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- EMDB-55521: Cryo-EM structure of alphaM/beta2:C3d-anti-CR3-Nb headpiece compl... -

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Basic information

Entry
Database: EMDB / ID: EMD-55521
TitleCryo-EM structure of alphaM/beta2:C3d-anti-CR3-Nb headpiece complex (HPO2 3D class reconstruction)
Map data
Sample
  • Complex: Complement C3d-alphaM/beta2 headpiece complex (wt HPO2)
    • Complex: AlphaM/beta2 headpiece complex
      • Protein or peptide: Isoform 2 of Integrin alpha-M
      • Protein or peptide: Integrin beta-2
    • Complex: Nanobody fused with C3d with flexible linkers
      • Protein or peptide: Nanobody,Complement C3dg fragment
  • Ligand: CALCIUM ION
  • Ligand: MANGANESE (II) ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
Keywordsphagocytosis / integrin / opsonisation / IMMUNE SYSTEM
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsAndersen GR / Fruergaard MU
Funding support1 items
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 GR / Fruergaard MU
History
DepositionOct 30, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55521.png

Downloads & links

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Map

FileDownload / File: emd_55521.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.29 Å/pix.
x 256 pix.
= 331.264 Å		1.29 Å/pix.
x 256 pix.
= 331.264 Å		1.29 Å/pix.
x 256 pix.
= 331.264 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.294 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.49597356 - 1.1864917
Average (Standard dev.)0.0011476451 (±0.023692315)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 331.264 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_55521_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_55521_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complement C3d-alphaM/beta2 headpiece complex (wt HPO2)

EntireName: Complement C3d-alphaM/beta2 headpiece complex (wt HPO2)
Components
  • Complex: Complement C3d-alphaM/beta2 headpiece complex (wt HPO2)
    • Complex: AlphaM/beta2 headpiece complex
      • Protein or peptide: Isoform 2 of Integrin alpha-M
      • Protein or peptide: Integrin beta-2
    • Complex: Nanobody fused with C3d with flexible linkers
      • Protein or peptide: Nanobody,Complement C3dg fragment
  • Ligand: CALCIUM ION
  • Ligand: MANGANESE (II) ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: Complement C3d-alphaM/beta2 headpiece complex (wt HPO2)

SupramoleculeName: Complement C3d-alphaM/beta2 headpiece complex (wt HPO2)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Headpiece of alphaM/beta2 complex in complex with C3d-anti-CR3-Nb fusion ligand (HPO2 orientation)
Molecular weightTheoretical: 190 kDa/nm

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Supramolecule #2: AlphaM/beta2 headpiece complex

SupramoleculeName: AlphaM/beta2 headpiece complex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Nanobody fused with C3d with flexible linkers

SupramoleculeName: Nanobody fused with C3d with flexible linkers / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Isoform 2 of Integrin alpha-M

MacromoleculeName: Isoform 2 of Integrin alpha-M / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 83.989734 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: FNLDTENAMT FQENARGFGQ SVVQLQGSRV VVGAPQEIVA ANQRGSLYQC DYSTGSCEPI RLQVPVEAVN MSLGLSLAAT TSPPQLLAC GPTVHQTCSE NTYVKGLCFL FGSNLRQQPQ KFPEALRGCP QEDSDIAFLI DGSGSIIPHD FRRMKEFVST V MEQLKKSK ...String:
FNLDTENAMT FQENARGFGQ SVVQLQGSRV VVGAPQEIVA ANQRGSLYQC DYSTGSCEPI RLQVPVEAVN MSLGLSLAAT TSPPQLLAC GPTVHQTCSE NTYVKGLCFL FGSNLRQQPQ KFPEALRGCP QEDSDIAFLI DGSGSIIPHD FRRMKEFVST V MEQLKKSK TLFSLMQYSE EFRIHFTFKE FQNNPNPRSL VKPITQLLGR THTATGIRKV VRELFNITNG ARKNAFKILV VI TDGEKFG DPLGYEDVIP EADREGVIRY VIGVGDAFRS EKSRQELNTI ASKPPRDHVF QVNNFEALKT IQNQLREKIF AIE GTQTGS SSSFEHEMSQ EGFSAAITSN GPLLSTVGSY DWAGGVFLYT SKEKSTFINM TRVDSDMNDA YLGYAAAIIL RNRV QSLVL GAPRYQHIGL VAMFRQNTGM WESNANVKGT QIGAYFGASL CSVDVDSNGS TDLVLIGAPH YYEQTRGGQV SVCPL PRGQ RARWQCDAVL YGEQGQPWGR FGAALTVLGD VNGDKLTDVA IGAPGEEDNR GAVYLFHGTS GSGISPSHSQ RIAGSK LSP RLQYFGQSLS GGQDLTMDGL VDLTVGAQGH VLLLRSQPVL RVKAIMEFNP REVARNVFEC NDQVVKGKEA GEVRVCL HV QKSTRDRLRE GQIQSVVTYD LALDSGRPHS RAVFNETKNS TRRQTQVLGL TQTCETLKLQ LPNCIEDPVS PIVLRLNF S LVGTPLSAFG NLRPVLAEDA QRLFTALFPF EKNTGGENLY FQ

UniProtKB: Integrin alpha-M

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Macromolecule #2: Integrin beta-2

MacromoleculeName: Integrin beta-2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.281094 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QECTKFKVSS CRECIESGPG CTWCQKLNFT GPGDPDSIRC DTRPQLLMRG CAADDIMDPT SLAETQEDHN GGQKQLSPQK VTLYLRPGQ AAAFNVTFRR AKGYPIDLYY LMDLSYSMLD DLRNVKKLGG DLLRALNEIT ESGRIGFGSF VDKTVLPFVN T HPDKLRNP ...String:
QECTKFKVSS CRECIESGPG CTWCQKLNFT GPGDPDSIRC DTRPQLLMRG CAADDIMDPT SLAETQEDHN GGQKQLSPQK VTLYLRPGQ AAAFNVTFRR AKGYPIDLYY LMDLSYSMLD DLRNVKKLGG DLLRALNEIT ESGRIGFGSF VDKTVLPFVN T HPDKLRNP CPNKEKECQP PFAFRHVLKL TNNSNQFQTE VGKQLISGNL DAPEGGLDAM MQVAACPEEI GWRNVTRLLV FA TDDGFHF AGDGKLGAIL TPNDGRCHLE DNLYKRSNEF DYPSVGQLAH KLAENNIQPI FAVTSRMVKT YEKLTEIIPK SAV GELSED SSNVVHLIKN AYNKLSSRVF LDHNALPDTL KVTYDSFCSN GVTHRNQPRG DCDGVQINVP ITFQVKVTAT ECIQ EQSFV IRALGFTDIV TVQVLPQCEC RCRDQSRDRS LCHGKGFLEC GICRCDTGYI GKNCEPAAEN LYFQ

UniProtKB: Integrin beta-2

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Macromolecule #3: Nanobody,Complement C3dg fragment

MacromoleculeName: Nanobody,Complement C3dg fragment / type: protein_or_peptide / ID: 3 / Details: Nb fused with C3d with flexible linkers / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 49.171129 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVESGGG LVQAGGSLRL SCTTSGFTFD DYAIGWFRQA PGKEREGVSC ISSSEGKYYS DGGGGSGGGG SGGGGSVDAE RLKHLIVTP SGSGEQNMIG MTPTVIAVHY LDETEQWEKF GLEKRQGALE LIKKGYTQQL AFRQPSSAFA AFVKRAPSTW L TAYVVKVF ...String:
QVQLVESGGG LVQAGGSLRL SCTTSGFTFD DYAIGWFRQA PGKEREGVSC ISSSEGKYYS DGGGGSGGGG SGGGGSVDAE RLKHLIVTP SGSGEQNMIG MTPTVIAVHY LDETEQWEKF GLEKRQGALE LIKKGYTQQL AFRQPSSAFA AFVKRAPSTW L TAYVVKVF SLAVNLIAID SQVLCGAVKW LILEKQKPDG VFQEDAPVIH QEMIGGLRNN NEKDMALTAF VLISLQEAKD IC EEQVNSL PGSITKAGDF LEANYMNLQR SYTVAIAGYA LAQMGRLKGP LLNKFLTTAK DKNRWEDPGK QLYNVEATSY ALL ALLQLK DFDFVPPVVR WLNEQRYYGG GYGSTQATFM VFQALAQYQK DAPDHKGGGG SGRFTISSDN AKNTVYLQMN NLKP EDTAV YYCAAEWNNF GRLCMYPDYW GQGTQVTVSS ENLYFQGHHH HHH

UniProtKB: Complement C3

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Macromolecule #7: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 7 / Number of copies: 5 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #8: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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Macromolecule #9: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 9 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #10: water

MacromoleculeName: water / type: ligand / ID: 10 / Number of copies: 9 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.88 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
0.02 MC8H18N2O4SHEPES
0.15 MNaClsodium chloride
0.001 MMnCl2manganese chloride
2e-05 MCaCl2calcium chloride
GridModel: UltrAuFoil R0./1 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 180 sec. / Details: 25 mA current
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: 0.02 % w/v CHAPS added to sample just before vitrification.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 43930
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9t3y:
Cryo-EM structure of alphaM/beta2:C3d-anti-CR3-Nb headpiece complex (HPO2 3D class reconstruction)

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