymers70,2803
Non-polymers2545
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6900 Å2
ΔGint-54 kcal/mol
Surface area27360 Å2
MethodPISA
4
J: Antibody Light Chain
K: Antibody Heavy chain
L: Integrin alpha-M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,16417
Polymers70,2803
Non-polymers88414
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8460 Å2
ΔGint-41 kcal/mol
Surface area27960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.939, 157.218, 232.128
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules GEIL

#3: 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: 21778.887 Da / Num. of mol.: 4 / Fragment: UNP residues 148-337
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGAM, CD11B, CR3A / Production host: Escherichia coli (E. coli) / References: UniProt: P11215

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Antibody , 2 types, 8 molecules CAFJDBHK

#1: Antibody
Antibody Light Chain


Mass: 24457.043 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody
Antibody Heavy chain


Mass: 24043.818 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Non-polymers , 7 types, 369 molecules

#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#8: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.66 Å3/Da / Density % sol: 53.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 15% PEG4000, Tris pH 8.2, 0.3M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 16, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 81032 / % possible obs: 97.2 % / Redundancy: 4.2 % / Biso Wilson estimate: 68.74 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 11.31
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 1.2 / % possible all: 80.8

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Processing

Software
NameVersionClassification
PHASER2.1.4phasing
BUSTER2.8.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→47.76 Å / Cor.coef. Fo:Fc: 0.9174 / Cor.coef. Fo:Fc free: 0.89 / Cross valid method: THROUGHOUT / σ(F): 0
Details: NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION
RfactorNum. reflection% reflectionSelection details
Rfree0.2442 4048 5 %RANDOM
Rwork0.2108 ---
obs0.2125 80896 --
Displacement parametersBiso mean: 54.01 Å2
Baniso -1Baniso -2Baniso -3
1-4.4166 Å20 Å20 Å2
2---6.9525 Å20 Å2
3---2.5359 Å2
Refine analyzeLuzzati coordinate error obs: 0.405 Å
Refinement stepCycle: LAST / Resolution: 2.7→47.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19752 0 185 320 20257
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00920352HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1927570HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6945SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes500HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2900HARMONIC5
X-RAY DIFFRACTIONt_it20352HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.96
X-RAY DIFFRACTIONt_other_torsion19.94
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion27125
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_contact223074
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3393 219 4.63 %
Rwork0.2829 4508 -
all0.2855 4727 -

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