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- PDB-9t3y: Cryo-EM structure of alphaM/beta2:C3d-anti-CR3-Nb headpiece compl... -

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Basic information

Entry
Database: PDB / ID: 9t3y
TitleCryo-EM structure of alphaM/beta2:C3d-anti-CR3-Nb headpiece complex (HPO2 3D class reconstruction)
Components
  • Integrin beta-2
  • Isoform 2 of Integrin alpha-M
  • Nanobody,Complement C3dg fragment
KeywordsIMMUNE SYSTEM / phagocytosis / integrin / opsonisation
Function / homology
Function and homology information


integrin alphaD-beta2 complex / integrin alphaX-beta2 complex / ectodermal cell differentiation / cellular extravasation / integrin alphaM-beta2 complex / positive regulation of neutrophil degranulation / integrin alphaL-beta2 complex / ICAM-3 receptor activity / response to Gram-positive bacterium / response to curcumin ...integrin alphaD-beta2 complex / integrin alphaX-beta2 complex / ectodermal cell differentiation / cellular extravasation / integrin alphaM-beta2 complex / positive regulation of neutrophil degranulation / integrin alphaL-beta2 complex / ICAM-3 receptor activity / response to Gram-positive bacterium / response to curcumin / positive regulation of microglial cell mediated cytotoxicity / C5L2 anaphylatoxin chemotactic receptor binding / oviduct epithelium development / regulation of triglyceride biosynthetic process / positive regulation of activation of membrane attack complex / vertebrate eye-specific patterning / leukocyte migration involved in inflammatory response / positive regulation of apoptotic cell clearance / complement component C3b binding / Alternative complement activation / complement-mediated synapse pruning / Toll Like Receptor 4 (TLR4) Cascade / : / neutrophil migration / positive regulation of type IIa hypersensitivity / Activation of C3 and C5 / positive regulation of lipid storage / positive regulation of phagocytosis, engulfment / complement activation, GZMK pathway / positive regulation of G protein-coupled receptor signaling pathway / complement-dependent cytotoxicity / positive regulation of D-glucose transmembrane transport / complement receptor mediated signaling pathway / complement activation, alternative pathway / complement activation / positive regulation of leukocyte adhesion to vascular endothelial cell / integrin complex / cell adhesion mediated by integrin / heterotypic cell-cell adhesion / cargo receptor activity / regulation of peptidyl-tyrosine phosphorylation / phagocytosis, engulfment / leukocyte cell-cell adhesion / neuron remodeling / endopeptidase inhibitor activity / negative regulation of dopamine metabolic process / receptor clustering / forebrain development / endodermal cell differentiation / amyloid-beta clearance / B cell activation / tertiary granule membrane / ficolin-1-rich granule membrane / complement activation, classical pathway / plasma membrane raft / positive regulation of vascular endothelial growth factor production / positive regulation of protein targeting to membrane / Integrin cell surface interactions / cellular response to low-density lipoprotein particle stimulus / response to mechanical stimulus / endothelial cell migration / Purinergic signaling in leishmaniasis infection / specific granule membrane / positive regulation of superoxide anion generation / heat shock protein binding / neutrophil chemotaxis / cell adhesion molecule binding / receptor-mediated endocytosis / Regulation of Complement cascade / response to ischemia / Peptide ligand-binding receptors / cell-matrix adhesion / Cell surface interactions at the vascular wall / response to amphetamine / integrin-mediated signaling pathway / Post-translational protein phosphorylation / response to bacterium / microglial cell activation / fatty acid metabolic process / cell-cell adhesion / positive regulation of protein phosphorylation / receptor internalization / positive regulation of receptor-mediated endocytosis / integrin binding / 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 / positive regulation of angiogenesis / positive regulation of nitric oxide biosynthetic process / azurophil granule lumen / response to estradiol / cell-cell signaling / regulation of cell shape / extracellular vesicle / amyloid-beta binding / signaling receptor activity / Interleukin-4 and Interleukin-13 signaling / secretory granule lumen / blood microparticle / G alpha (i) signalling events / cell adhesion
Similarity search - Function
Integrin beta-2 subunit / : / Integrin alpha-X-like, Ig-like domain 3 / Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 ...Integrin beta-2 subunit / : / Integrin alpha-X-like, Ig-like domain 3 / Complement C3-like, NTR domain / : / : / Complement component 3, CUB domain, second segment / Complement component 3, CUB domain, first segment / Complement C3/4/5, macroglobulin domain MG1 / Macroglobulin domain MG1 / Alpha-2-macroglobulin, conserved site / Alpha-2-macroglobulin family thiolester region signature. / Anaphylatoxin, complement system domain / : / Alpha-macro-globulin thiol-ester bond-forming region / 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 / Macroglobulin domain MG4 / Macroglobulin domain MG4 / Alpha-macroglobulin, receptor-binding / Alpha-macroglobulin, receptor-binding domain superfamily / Macroglobulin domain MG3 / : / A-macroglobulin receptor binding domain / Macroglobulin domain MG3 / A-macroglobulin receptor / Netrin domain / NTR domain profile. / Alpha-2-macroglobulin / Macroglobulin domain / Tissue inhibitor of metalloproteinases-like, OB-fold / 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 beta subunit, cytoplasmic domain / Integrin beta tail domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin alpha cytoplasmic region / : / Integrins beta chain EGF (I-EGF) domain profile. / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain EGF (I-EGF) domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / Integrin alpha chain / Integrin alpha beta-propellor / : / Integrin alpha Ig-like domain 2 / 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 / PSI domain / domain found in Plexins, Semaphorins and Integrins / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / Immunoglobulin-like fold
Similarity search - Domain/homology
: / Complement C3 / Integrin beta-2 / Integrin alpha-M
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsAndersen, G.R. / Fruergaard, M.U.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: Cryo-EM structure of alphaM/beta2:C3d-anti-CR3-Nb headpiece complex (HPO2 3D class reconstruction)
Authors: Andersen, G.R. / Fruergaard, M.U.
History
DepositionOct 30, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 2 of Integrin alpha-M
B: Integrin beta-2
C: Nanobody,Complement C3dg fragment
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,67318
Polymers185,4423
Non-polymers4,23115
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Isoform 2 of 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: 83989.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGAM, CD11B, CR3A / Production host: Homo sapiens (human) / References: UniProt: P11215
#2: Protein Integrin beta-2 / Cell surface adhesion glycoproteins LFA-1/CR3/p150 / 95 subunit beta / Complement receptor C3 subunit beta


Mass: 52281.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB2, CD18, MFI7 / Production host: Homo sapiens (human) / References: UniProt: P05107

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Antibody , 1 types, 1 molecules C

#3: Antibody Nanobody,Complement C3dg fragment


Mass: 49171.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Nb fused with C3d with flexible linkers
Source: (gene. exp.) Lama glama (llama), (gene. exp.) Homo sapiens (human)
Gene: C3, CPAMD1 / Production host: Homo sapiens (human) / References: UniProt: P01024

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Sugars , 4 types, 8 molecules

#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-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
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#6: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}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.: 3 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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 , 3 types, 16 molecules

#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Complement C3d-alphaM/beta2 headpiece complex (wt HPO2)COMPLEXHeadpiece of alphaM/beta2 complex in complex with C3d-anti-CR3-Nb fusion ligand (HPO2 orientation)#1-#30MULTIPLE SOURCES
2AlphaM/beta2 headpiece complexCOMPLEX#1-#21RECOMBINANT
3Nanobody fused with C3d with flexible linkersCOMPLEX#31RECOMBINANT
Molecular weightValue: 190 kDa/nm / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Homo sapiens (human)9606
43Lama glama (llama)9844
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Homo sapiens (human)9606
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
10.02 MHEPESC8H18N2O4S1
20.15 Msodium chlorideNaCl1
30.001 Mmanganese chlorideMnCl21
40.00002 Mcalcium chlorideCaCl21
SpecimenConc.: 2.88 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 25 mA current / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R0./1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
Details: 0.02 % w/v CHAPS added to sample just before vitrification

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60.1 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2EPUimage acquisition
12cryoSPARC3D reconstruction
13PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43930 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
RefinementHighest resolution: 3.44 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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