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- PDB-7akk: Structure of a complement factor-receptor complex -

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Basic information

Entry
Database: PDB / ID: 7akk
TitleStructure of a complement factor-receptor complex
Components
  • Complement C3 beta chain
  • Complement C3b alpha' chain
  • Integrin alpha-M
KeywordsIMMUNE SYSTEM / Immunology / Complement / iC3b / Integrin / CR3
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 / : / 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 / 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 / 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
Similarity search - Domain/homology
: / Complement C3 / Integrin alpha-M
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.395 Å
AuthorsFernandez, F.J. / Santos-Lopez, J. / Martinez-Barricarte, R. / Querol-Garcia, J. / Navas-Yuste, S. / Savko, M. / Shepard, W.E. / Rodriguez de Cordoba, S. / Vega, M.C.
Funding support Spain, 5items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesRTI2018-102242-B-I00 Spain
Spanish Ministry of Economy and CompetitivenessSAF2015-72961-EXP Spain
Spanish Ministry of Economy and CompetitivenessSAF2015-66287-R Spain
Other governmentS2017/BMD-3673 Spain
Spanish National Research CouncilPIE-201620E064 Spain
CitationJournal: Nat Commun / Year: 2022
Title: The crystal structure of iC3b-CR3 alpha I reveals a modular recognition of the main opsonin iC3b by the CR3 integrin receptor
Authors: Fernandez, F.J. / Santos-Lopez, J. / Martinez-Barricarte, R. / Querol-Garcia, J. / Martin-Merinero, H. / Navas-Yuste, S. / Savko, M. / Shepard, W.E. / Rodriguez de Cordoba, S. / Vega, M.C.
History
DepositionOct 1, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 31, 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

Downloads & links

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Assembly

Deposited unit
B: Complement C3 beta chain
A: Complement C3b alpha' chain
D: Integrin alpha-M
C: Complement C3 beta chain
E: Complement C3b alpha' chain
H: Integrin alpha-M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)393,31816
Polymers391,3596
Non-polymers1,96010
Water37821
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Heterodimeric complex iC3b-CR3 alphaI domain.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28030 Å2
ΔGint-119 kcal/mol
Surface area143920 Å2
Unit cell
Length a, b, c (Å)111.290, 150.730, 111.300
Angle α, β, γ (deg.)90.000, 92.800, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 3 types, 6 molecules BCAEDH

#1: Protein Complement C3 beta chain


Mass: 71393.320 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01024
#2: Protein Complement C3b alpha' chain


Mass: 102064.844 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01024
#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: 22221.268 Da / Num. of mol.: 2 / Mutation: C128S,I316G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGAM, CD11B, CR3A / Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P11215

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Sugars , 3 types, 3 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...beta-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-6DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1122h-1b_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(6+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#9: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 28 molecules

#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 48.37 % / Description: Long needles
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 100 mM Tris-HCl (pH 8.0), 8% (w/v) polyethylene glycol (PEG) 8000
PH range: 8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98001 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 21, 2020
RadiationMonochromator: Cryogenically cooled channel cut crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98001 Å / Relative weight: 1
Reflection twinOperator: l,-k,h / Fraction: 0.5
ReflectionResolution: 3.34→53.775 Å / Num. obs: 50383 / % possible obs: 99.62 % / Redundancy: 3.6 % / Biso Wilson estimate: 105.46 Å2 / CC1/2: 0.973 / CC star: 0.993 / Rmerge(I) obs: 0.338 / Rpim(I) all: 0.209 / Rrim(I) all: 0.398 / Net I/σ(I): 4.03
Reflection shellResolution: 3.39→3.52 Å / Redundancy: 3.6 % / Rmerge(I) obs: 2.422 / Mean I/σ(I) obs: 0.53 / Num. unique obs: 4854 / CC1/2: 0.167 / CC star: 0.547 / Rpim(I) all: 1.486 / Rrim(I) all: 2.847 / % possible all: 96.71

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSJan 31, 2020 BUILT=20200131data reduction
DIALS3.3data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: wwPDB 2A74/2I07/4M76

2a74

2i07

4m76


Resolution: 3.395→53.775 Å / Cross valid method: THROUGHOUT / Phase error: 20.03 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2294 2529 5.02 %
Rwork0.1921 47861 -
obs-50383 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 208 Å2 / Biso mean: 112.4737 Å2 / Biso min: 25 Å2
Refinement stepCycle: final / Resolution: 3.395→53.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23866 0 125 21 24012
Biso mean--124.06 56.8 -
Num. residues----3006
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.3954-3.46070.59731290.5844243786
3.4607-3.53130.56871380.5712262395
3.5313-3.60810.56551390.563264395
3.6081-3.6920.5471410.5609267695
3.692-3.78430.55831400.5568266995
3.7843-3.88660.5331400.5416265695
3.8866-4.00090.5291400.5278266895
4.0009-4.130.55361420.5284268295
4.13-4.27750.51961410.5185269195
4.2775-4.44870.53231400.5195265695
4.4487-4.65110.48961400.4929265695
4.6511-4.89610.46461410.4679268095
4.8961-5.20260.43791400.4399266095
5.2026-5.60390.41451420.3901269295
5.6039-6.1670.38441400.3537267095
6.167-7.05750.38051410.3566267795
7.0575-8.88460.39481420.3699269195
8.8846-52.15680.48341440.4539273494
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)
10.6922-0.6126-0.42021.00920.19580.6484-0.00150.2514-0.3145-0.5265-0.0421-0.37540.1944-0.10660.02820.7451-0.01450.16940.3164-0.06350.5887116.6696-60.120681.6572
20.233-0.4937-0.13670.7033-0.05260.12880.21370.1654-0.0013-0.3137-0.1590.24310.0018-0.0752-0.01640.5781-0.017-0.09720.4480.05240.748657.4656-17.838681.6967
30.3001-0.14060.00990.82240.18640.550.00990.0121-0.03910.06730.02460.44320.0076-0.2735-0.02560.6439-0.06760.06330.59460.02361.159152.2607-56.6343108.1565
40.33630.2054-0.07120.3413-0.09030.3134-0.10090.1449-0.1669-0.41080.07490.00010.1001-0.1266-0.06641.0447-0.08030.15030.46290.02490.58666.834222.633885.827
50.4771-0.2913-0.39980.84940.2350.75550.02010.23410.11830.4120.05180.3742-0.2316-0.2905-0.11580.69450.03660.13520.30370.02630.667676.1494-15.9545120.6664
60.6678-0.1866-0.1550.6969-0.01090.6671-0.09370.0821-0.208-0.23680.0739-0.1020.04960.0422-0.03920.4299-0.02010.03610.2429-0.02790.3575105.1091-18.862386.7169
70.6123-0.25460.20350.7402-0.04940.34710.17610.2261-0.1405-0.4491-0.0534-0.0150.32550.05850.06131.16680.08670.150.57250.04830.7219106.1318-19.967357.7044
80.4016-0.0749-0.03110.59660.17040.3961-0.1388-0.0363-0.02370.1999-0.0469-0.1761-0.0270.16070.12320.51260.0107-0.06310.4089-0.06040.8505132.1514-23.361699.9614
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resseq 1:2004)A1 - 2004
2X-RAY DIFFRACTION2(chain B and resseq 730:2002)B730 - 2002
3X-RAY DIFFRACTION3(chain C and resseq 1335:1641)C1335 - 1641
4X-RAY DIFFRACTION4(chain D and resseq 131:2101)D131 - 2101
5X-RAY DIFFRACTION5(chain E and resseq 1:2005)E1 - 2005
6X-RAY DIFFRACTION6(chain F and resseq 728:2101)F728 - 2101
7X-RAY DIFFRACTION7(chain G and resseq 1335:1641)G1335 - 1641
8X-RAY DIFFRACTION8(chain H and resseq 131:2001)H131 - 2001

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