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- PDB-4m76: Integrin I domain of complement receptor 3 in complex with C3d -

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Basic information

Entry
Database: PDB / ID: 4m76
TitleIntegrin I domain of complement receptor 3 in complex with C3d
Components
  • Complement C3
  • Integrin alpha-M
KeywordsCELL ADHESION / integrin / complement receptor / immunity / innate immunity / inflammation / phagocytosis / Mac-1 / CD11b/CD18 / alphaMbeta2 / macrophage / Rossmann fold / I domain / Von Willebrand Factor A (VWA) / alpha-alpha barrel / adhesion
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 / positive regulation of microglial cell mediated cytotoxicity / response to Gram-positive bacterium / oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process ...ectodermal cell differentiation / positive regulation of prostaglandin-E synthase activity / response to curcumin / positive regulation of neutrophil degranulation / integrin alphaM-beta2 complex / positive regulation of microglial cell mediated cytotoxicity / response to Gram-positive bacterium / oviduct epithelium development / C5L2 anaphylatoxin chemotactic receptor binding / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / complement component C3b binding / vertebrate eye-specific patterning / positive regulation of apoptotic cell clearance / complement-mediated synapse pruning / Toll Like Receptor 4 (TLR4) Cascade / negative regulation of dopamine metabolic process / Alternative complement activation / cell-cell adhesion via plasma-membrane adhesion molecules / positive regulation of lipid storage / positive regulation of phagocytosis, engulfment / positive regulation of G protein-coupled receptor signaling pathway / complement receptor mediated signaling pathway / Activation of C3 and C5 / positive regulation of type IIa hypersensitivity / positive regulation of glucose transmembrane transport / complement-dependent cytotoxicity / complement activation, alternative pathway / complement activation / heterotypic cell-cell adhesion / integrin complex / cargo receptor activity / cell adhesion mediated by integrin / endopeptidase inhibitor activity / neuron remodeling / phagocytosis, engulfment / amyloid-beta clearance / plasma membrane raft / tertiary granule membrane / positive regulation of vascular endothelial growth factor production / positive regulation of protein targeting to membrane / Integrin cell surface interactions / Purinergic signaling in leishmaniasis infection / specific granule membrane / response to mechanical stimulus / forebrain development / heat shock protein binding / Peptide ligand-binding receptors / receptor-mediated endocytosis / cell-matrix adhesion / complement activation, classical pathway / positive regulation of superoxide anion generation / fatty acid metabolic process / Regulation of Complement cascade / response to ischemia / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / Post-translational protein phosphorylation / response to bacterium / microglial cell activation / cell-cell adhesion / positive regulation of receptor-mediated endocytosis / positive regulation of angiogenesis / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / azurophil granule lumen / integrin binding / response to estradiol / amyloid-beta binding / G alpha (i) signalling events / Interleukin-4 and Interleukin-13 signaling / secretory granule lumen / blood microparticle / cell adhesion / inflammatory response / immune response / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / external side of plasma membrane / innate immune response / signaling receptor binding / Neutrophil degranulation / cell surface / signal transduction / protein-containing complex / extracellular space / extracellular exosome / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
: / Integrin alpha-X-like, Ig-like domain 3 / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Complement C3-like, NTR domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 ...: / Integrin alpha-X-like, Ig-like domain 3 / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Complement C3-like, NTR domain / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / : / Alpha-macro-globulin thiol-ester bond-forming region / Anaphylatoxin, complement system domain / Anaphylatoxin domain signature. / Anaphylatoxin, complement system / Anaphylatoxin/fibulin / Anaphylotoxin-like domain / Anaphylatoxin domain profile. / Anaphylatoxin homologous domain / Netrin C-terminal Domain / Netrin module, non-TIMP type / UNC-6/NTR/C345C module / Glycosyltransferase - #20 / : / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor binding domain / Macroglobulin domain MG4 / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Tissue inhibitor of metalloproteinases-like, OB-fold / Alpha-2-macroglobulin / Macroglobulin domain / Alpha-2-macroglobulin, bait region domain / Alpha-macroglobulin-like, TED domain / Alpha-2-macroglobulin family / MG2 domain / A-macroglobulin TED domain / Alpha-2-macroglobulin bait region domain / Alpha-2-Macroglobulin / Alpha-2-macroglobulin family / 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 / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Glycosyltransferase / Alpha/alpha barrel / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Immunoglobulin-like fold / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Complement C3 / Integrin alpha-M
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.804 Å
AuthorsBajic, G. / Yatime, L. / Vorup-Jensen, T. / Andersen, G.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural insight on the recognition of surface-bound opsonins by the integrin I domain of complement receptor 3.
Authors: Bajic, G. / Yatime, L. / Sim, R.B. / Vorup-Jensen, T. / Andersen, G.R.
History
DepositionAug 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Nov 6, 2013Group: Structure summary
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Sep 20, 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_auth_seq_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
A: Complement C3
B: Integrin alpha-M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7974
Polymers55,6802
Non-polymers1172
Water59433
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.460, 65.120, 62.540
Angle α, β, γ (deg.)90.00, 115.69, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Complement C3 / C3 and PZP-like alpha-2-macroglobulin domain-containing protein 1 / Complement C3 beta chain / ...C3 and PZP-like alpha-2-macroglobulin domain-containing protein 1 / Complement C3 beta chain / Complement C3 alpha chain / C3a anaphylatoxin / Acylation stimulating protein / ASP / C3adesArg / Complement C3b alpha' chain / Complement C3c alpha' chain fragment 1 / Complement C3dg fragment / Complement C3g fragment / Complement C3d fragment / Complement C3f fragment / Complement C3c alpha' chain fragment 2


Mass: 33198.996 Da / Num. of mol.: 1 / Fragment: unp residues 994-1288 / Mutation: C1010A, C144A, I332G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C3, CPAMD1 / Plasmid: pETM-20 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01024
#2: 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 143-337
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD11B, CR3A, ITGAM / Plasmid: pETM-11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P11215
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.38 Å3/Da / Density % sol: 48.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3350, pH 7, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.8→98.895 Å / Num. obs: 12888 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 67.17 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 16.77
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.8-30.2914.47194.3
3-3.30.1628.19199.4
3.3-3.50.09912.47199.5
3.5-3.80.06617.03198.6
3.8-40.0521.52199.6
4-50.03826.75198.8
5-60.03726.48198.8
6-80.03430.88198.6
8-100.02734.48198.3
10-200.02634.87198.2
20-400.02834.19197.1
40-500.01230.211100
501

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 1IDO, 1C3D

1ido

1c3d


Resolution: 2.804→45.107 Å / Occupancy max: 1 / Occupancy min: 0.63 / SU ML: 0.4 / σ(F): 2.02 / Phase error: 28.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2419 972 7.54 %
Rwork0.194 --
obs0.1979 12885 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.3487 Å2
Refinement stepCycle: LAST / Resolution: 2.804→45.107 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3769 0 2 33 3804
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023848
X-RAY DIFFRACTIONf_angle_d0.6575201
X-RAY DIFFRACTIONf_dihedral_angle_d11.0051435
X-RAY DIFFRACTIONf_chiral_restr0.043577
X-RAY DIFFRACTIONf_plane_restr0.002675
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.804-2.95180.33761200.28711676X-RAY DIFFRACTION96
2.9518-3.13670.33541440.23841691X-RAY DIFFRACTION100
3.1367-3.37880.27841410.2341682X-RAY DIFFRACTION100
3.3788-3.71870.2631420.20381701X-RAY DIFFRACTION99
3.7187-4.25640.25311210.1861718X-RAY DIFFRACTION99
4.2564-5.36130.21111500.16931704X-RAY DIFFRACTION99
5.3613-45.11280.20821540.17531741X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1137-0.10050.11580.0876-0.10030.1105-0.11510.25990.1339-0.0625-0.0754-0.2378-0.03080.0879-0.27080.483-0.23840.23510.5828-0.1210.722317.0658-15.34459.489
20.15990.0267-0.00050.1935-0.12630.2953-0.20390.050.08340.1235-0.153-0.2603-0.24130.0581-0.37230.5692-0.24690.01480.4621-0.22690.964925.0717-7.818222.4205
30.056-0.1-0.030.33680.05960.02060.0459-0.0720.05610.2675-0.0167-0.15530.06980.0343-0.03390.1901-0.0581-0.2032-0.2727-0.33240.257214.2597-13.784231.7924
40.0391-0.08650.07850.70960.15740.3950.035-0.0460.11280.6487-0.16420.13490.155-0.3151-0.1380.3214-0.08730.00770.3194-0.0050.1555-1.7691-21.60429.3424
50.3167-0.18880.07160.1644-0.01150.0389-0.07070.0890.0890.00530.0366-0.1122-0.0764-0.1109-0.03220.2444-0.04040.00360.1899-0.01160.06281.5152-20.176714.9636
60.282-0.05620.40580.0128-0.08090.5844-0.11870.04240.0674-0.0002-0.0576-0.03730.01910.0389-0.11710.1892-0.04390.12540.2703-0.00180.39969.3384-22.30315.0609
70.0685-0.0870.05920.1072-0.07340.05270.02160.0632-0.1051-0.038-0.01760.0830.0896-0.07970.09970.3186-0.25510.0910.6676-0.3160.4288-16.06-43.67038.0613
80.006-0.0075-0.01040.00780.01150.0203-0.07730.01360.0243-0.0080.00190.001-0.0231-0.0351-0.04720.4131-0.28110.00370.7229-0.17890.2665-14.0489-39.246-0.5886
90.00730.0097-0.00510.01-0.00580.00330.0185-0.0201-0.0268-0.02090.00770.0417-0.00730.00460.00160.3252-0.28040.05810.6115-0.15810.4403-23.7288-46.69572.694
100.00260.00390.0010.04730.01270.0133-0.04750.01440.01720.08810.06670.05240.0025-0.0026-0.00120.3369-0.07210.15250.5805-0.11150.5242-20.6471-37.042413.8782
110.0437-0.01690.00210.0712-0.01350.0018-0.04150.0190.00070.03990.0088-0.05350.0384-0.0901-0.00860.1946-0.22170.00710.4878-0.08770.2856-21.8463-40.28069.9718
120.18820.0182-0.00070.212-0.09240.04130.03490.00550.00160.00730.06630.01960.0105-0.01110.26850.3882-0.2940.2330.5587-0.28220.5211-25.5264-51.587211.0423
130.005-0.00310.00660.0103-0.00020.00960.08790.0232-0.03610.02680.0594-0.0202-0.01590.06220.00530.6677-0.19930.1190.4057-0.12940.5248-8.0064-45.675420.8486
140.01410.04380.0220.23350.06870.0325-0.0126-0.0043-0.05310.08960.0017-0.0750.0270.03170.00720.5911-0.310.30530.7176-0.41250.9088-10.3114-52.122312.1806
150.0095-0.00460.00520.0106-0.00910.00880.05540.0019-0.0214-0.05410.00730.07250.07070.01540.02740.7155-0.16980.22940.5471-0.39331.0097-5.0266-54.982311.0408
160.0188-0.03460.02560.092-0.06790.05020.0365-0.00780.0199-0.05020.0242-0.036-0.0174-0.01490.0420.87240.0970.12370.9153-0.47050.739-10.972-52.1646-2.7103
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 992:1038 )A992 - 1038
2X-RAY DIFFRACTION2( CHAIN A AND RESID 1039:1075 )A1039 - 1075
3X-RAY DIFFRACTION3( CHAIN A AND RESID 1076:1164 )A1076 - 1164
4X-RAY DIFFRACTION4( CHAIN A AND RESID 1165:1225 )A1165 - 1225
5X-RAY DIFFRACTION5( CHAIN A AND RESID 1226:1268 )A1226 - 1268
6X-RAY DIFFRACTION6( CHAIN A AND RESID 1269:1287 )A1269 - 1287
7X-RAY DIFFRACTION7( CHAIN B AND RESID 132:146 )B132 - 146
8X-RAY DIFFRACTION8( CHAIN B AND RESID 147:162 )B147 - 162
9X-RAY DIFFRACTION9( CHAIN B AND RESID 163:176 )B163 - 176
10X-RAY DIFFRACTION10( CHAIN B AND RESID 178:185 )B178 - 185
11X-RAY DIFFRACTION11( CHAIN B AND RESID 186:221 )B186 - 221
12X-RAY DIFFRACTION12( CHAIN B AND RESID 222:241 )B222 - 241
13X-RAY DIFFRACTION13( CHAIN B AND RESID 242:255 )B242 - 255
14X-RAY DIFFRACTION14( CHAIN B AND RESID 256:278 )B256 - 278
15X-RAY DIFFRACTION15( CHAIN B AND RESID 279:294 )B279 - 294
16X-RAY DIFFRACTION16( CHAIN B AND RESID 295:310 )B295 - 310

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