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- EMDB-54053: Cryo-EM structure of alphaM I-domain:C3d-anti-CR3-Nb complex focu... -

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Basic information

Entry
Database: EMDB / ID: EMD-54053
TitleCryo-EM structure of alphaM I-domain:C3d-anti-CR3-Nb complex focused refinement from the alphaM/beta2:C3d-anti-CR3-Nb headpiece complex
Map dataFocus map
Sample
  • Complex: alphaM I-domain:C3d-anti-CR3-Nb complex
    • Protein or peptide: Isoform 2 of Integrin alpha-M
    • Protein or peptide: C3d-anti-CR3-Nb fusion ligand
  • Ligand: MANGANESE (II) ION
  • Ligand: water
Keywordsphagocytosis / integrin / opsonisation / IMMUNE SYSTEM
Function / homology
Function and homology information


ectodermal cell differentiation / integrin alphaM-beta2 complex / positive regulation of neutrophil degranulation / response to Gram-positive bacterium / response to curcumin / positive regulation of microglial cell mediated cytotoxicity / vertebrate eye-specific patterning / complement component C3b binding / complement-mediated synapse pruning / Toll Like Receptor 4 (TLR4) Cascade ...ectodermal cell differentiation / integrin alphaM-beta2 complex / positive regulation of neutrophil degranulation / response to Gram-positive bacterium / response to curcumin / positive regulation of microglial cell mediated cytotoxicity / vertebrate eye-specific patterning / complement component C3b binding / complement-mediated synapse pruning / Toll Like Receptor 4 (TLR4) Cascade / : / complement receptor mediated signaling pathway / integrin complex / heterotypic cell-cell adhesion / cargo receptor activity / phagocytosis, engulfment / negative regulation of dopamine metabolic process / forebrain development / amyloid-beta clearance / tertiary granule membrane / plasma membrane raft / positive regulation of protein targeting to membrane / Integrin cell surface interactions / response to mechanical stimulus / specific granule membrane / positive regulation of superoxide anion generation / heat shock protein binding / receptor-mediated endocytosis / response to ischemia / cell-matrix adhesion / Cell surface interactions at the vascular wall / response to amphetamine / integrin-mediated signaling pathway / microglial cell activation / cell-cell adhesion / integrin binding / response to estradiol / amyloid-beta binding / signaling receptor activity / Interleukin-4 and Interleukin-13 signaling / cell adhesion / external side of plasma membrane / innate immune response / Neutrophil degranulation / cell surface / : / 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 / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / 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 / 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 / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.94 Å
AuthorsFruergaard MU / Andersen GR
Funding support1 items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: Cryo-EM structure of alphaM I-domain:C3d-anti-CR3-Nb complex focused refinement from the alphaM/beta2:C3d-anti-CR3-Nb headpiece complex
Authors: Fruergaard MU / Andersen GR
History
DepositionJun 18, 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_54053.png

Downloads & links

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Map

FileDownload / File: emd_54053.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFocus map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.29 Å/pix.
x 256 pix.
= 330.24 Å		1.29 Å/pix.
x 256 pix.
= 330.24 Å		1.29 Å/pix.
x 256 pix.
= 330.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.29 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.2954112 - 2.1868095
Average (Standard dev.)0.0014333692 (±0.020059055)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 330.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54053_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_54053_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_54053_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : alphaM I-domain:C3d-anti-CR3-Nb complex

EntireName: alphaM I-domain:C3d-anti-CR3-Nb complex
Components
  • Complex: alphaM I-domain:C3d-anti-CR3-Nb complex
    • Protein or peptide: Isoform 2 of Integrin alpha-M
    • Protein or peptide: C3d-anti-CR3-Nb fusion ligand
  • Ligand: MANGANESE (II) ION
  • Ligand: water

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Supramolecule #1: alphaM I-domain:C3d-anti-CR3-Nb complex

SupramoleculeName: alphaM I-domain:C3d-anti-CR3-Nb complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: alphaM I-domain:C3d-anti-CR3-Nb complex focused refinement from the alphaM/beta2:C3d-anti-CR3-Nb headpiece complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 190 kDa/nm

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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: C3d-anti-CR3-Nb fusion ligand

MacromoleculeName: C3d-anti-CR3-Nb fusion ligand / type: protein_or_peptide / ID: 2 / Details: Fused with a flexible linker to C3d / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 51.073422 KDa
Recombinant expressionOrganism: Lama glama (llama)
SequenceString: MGWSCIILFL VATATGVHQV QLVESGGGLV QAGGSLRLSC TTSGFTFDDY AIGWFRQAPG KEREGVSCIS SSEGKYYSDG GGGSGGGGS GGGGSVDAER LKHLIVTPSG SGEQNMIGMT PTVIAVHYLD ETEQWEKFGL EKRQGALELI KKGYTQQLAF R QPSSAFAA ...String:
MGWSCIILFL VATATGVHQV QLVESGGGLV QAGGSLRLSC TTSGFTFDDY AIGWFRQAPG KEREGVSCIS SSEGKYYSDG GGGSGGGGS GGGGSVDAER LKHLIVTPSG SGEQNMIGMT PTVIAVHYLD ETEQWEKFGL EKRQGALELI KKGYTQQLAF R QPSSAFAA FVKRAPSTWL TAYVVKVFSL AVNLIAIDSQ VLCGAVKWLI LEKQKPDGVF QEDAPVIHQE MIGGLRNNNE KD MALTAFV LISLQEAKDI CEEQVNSLPG SITKAGDFLE ANYMNLQRSY TVAIAGYALA QMGRLKGPLL NKFLTTAKDK NRW EDPGKQ LYNVEATSYA LLALLQLKDF DFVPPVVRWL NEQRYYGGGY GSTQATFMVF QALAQYQKDA PDHKGGGGSG RFTI SSDNA KNTVYLQMNN LKPEDTAVYY CAAEWNNFGR LCMYPDYWGQ GTQVTVSSEN LYFQGHHHHH H

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Macromolecule #4: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 2 / 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 MMnCl2mangenese 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: 3.94 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 184079
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-9rma:
Cryo-EM structure of alphaM I-domain:C3d-anti-CR3-Nb complex focused refinement from the alphaM/beta2:C3d-anti-CR3-Nb headpiece complex

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