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- EMDB-35465: Cryo-EM structure of Integrin AVB3 -

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Basic information

Entry
Database: EMDB / ID: EMD-35465
TitleCryo-EM structure of Integrin AVB3
Map data
Sample
  • Complex: Cryo-EM structure of integrin AVB3
    • Protein or peptide: Integrin beta-3
    • Protein or peptide: Integrin alpha-V heavy chain
KeywordsIntegrin alphaV beta3 / MEMBRANE PROTEIN
Function / homology
Function and homology information


integrin alphav-beta8 complex / integrin alphav-beta6 complex / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / opsonin binding / integrin alphav-beta1 complex / Cross-presentation of particulate exogenous antigens (phagosomes) / extracellular matrix protein binding / regulation of serotonin uptake ...integrin alphav-beta8 complex / integrin alphav-beta6 complex / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / opsonin binding / integrin alphav-beta1 complex / Cross-presentation of particulate exogenous antigens (phagosomes) / extracellular matrix protein binding / regulation of serotonin uptake / positive regulation of adenylate cyclase-inhibiting opioid receptor signaling pathway / tube development / alpha9-beta1 integrin-ADAM8 complex / regulation of trophoblast cell migration / integrin alphaIIb-beta3 complex / regulation of postsynaptic neurotransmitter receptor diffusion trapping / alphav-beta3 integrin-vitronectin complex / maintenance of postsynaptic specialization structure / regulation of extracellular matrix organization / platelet alpha granule membrane / Laminin interactions / positive regulation of glomerular mesangial cell proliferation / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / alphav-beta3 integrin-PKCalpha complex / entry into host cell by a symbiont-containing vacuole / fibrinogen binding / positive regulation of small GTPase mediated signal transduction / alphav-beta3 integrin-HMGB1 complex / vascular endothelial growth factor receptor 2 binding / negative regulation of lipid transport / regulation of phagocytosis / positive regulation of vascular endothelial growth factor signaling pathway / Elastic fibre formation / cell-substrate junction assembly / alphav-beta3 integrin-IGF-1-IGF1R complex / positive regulation of bone resorption / platelet-derived growth factor receptor binding / transforming growth factor beta binding / mesodermal cell differentiation / glycinergic synapse / extracellular matrix binding / filopodium membrane / regulation of release of sequestered calcium ion into cytosol / positive regulation of vascular endothelial growth factor receptor signaling pathway / positive regulation of cell adhesion mediated by integrin / apolipoprotein A-I-mediated signaling pathway / negative regulation of low-density lipoprotein particle clearance / regulation of bone resorption / angiogenesis involved in wound healing / wound healing, spreading of epidermal cells / apoptotic cell clearance / positive regulation of fibroblast migration / integrin complex / cell adhesion mediated by integrin / smooth muscle cell migration / Molecules associated with elastic fibres / heterotypic cell-cell adhesion / positive regulation of smooth muscle cell migration / negative chemotaxis / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / Syndecan interactions / positive regulation of cell-matrix adhesion / p130Cas linkage to MAPK signaling for integrins / regulation of postsynaptic neurotransmitter receptor internalization / cellular response to insulin-like growth factor stimulus / positive regulation of osteoblast proliferation / protein disulfide isomerase activity / microvillus membrane / cell-substrate adhesion / platelet-derived growth factor receptor signaling pathway / PECAM1 interactions / GRB2:SOS provides linkage to MAPK signaling for Integrins / endodermal cell differentiation / TGF-beta receptor signaling activates SMADs / fibronectin binding / lamellipodium membrane / positive regulation of intracellular signal transduction / negative regulation of macrophage derived foam cell differentiation / negative regulation of lipid storage / blood coagulation, fibrin clot formation / ECM proteoglycans / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / positive regulation of T cell migration / vasculogenesis / specific granule membrane / coreceptor activity / phagocytic vesicle / ERK1 and ERK2 cascade / cellular response to platelet-derived growth factor stimulus / extrinsic apoptotic signaling pathway in absence of ligand / Integrin signaling / positive regulation of endothelial cell proliferation / positive regulation of substrate adhesion-dependent cell spreading / substrate adhesion-dependent cell spreading / embryo implantation / cell adhesion molecule binding / positive regulation of endothelial cell migration / positive regulation of smooth muscle cell proliferation
Similarity search - Function
Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / : / Integrin alpha 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, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / : / Integrin alpha Ig-like domain 3 / Integrin beta subunit, cytoplasmic domain / Integrin beta tail domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin EGF domain / EGF-like domain, extracellular / EGF-like 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 / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2.
Similarity search - Domain/homology
Integrin beta-3 / Integrin alpha-V
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsZhang X / Wu C / Gao Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: cryo-EM Structure of Integrin AVB3
Authors: Xi Z / Cang W / Yuanzhu G
History
DepositionFeb 26, 2023-
Header (metadata) releaseFeb 28, 2024-
Map releaseFeb 28, 2024-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35465.png

Downloads & links

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Map

FileDownload / File: emd_35465.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 320 pix.
= 422.4 Å		1.32 Å/pix.
x 320 pix.
= 422.4 Å		1.32 Å/pix.
x 320 pix.
= 422.4 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.02867533 - 1.7837577
Average (Standard dev.)0.00034089174 (±0.011867563)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_35465_msk_1.map
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AxesZYX

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Half map: #2

Fileemd_35465_half_map_1.map
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Half map: #1

Fileemd_35465_half_map_2.map
Projections & Slices
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Sample components

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Entire : Cryo-EM structure of integrin AVB3

EntireName: Cryo-EM structure of integrin AVB3
Components
  • Complex: Cryo-EM structure of integrin AVB3
    • Protein or peptide: Integrin beta-3
    • Protein or peptide: Integrin alpha-V heavy chain

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Supramolecule #1: Cryo-EM structure of integrin AVB3

SupramoleculeName: Cryo-EM structure of integrin AVB3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Integrin beta-3

MacromoleculeName: Integrin beta-3 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.577367 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: CTTRGVSSCQ QCLAVSPMCA WCSDEALPLG SPRCDLKENL LKDNCAPESI EFPVSEARVL EDRPLSDKGS GDSSQVTQVS PQRIALRLR PDDSKNFSIQ VRQVEDYPVD IYYLMDLSYS MKDDLWSIQN LGTKLATQMR KLTSNLRIGF GAFVDKPVSP Y MYISPPEA ...String:
CTTRGVSSCQ QCLAVSPMCA WCSDEALPLG SPRCDLKENL LKDNCAPESI EFPVSEARVL EDRPLSDKGS GDSSQVTQVS PQRIALRLR PDDSKNFSIQ VRQVEDYPVD IYYLMDLSYS MKDDLWSIQN LGTKLATQMR KLTSNLRIGF GAFVDKPVSP Y MYISPPEA LENPCYDMKT TCLPMFGYKH VLTLTDQVTR FNEEVKKQSV SRNRDAPEGG FDAIMQATVC DEKIGWRNDA SH LLVFTTD AKTHIALDGR LAGIVQPNDG QCHVGSDNHY SASTTMDYPS LGLMTEKLSQ KNINLIFAVT ENVVNLYQNY SEL IPGTTV GVLSMDSSNV LQLIVDAYGK IRSKVELEVR DLPEELSLSF NATCLNNEVI PGLKSCMGLK IGDTVSFSIE AKVR GCPQE KEKSFTIKPV GFKDSLIVQV TFDCDCACQA QAEPNSHRCN NGNGTFECGV CRCGPGWLGS QC

UniProtKB: Integrin beta-3

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Macromolecule #2: Integrin alpha-V heavy chain

MacromoleculeName: Integrin alpha-V heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 65.268188 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: FNLDVDSPAE YSGPEGSYFG FAVDFFVPSA SSRMFLLVGA PKANTTQPGI VEGGQVLKCD WSSTRRCQPI EFDATGNRDY AKDDPLEFK SHQWFGASVR SKQDKILACA PLYHWRTEMK QEREPVGTCF LQDGTKTVEY APCRSQDIDA DGQGFCQGGF S IDFTKADR ...String:
FNLDVDSPAE YSGPEGSYFG FAVDFFVPSA SSRMFLLVGA PKANTTQPGI VEGGQVLKCD WSSTRRCQPI EFDATGNRDY AKDDPLEFK SHQWFGASVR SKQDKILACA PLYHWRTEMK QEREPVGTCF LQDGTKTVEY APCRSQDIDA DGQGFCQGGF S IDFTKADR VLLGGPGSFY WQGQLISDQV AEIVSKYDPN VYSIKYNNQL ATRTAQAIFD DSYLGYSVAV GDFNGDGIDD FV SGVPRAA RTLGMVYIYD GKNMSSLYNF TGEQMAAYFG FSVAATDING DDYADVFIGA PLFMDRGSDG KLQEVGQVSV SLQ RASGDF QTTKLNGFEV FARFGSAIAP LGDLDQDGFN DIAIAAPYGG EDKKGIVYIF NGRSTGLNAV PSQILEGQWA ARSM PPSFG YSMKGATDID KNGYPDLIVG AFGVDRAILY RARPVITVNA GLEVYPSILN QDNKTCSLPG TALKVSCFNV RFCLK ADGK GVLPRKLNFQ VELLLDKLKQ KGAIRRALFL YSRSPSHSKN MTISRGGLMQ CEELIAYLRD ESEFRDKLTP ITIFME YRL DYRTAADTTG LQPILNQFTP ANISRQAHIL

UniProtKB: Integrin alpha-V

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 69506
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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