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- EMDB-54200: Complex of peptidisc-embedded alpha5beta1 integrin and galectin-3 -

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Basic information

Entry
Database: EMDB / ID: EMD-54200
TitleComplex of peptidisc-embedded alpha5beta1 integrin and galectin-3
Map dataMain map, local filtered
Sample
  • Complex: peptidisc-embedded Alpha5beta1 integrin heterodimer in complex with two Galectin-3
    • Complex: Alpha5beta1 integrin heterodimer
      • Protein or peptide: rat alpha5 integrin
      • Protein or peptide: rat beta1 integrin
    • Complex: Galectin-3
      • Protein or peptide: Galectin-3 (human)
Keywordsintegrin / clathrin-independent endocytosis / galectin / glycoprotein / ENDOCYTOSIS
Function / homology
Function and homology information


synaptic membrane adhesion to extracellular matrix / Elastic fibre formation / Fibronectin matrix formation / Molecules associated with elastic fibres / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / MET interacts with TNS proteins / protein transport within lipid bilayer / response to gonadotropin / Laminin interactions / MET activates PTK2 signaling ...synaptic membrane adhesion to extracellular matrix / Elastic fibre formation / Fibronectin matrix formation / Molecules associated with elastic fibres / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / MET interacts with TNS proteins / protein transport within lipid bilayer / response to gonadotropin / Laminin interactions / MET activates PTK2 signaling / TGF-beta receptor signaling activates SMADs / negative regulation of cell projection organization / Integrin cell surface interactions / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / Syndecan interactions / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / ECM proteoglycans / Basigin interactions / Cell surface interactions at the vascular wall / GPER1 signaling / RAC2 GTPase cycle / RHOG GTPase cycle / RAC1 GTPase cycle / integrin alpha3-beta1 complex / integrin alpha5-beta1 complex / integrin alpha6-beta1 complex / integrin alpha7-beta1 complex / integrin alpha10-beta1 complex / integrin alpha11-beta1 complex / positive regulation of glutamate uptake involved in transmission of nerve impulse / myoblast fate specification / integrin alpha9-beta1 complex / regulation of collagen catabolic process / cardiac cell fate specification / integrin alpha1-beta1 complex / integrin binding involved in cell-matrix adhesion / integrin alpha4-beta1 complex / hemidesmosome / cell-cell adhesion mediated by integrin / establishment of Sertoli cell barrier / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / reactive gliosis / formation of radial glial scaffolds / Signal transduction by L1 / response to transforming growth factor beta / cerebellar climbing fiber to Purkinje cell synapse / myelin sheath abaxonal region / CD40 signaling pathway / calcium-independent cell-matrix adhesion / positive regulation of fibroblast growth factor receptor signaling pathway / regulation of synapse pruning / integrin alphav-beta1 complex / negative regulation of NK T cell activation / basement membrane organization / negative regulation of immunological synapse formation / cardiac muscle cell myoblast differentiation / disaccharide binding / regulation of postsynaptic neurotransmitter receptor diffusion trapping / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / RUNX2 regulates genes involved in differentiation of myeloid cells / maintenance of postsynaptic specialization structure / regulation of T cell apoptotic process / bicellular tight junction assembly / mononuclear cell migration / tissue homeostasis / receptor ligand inhibitor activity / cellular response to vitamin D / cardiac muscle cell differentiation / positive regulation of mononuclear cell migration / germ cell migration / leukocyte tethering or rolling / negative regulation of endocytosis / regulation of G protein-coupled receptor signaling pathway / IgE binding / eosinophil chemotaxis / cell projection organization / myoblast fusion / positive regulation of vascular endothelial growth factor signaling pathway / mesodermal cell differentiation / glycinergic synapse / cell-substrate junction assembly / regulation of extrinsic apoptotic signaling pathway via death domain receptors / myoblast differentiation / axon extension / cell migration involved in sprouting angiogenesis / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / signaling receptor inhibitor activity / positive regulation of cell-substrate adhesion / regulation of spontaneous synaptic transmission / heterophilic cell-cell adhesion / wound healing, spreading of epidermal cells / epidermal growth factor receptor binding / positive regulation of fibroblast migration / integrin complex / lamellipodium assembly / sarcomere organization / heterotypic cell-cell adhesion / negative regulation of vasoconstriction / leukocyte cell-cell adhesion
Similarity search - Function
Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta tail domain / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin alpha Ig-like domain 3 / Integrin EGF domain / Integrin beta subunit, tail ...Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta tail domain / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin alpha Ig-like domain 3 / Integrin EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / EGF-like domain, extracellular / EGF-like domain / 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 / 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 / Galectin-like / Galactoside-binding lectin / Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor A-like domain superfamily / EGF-like domain signature 1. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Integrin subunit alpha 5 / Galectin-3 / Integrin beta-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.9 Å
AuthorsRoderer D / Hamitouche I / Dransart E / Shafaq-Zadah M / Johannes L
Funding support France, 1 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: To Be Published
Title: Spatial N-glycan rearrangement on alpha5beta1 integrin nucleates galectin-3 oligomers to determine endocytic fate
Authors: Shafaq-Zadah M / Dransart E / Hamitouche I / Wunder C / Chambon V / Valades-Cruz C / Leconte L / Sarangi NK / Robinson J / Bai S-K / Regmi R / Di Cicco A / Hovasse A / Bartels R / Nilsson UJ ...Authors: Shafaq-Zadah M / Dransart E / Hamitouche I / Wunder C / Chambon V / Valades-Cruz C / Leconte L / Sarangi NK / Robinson J / Bai S-K / Regmi R / Di Cicco A / Hovasse A / Bartels R / Nilsson UJ / Cianferani-Sanglier S / Leffler H / Keyes TE / Levy D / Raunser S / Roderer D / Johannes L
History
DepositionJun 30, 2025-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54200.png

Downloads & links

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Map

FileDownload / File: emd_54200.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map, local filtered
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 320 pix.
= 339.2 Å		1.06 Å/pix.
x 320 pix.
= 339.2 Å		1.06 Å/pix.
x 320 pix.
= 339.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.031
Minimum - Maximum-0.14041336 - 0.3021151
Average (Standard dev.)0.0004362652 (±0.0072487965)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 339.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_54200_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_54200_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : peptidisc-embedded Alpha5beta1 integrin heterodimer in complex wi...

EntireName: peptidisc-embedded Alpha5beta1 integrin heterodimer in complex with two Galectin-3
Components
  • Complex: peptidisc-embedded Alpha5beta1 integrin heterodimer in complex with two Galectin-3
    • Complex: Alpha5beta1 integrin heterodimer
      • Protein or peptide: rat alpha5 integrin
      • Protein or peptide: rat beta1 integrin
    • Complex: Galectin-3
      • Protein or peptide: Galectin-3 (human)

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Supramolecule #1: peptidisc-embedded Alpha5beta1 integrin heterodimer in complex wi...

SupramoleculeName: peptidisc-embedded Alpha5beta1 integrin heterodimer in complex with two Galectin-3
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Alpha5beta1 integrin heterodimer

SupramoleculeName: Alpha5beta1 integrin heterodimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Supramolecule #3: Galectin-3

SupramoleculeName: Galectin-3 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: rat alpha5 integrin

MacromoleculeName: rat alpha5 integrin / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
SequenceString: FNLDAEAPAV LSGPPG SLF GFSVEFYRPG RDGVSVLVGA PKANTSQPGV LQGGAVYVCP WGTSPIQCST IQFDSKG SR ILESSLYSEE PVEYKSLQWF GATVRAHGSS ILACAPLYSW RTEKDPQNDP VGTCYLST E NFTRILEYAP CRSDFGSAAG QGYCQGGFSA ...String:
FNLDAEAPAV LSGPPG SLF GFSVEFYRPG RDGVSVLVGA PKANTSQPGV LQGGAVYVCP WGTSPIQCST IQFDSKG SR ILESSLYSEE PVEYKSLQWF GATVRAHGSS ILACAPLYSW RTEKDPQNDP VGTCYLST E NFTRILEYAP CRSDFGSAAG QGYCQGGFSA EFTKTGRVVL GGPGSYFWQG QILSATQEQ ISESYYPQYL INPVQGQLQT RQASSVYDDS YLGYSVAVGE FSGDDTEDFV AGVPKGNLTY GYVTVLNGS DIHSLYNVSG EQMASYFGYA VAATDTNGDG LDDLLVGAPL LMERTADGRP Q EVGRVYIY LQHPEGIEPT PSLTLTGQDE FGRFGSSLTP LGDLDQDGYN DVAIGAPFGG EA QQGVVFI FPGGPGGLNT KPSQVLQPLW AAGHTPDFFG SALRGGRDLD GNGYPDLIVG SFG VDKALV YRGRPIISAS ASLTIFPSMF NPEERSCSLE GNPVSCINLS FCLNASGKHV PNSI GFEVE LQLDWQKQKG GVRRALFLAS KQATLTQTLL IQNGAREDCR EMKIYLRNES EFRDK LSPI HIALNFSLDP KAPMDSHGLR PVLHYQSKSR IEDKAQILLD CGEDNICVPD LQLAVY GEK KHVYLGDKNA LNLTFLAQNL GEGGAYEAEL RVTAPLEAEY SGLVRHPGNF SSLSCDY FA VNQSRQLVCD LGNPMKAGTS IWGGLRFTVP HLQDTKKTIQ FDFQILSKNL NNSQSNMV S FPLSVEAQAQ VSLNGVSKPE AVIFPVSDWN PQDQPQKEGD LGPAVHHVYE LINQGPSSI SQGVLEISCP QALEGQQLLY VTKVTGLNNC TSNYTPNSQG LELDPEVSPH HLQRREAPGR SSTTSGTQV LKCPEAKCFR LRCEFGPLHR QESRSLQLHF RVWAKTFLQE YQPFSLQCEA L YEALKMPY QILPRQLPQK KLQVATAVQW TKAEGSNGVP LWIIILAILF GLLLLGLLIY VL YKLGFFK PNPPLSSNPP NLFKLCC

UniProtKB: Integrin subunit alpha 5

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Macromolecule #2: rat beta1 integrin

MacromoleculeName: rat beta1 integrin / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
SequenceString: QTDKNRCLKA NAKSCGECIQ AGPNCGWCTN TTFLQEGMPT SARCDDLEA LKKKGCHPSD IENPRGSQTI KKNKNVTNRS KGMAEKLRPE DITQIQPQQL L LKLRSGEP QKFTLKFKRA EDYPIDLYYL MDLSYSMKDD LENVKSLGTD LMNEMRRITS DF RIGFGSF ...String:
QTDKNRCLKA NAKSCGECIQ AGPNCGWCTN TTFLQEGMPT SARCDDLEA LKKKGCHPSD IENPRGSQTI KKNKNVTNRS KGMAEKLRPE DITQIQPQQL L LKLRSGEP QKFTLKFKRA EDYPIDLYYL MDLSYSMKDD LENVKSLGTD LMNEMRRITS DF RIGFGSF VEKTVMPYIS TTPAKLRNPC TSEQNCTSPF SYKNVLSLTD RGEFFNELVG QQR ISGNLD SPEGGFDAIM QVAVCGSLIG WRNVTRLLVF STDAGFHFAG DGKLGGIVLP NDGQ CHLEN NVYTMSHYYD YPSIAHLVQK LSENNIQTIF AVTEEFQPVY KELKNLIPKS AVGTL SGNS SNVIQLIIDA YNSLSSEVIL ENSKLPDGVT INYKSYCKNG VNGTGENGRK CSNISI GDE VQFEISITAN KCPNKESENQ LKLNPLGFTE EVEVVLQFIC KCNCQSHGIP ASPKCHE GN GTFECGACRC NEGRVGRHCE CSTDEVNSED MDAYCRKENS SEICSNNGEC VCGQCVCR K RENTNEIYSG KFCECDNFNC DRSNGLICGG NGVCRCRVCE CYPNYTGSAC DCSLDTVPC VATNGQICNG RGICECGACK CTDPKFQGPT CETCQTCLGV CAEHKECVQC RAFNKGEKKD TCAQECSHF NLTKVESREK LPQPVQVDPV THCKEKDIDD CWFYFTYSVN SKGEAHVHVV E TPDCPTGP DIIPIVAGVV AGIVLIGLAL LLIWKLLMII HDRREFAKFE KEKMNAKWDT GE NPIYKSA VTTVVNPKYE GK

UniProtKB: Integrin beta-1

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Macromolecule #3: Galectin-3 (human)

MacromoleculeName: Galectin-3 (human) / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MADNFSLHDA LSGSGNPNPQ GWPGAWGNQP AGAGGYPGAS YPGAYPGQAP PGAYPGQAPP GAYPGAPGA YPGAPAPGVY PGPPSGPGAY PSSGQPSATG AYPATGPYGA PAGPLIVPYN L PLPGGVVP RMLITILGTV KPNANRIALD FQRGNDVAFH FNPRFNENNR ...String:
MADNFSLHDA LSGSGNPNPQ GWPGAWGNQP AGAGGYPGAS YPGAYPGQAP PGAYPGQAPP GAYPGAPGA YPGAPAPGVY PGPPSGPGAY PSSGQPSATG AYPATGPYGA PAGPLIVPYN L PLPGGVVP RMLITILGTV KPNANRIALD FQRGNDVAFH FNPRFNENNR RVIVCNTKLD NN WGREERQ SVFPFESGKP FKIQVLVEPD HFKVAVNDAH LLQYNHRVKK LNEISKLGIS GDI DLTSAS YTMI

UniProtKB: Galectin-3

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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: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 285 K / Instrument: FEI VITROBOT MARK IV / Details: blot force -1, blotting time 3.5 sec.
DetailsPeptidisc-embedded protein complex. Vitrification immediately after elution from NiNTA beads to minimize dissociation.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsSpherical aberration corrector: No Cs corrector / Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 16353 / Average exposure time: 3.0 sec. / Average electron dose: 61.0 e/Å2
Details: Two data sets with 6028 and 10325 images recorded under identical conditions
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
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

Particle selectionNumber selected: 5222335
Details: template-based picking after initial blob picking in CryoSPARC
CTF correctionSoftware - Name: cryoSPARC (ver. 4.0.3) / Software - details: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0.3) / Number images used: 111869
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0.3)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.0.3)
FSC plot (resolution estimation)

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Atomic model buiding 1

DetailsModels were rigid-body fitted using UCSF Chimera and ChimeraX
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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