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- PDB-7usl: Integrin alphaM/beta2 ectodomain in complex with adenylate cyclas... -

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Basic information

Entry
Database: PDB / ID: 7usl
TitleIntegrin alphaM/beta2 ectodomain in complex with adenylate cyclase toxin RTX751 and M1F5 Fab
Components
  • Bifunctional hemolysin-adenylate cyclase
  • Integrin alpha-M
  • Integrin beta
  • M1F5 fab heavy chain
  • M1F5 fab light chain
KeywordsTOXIN / Receptor / Complex / Integrin
Function / homology
Function and homology information


ectodermal cell differentiation / positive regulation of neutrophil degranulation / cellular extravasation / integrin alphaM-beta2 complex / response to Gram-positive bacterium / hemolysis in another organism / response to curcumin / positive regulation of microglial cell mediated cytotoxicity / vertebrate eye-specific patterning / : ...ectodermal cell differentiation / positive regulation of neutrophil degranulation / cellular extravasation / integrin alphaM-beta2 complex / response to Gram-positive bacterium / hemolysis in another organism / 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 / leukocyte migration involved in inflammatory response / complement receptor mediated signaling pathway / cAMP biosynthetic process / cargo receptor activity / integrin complex / heterotypic cell-cell adhesion / leukocyte cell-cell adhesion / phagocytosis, engulfment / cell adhesion mediated by integrin / negative regulation of dopamine metabolic process / forebrain development / amyloid-beta clearance / tertiary granule membrane / plasma membrane raft / positive regulation of protein targeting to membrane / phagocytosis / Integrin cell surface interactions / response to mechanical stimulus / endothelial cell migration / specific granule membrane / positive regulation of superoxide anion generation / cell adhesion molecule binding / heat shock protein binding / receptor-mediated endocytosis / response to ischemia / cell-matrix adhesion / integrin-mediated signaling pathway / Cell surface interactions at the vascular wall / microglial cell activation / cell-cell adhesion / integrin binding / positive regulation of angiogenesis / positive regulation of nitric oxide biosynthetic process / response to estradiol / amyloid-beta binding / channel activity / toxin activity / Interleukin-4 and Interleukin-13 signaling / calmodulin binding / cell adhesion / lyase activity / membrane raft / innate immune response / external side of plasma membrane / calcium ion binding / Neutrophil degranulation / protein-containing complex binding / host cell plasma membrane / cell surface / extracellular space / extracellular exosome / extracellular region / ATP binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
RTX, pore-forming domain / N-terminal domain in RTX protein / RTX toxin determinant A / Haemolysin-type calcium binding-related / Haemolysin-type calcium binding protein related domain / Integrin beta-2 subunit / : / : / Integrin alpha-X-like, Ig-like domain 3 / Hemolysin-type calcium-binding conserved site ...RTX, pore-forming domain / N-terminal domain in RTX protein / RTX toxin determinant A / Haemolysin-type calcium binding-related / Haemolysin-type calcium binding protein related domain / Integrin beta-2 subunit / : / : / Integrin alpha-X-like, Ig-like domain 3 / Hemolysin-type calcium-binding conserved site / Hemolysin-type calcium-binding region signature. / RTX calcium-binding nonapeptide repeat / RTX calcium-binding nonapeptide repeat (4 copies) / Serralysin-like metalloprotease, C-terminal / Integrin beta tail domain / Integrin beta subunit, cytoplasmic 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 alpha, N-terminal / Integrin domain superfamily / 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 / von Willebrand factor A-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Integrin beta / Bifunctional hemolysin/adenylate cyclase / Integrin alpha-M
Similarity search - Component
Biological speciesHomo sapiens (human)
Bordetella pertussis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsGoldsmith, J.A. / McLellan, J.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI155453 United States
CitationJournal: Cell Rep / Year: 2022
Title: Structural basis for non-canonical integrin engagement by Bordetella adenylate cyclase toxin.
Authors: Jory A Goldsmith / Andrea M DiVenere / Jennifer A Maynard / Jason S McLellan /
Abstract: Integrins are ubiquitous cell-surface heterodimers that are exploited by pathogens and toxins, including leukotoxins that target β integrins on phagocytes. The Bordetella adenylate cyclase toxin ...Integrins are ubiquitous cell-surface heterodimers that are exploited by pathogens and toxins, including leukotoxins that target β integrins on phagocytes. The Bordetella adenylate cyclase toxin (ACT) uses the αβ integrin as a receptor, but the structural basis for integrin binding and neutralization by antibodies is poorly understood. Here, we use cryoelectron microscopy to determine a 2.7 Å resolution structure of an ACT fragment bound to αβ. This structure reveals that ACT interacts with the headpiece and calf-2 of the α subunit in a non-canonical manner specific to bent, inactive αβ. Neutralizing antibody epitopes map to ACT residues involved in α binding, providing the basis for antibody-mediated attachment inhibition. Furthermore, binding to αβ positions the essential ACT acylation sites, which are conserved among toxins exported by type I secretion systems, at the cell membrane. These findings reveal a structural mechanism for integrin-mediated attachment and explain antibody-mediated neutralization of ACT intoxication.
History
DepositionApr 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation
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.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrin alpha-M
B: Integrin beta
C: Bifunctional hemolysin-adenylate cyclase
H: M1F5 fab heavy chain
L: M1F5 fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)362,30451
Polymers357,5535
Non-polymers4,75146
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: immunoprecipitation
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 3 types, 3 molecules ABC

#1: 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: 128455.289 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


Mass: 80784.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB2 / Production host: Homo sapiens (human) / References: UniProt: A0A494C0X7
#3: Protein Bifunctional hemolysin-adenylate cyclase


Mass: 100286.688 Da / Num. of mol.: 1 / Fragment: C-terminal fragment RTX751, residues 270-1225
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella pertussis (bacteria) / Gene: cyaA / Production host: Escherichia coli (E. coli) / References: UniProt: A5JW88

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Antibody , 2 types, 2 molecules HL

#4: Antibody M1F5 fab heavy chain


Mass: 24665.729 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Antibody M1F5 fab light chain


Mass: 23360.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 3 types, 13 molecules

#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.: 1
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
#7: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}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.: 11 / 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 , 1 types, 33 molecules

#8: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: Ca

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Details

Has ligand of interestN
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

ComponentName: Ternary complex of integrin alphaM/beta2 ectodomain with adenylate cyclase toxin RTX domain and M1F5 Fab
Type: COMPLEX / Entity ID: #1-#5 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 80 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

Software
NameVersionClassification
phenix.real_space_refine1.19.1_4122+SVNrefinement
PHENIX1.19.1_4122+SVNrefinement
CTF correctionType: NONE
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 347508 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 57.74 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003319369
ELECTRON MICROSCOPYf_angle_d0.582526229
ELECTRON MICROSCOPYf_chiral_restr0.0452937
ELECTRON MICROSCOPYf_plane_restr0.0043481
ELECTRON MICROSCOPYf_dihedral_angle_d5.08132758

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