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- PDB-3qa3: Crystal Structure of A-domain in complex with antibody -

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Basic information

Entry
Database: PDB / ID: 3qa3
TitleCrystal Structure of A-domain in complex with antibody
Components
  • Antibody Heavy chainImmunoglobulin heavy chain
  • Antibody Light chainImmunoglobulin light chain
  • Integrin alpha-M
KeywordsIMMUNE SYSTEM/ cell adhesion / IMMUNE SYSTEM- cell adhesion complex
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 / 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 / complement component C3b binding / vertebrate eye-specific patterning / 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 / integrin-mediated signaling pathway / response to ischemia / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 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
DepositionJan 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2011Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)282,01229
Polymers280,89512
Non-polymers1,11717
Water1,35175
1
C: Antibody Light chain
D: Antibody Heavy chain
G: Integrin alpha-M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,78811
Polymers70,2243
Non-polymers5658
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7250 Å2
ΔGint-33 kcal/mol
Surface area27060 Å2
MethodPISA
2
A: Antibody Light chain
B: Antibody Heavy chain
E: Integrin alpha-M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4486
Polymers70,2243
Non-polymers2243
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-41 kcal/mol
Surface area27380 Å2
MethodPISA
3
F: Antibody Light chain
H: Antibody Heavy chain
I: Integrin alpha-M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3265
Polymers70,2243
Non-polymers1022
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-42 kcal/mol
Surface area27970 Å2
MethodPISA
4
J: Antibody Light chain
K: Antibody Heavy chain
L: Integrin alpha-M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,4507
Polymers70,2243
Non-polymers2264
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6500 Å2
ΔGint-34 kcal/mol
Surface area27820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.604, 158.346, 233.319
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: 21722.779 Da / Num. of mol.: 4 / Fragment: UNP residues 148-337 / Mutation: I316G
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 / Immunoglobulin 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 / Immunoglobulin 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 , 4 types, 92 molecules

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


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.72 Å3/Da / Density % sol: 54.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 13% PEG8000, Tris pH 8.2, 0.25M NaCl, 10mM CaCl2, 1mM PMSF, 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: 0.97934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3.001→47.648 Å / Num. obs: 61325 / % possible obs: 99.1 % / Redundancy: 5.9 % / Biso Wilson estimate: 60.31 Å2 / Rmerge(I) obs: 0.156 / Net I/σ(I): 10.92
Reflection shellResolution: 3→3.05 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.814 / Mean I/σ(I) obs: 2.66 / % possible all: 97.9

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER2.1.4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q3G

3q3g


Resolution: 3→47.65 Å / Cor.coef. Fo:Fc: 0.9184 / Cor.coef. Fo:Fc free: 0.8874 / Cross valid method: THROUGHOUT / σ(F): 0
Details: NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION
RfactorNum. reflection% reflectionSelection details
Rfree0.2244 3095 5.06 %RANDOM
Rwork0.1941 ---
obs0.1956 61169 --
Displacement parametersBiso mean: 49.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.3463 Å20 Å20 Å2
2---3.407 Å20 Å2
3---3.7533 Å2
Refine analyzeLuzzati coordinate error obs: 0.396 Å
Refinement stepCycle: LAST / Resolution: 3→47.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19631 0 66 75 19772
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.009201422
X-RAY DIFFRACTIONt_angle_deg1.18273322
X-RAY DIFFRACTIONt_dihedral_angle_d68692
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes4962
X-RAY DIFFRACTIONt_gen_planes28855
X-RAY DIFFRACTIONt_it2014220
X-RAY DIFFRACTIONt_nbd05
X-RAY DIFFRACTIONt_omega_torsion2.88
X-RAY DIFFRACTIONt_other_torsion20.72
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion26875
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_contact217084
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2997 188 4.59 %
Rwork0.2618 3908 -
all0.2635 4096 -

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