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- EMDB-55599: Cryo-EM structure of alphaM/beta2:MEM148-Fab headpiece complex (w... -

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Basic information

Entry
Database: EMDB / ID: EMD-55599
TitleCryo-EM structure of alphaM/beta2:MEM148-Fab headpiece complex (without alphaM I-domain)
Map dataConsensus map (no Sharp)
Sample
  • Complex: Headpiece of alphaM/beta2 in complex with MEM148 Fab
    • Protein or peptide: Integrin alpha-M
    • Protein or peptide: Integrin beta-2
    • Protein or peptide: Murine IgG1 MEM148 heavy chain
    • Protein or peptide: Anti-colorectal carcinoma light chain
  • 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 / vertebrate eye-specific patterning / complement component C3b binding / leukocyte migration involved in inflammatory response / : / complement-mediated synapse pruning / Toll Like Receptor 4 (TLR4) Cascade / neutrophil migration / complement receptor mediated signaling pathway / positive regulation of leukocyte adhesion to vascular endothelial cell / integrin complex / cell adhesion mediated by integrin / heterotypic cell-cell adhesion / regulation of peptidyl-tyrosine phosphorylation / cargo receptor activity / phagocytosis, engulfment / leukocyte cell-cell adhesion / negative regulation of dopamine metabolic process / forebrain development / receptor clustering / endodermal cell differentiation / amyloid-beta clearance / tertiary granule membrane / ficolin-1-rich granule membrane / plasma membrane raft / Integrin cell surface interactions / cellular response to low-density lipoprotein particle stimulus / positive regulation of protein targeting to membrane / endothelial cell migration / response to mechanical stimulus / specific granule membrane / positive regulation of superoxide anion generation / heat shock protein binding / neutrophil chemotaxis / cell adhesion molecule binding / receptor-mediated endocytosis / response to ischemia / cell-matrix adhesion / Cell surface interactions at the vascular wall / integrin-mediated signaling pathway / response to amphetamine / microglial cell activation / cell-cell adhesion / receptor internalization / integrin binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of nitric oxide biosynthetic process / positive regulation of angiogenesis / response to estradiol / regulation of cell shape / cell-cell signaling / amyloid-beta binding / extracellular vesicle / signaling receptor activity / Interleukin-4 and Interleukin-13 signaling / cell adhesion / signaling receptor complex / inflammatory response / external side of plasma membrane / innate immune response / focal adhesion / apoptotic process / Neutrophil degranulation / protein kinase binding / cell surface / : / extracellular exosome / membrane / metal ion binding / plasma membrane
Similarity search - Function
Integrin beta-2 subunit / : / Integrin alpha-X-like, Ig-like domain 3 / 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-2 subunit / : / Integrin alpha-X-like, Ig-like domain 3 / 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 / VWFA domain profile. / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / EGF-like domain signature 1. / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2.
Similarity search - Domain/homology
Integrin beta-2 / Integrin alpha-M
Similarity search - Component
Biological speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsLorentzen J / Andersen GR
Funding support1 items
OrganizationGrant numberCountry
Other private
CitationJournal: Sci Adv / Year: 2026
Title: Three cryo-EM structures of complement C3d-bound αβ reveal an unexpected layer of dynamics for αI-containing integrin receptors.
Authors: Josefine Lorentzen / Marlene Uglebjerg Fruergaard / Szilvia Lukácsi / Martin Høgholm Jørgensen / Timo Lambertus Gerardus van Veghel / Rasmus Kjeldsen Jensen / Krzysztof Jakub Pietrzak- ...Authors: Josefine Lorentzen / Marlene Uglebjerg Fruergaard / Szilvia Lukácsi / Martin Høgholm Jørgensen / Timo Lambertus Gerardus van Veghel / Rasmus Kjeldsen Jensen / Krzysztof Jakub Pietrzak-Lichwa / Zsuzsa Bajtay / Václav Hořejší / Rasmus Kock Flygaard / Daan Vorselen / Simon Arnold Mortensen / Gregers Rom Andersen /
Abstract: Integrins are heterodimeric membrane proteins acting as mechanosensing receptors. Nine human α-subunits contain a ligand binding αI domain, but how ligands activate αI integrins are not understood. ...Integrins are heterodimeric membrane proteins acting as mechanosensing receptors. Nine human α-subunits contain a ligand binding αI domain, but how ligands activate αI integrins are not understood. We present cryo-EM structures of the αI integrin αβ in complex with the C3d ligand. The ligand-bound αI domain appears to have two major opposite orientations relative to the β subunit. Ligand binding induces an ordered conformation of the α internal ligand region that is tightly packed between the α β-propeller and the β βI-domain. Recognition of the internal ligand induces an open βI conformation practically identical to that of ligand-bound αI-less integrins confirming that ligand binding and signaling are coupled by a universal mechanism across all integrins. Integration of our findings with prior data allows us to propose a model for C3dg/iC3b-bound αβ in the phagocytotic cup and outline mechanistic models for external ligand-induced activation of αβ.
History
DepositionNov 6, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55599.png

Downloads & links

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Map

FileDownload / File: emd_55599.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConsensus map (no Sharp)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.29 Å/pix.
x 350 pix.
= 452.9 Å		1.29 Å/pix.
x 350 pix.
= 452.9 Å		1.29 Å/pix.
x 350 pix.
= 452.9 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: 0.006
Minimum - Maximum-0.02337944 - 0.061809108
Average (Standard dev.)0.000003898602 (±0.00069897855)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 452.90002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Consensus map (Sharp)

Fileemd_55599_additional_1.map
AnnotationConsensus map (Sharp)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_55599_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_55599_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Headpiece of alphaM/beta2 in complex with MEM148 Fab

EntireName: Headpiece of alphaM/beta2 in complex with MEM148 Fab
Components
  • Complex: Headpiece of alphaM/beta2 in complex with MEM148 Fab
    • Protein or peptide: Integrin alpha-M
    • Protein or peptide: Integrin beta-2
    • Protein or peptide: Murine IgG1 MEM148 heavy chain
    • Protein or peptide: Anti-colorectal carcinoma light chain
  • Ligand: CALCIUM ION
  • Ligand: MANGANESE (II) ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: Headpiece of alphaM/beta2 in complex with MEM148 Fab

SupramoleculeName: Headpiece of alphaM/beta2 in complex with MEM148 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: Headpiece of alphaM/beta2 in complex with MEM148 Fab-fragment from mouse IgG1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 240 kDa/nm

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Macromolecule #1: Integrin alpha-M

MacromoleculeName: Integrin alpha-M / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 83.912836 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 VRELFRITNG 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 PRGR TRWQCDAVLY GEQGQPWGRF GAALTVLGDV NGDKLTDVAI GAPGEEDNRG AVYLFHGTSG SGISPSHSQR IAGSKL SPR LQYFGQSLSG GQDLTMDGLV DLTVGAQGHV LLLRSQPVLR VKAIMEFNPR EVARNVFECN DQVVKGKEAG EVRVCLH VQ KSTRDRLREG QIQSVVTYDL ALDSGRPHSR AVFNETKRST RRQTQVLGLT QTCETLKLQL PNCIEDPVSP IVLRLNFS L VGTPLSAFGN LRPVLAEDAQ RLFTALFPFE KNTGGLEVLF Q

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: 52.217094 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 GKNCEPAALQ TLFQ

UniProtKB: Integrin beta-2

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Macromolecule #3: Murine IgG1 MEM148 heavy chain

MacromoleculeName: Murine IgG1 MEM148 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.865525 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: EVQLQESGPS LVKPSQTLSL TCSVTGDSIT SGYWNWIRKF PYNKLEYMGY ISYSGSTYYN PSLESRVSIT RDTSKNQYYL QLHSVTTED TATYHCARER DYAFDFWGQG TTLTVSSAKT TPPSVYPLAP GSAAQTNSMV TLGCLVKGYF PEPVTVTWNS G SLSSGVHT ...String:
EVQLQESGPS LVKPSQTLSL TCSVTGDSIT SGYWNWIRKF PYNKLEYMGY ISYSGSTYYN PSLESRVSIT RDTSKNQYYL QLHSVTTED TATYHCARER DYAFDFWGQG TTLTVSSAKT TPPSVYPLAP GSAAQTNSMV TLGCLVKGYF PEPVTVTWNS G SLSSGVHT FPAVLQSDLY TLSSSVTVPS SPRPSETVTC NVAHPASSTK VDKKIVPRDC

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Macromolecule #4: Anti-colorectal carcinoma light chain

MacromoleculeName: Anti-colorectal carcinoma light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.936613 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: DIKMTQSPSP MYASLGERVT VTCKASQDIN NYLSWFQQKP GKSPKTLIYR AKRLVDGVPS RFSGSGSGQD YSLTISSLEY EDMGIYYCL QYDEFPLTFG AGTKLELKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS ...String:
DIKMTQSPSP MYASLGERVT VTCKASQDIN NYLSWFQQKP GKSPKTLIYR AKRLVDGVPS RFSGSGSGQD YSLTISSLEY EDMGIYYCL QYDEFPLTFG AGTKLELKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS KDSTYSMSST LTLTKDEYER HNSYTCEATH KTSTSPIVKS FNRNEC

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Macromolecule #8: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 8 / Number of copies: 5 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #9: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 9 / Number of copies: 1 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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Macromolecule #10: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 10 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #11: water

MacromoleculeName: water / type: ligand / ID: 11 / Number of copies: 7 / 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

Concentration0.15 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: 60 sec. / Details: 25 mA current
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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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: 60.0 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: 2.2 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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 188421
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-9t5z:
Cryo-EM structure of alphaM/beta2:MEM148-Fab headpiece complex (without alphaM I-domain)

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