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- EMDB-17269: Rat alpha5beta1 integrin, headpiece -

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Basic information

Entry
Database: EMDB / ID: EMD-17269
TitleRat alpha5beta1 integrin, headpiece
Map dataSharpened map of alpha5beta1 integrin headpiece
Sample
  • Complex: Alpha5beta1 integrin from Rattus norvegicus
    • Protein or peptide: Integrin subunit alpha 5
    • Protein or peptide: Integrin beta-1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsintegrin / glycoprotein / membrane protein / CELL ADHESION
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 / 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 / RAC1 GTPase cycle / integrin alpha9-beta1 complex / regulation of collagen catabolic process / cardiac cell fate specification / integrin binding involved in cell-matrix adhesion / integrin alpha4-beta1 complex / cell-cell adhesion mediated by integrin / integrin alpha1-beta1 complex / hemidesmosome / establishment of Sertoli cell barrier / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / reactive gliosis / formation of radial glial scaffolds / cerebellar climbing fiber to Purkinje cell synapse / response to transforming growth factor beta / Signal transduction by L1 / positive regulation of fibroblast growth factor receptor signaling pathway / CD40 signaling pathway / calcium-independent cell-matrix adhesion / basement membrane organization / regulation of synapse pruning / integrin alphav-beta1 complex / myelin sheath abaxonal region / regulation of postsynaptic neurotransmitter receptor diffusion trapping / cardiac muscle cell myoblast differentiation / maintenance of postsynaptic specialization structure / bicellular tight junction assembly / tissue homeostasis / leukocyte tethering or rolling / cellular response to vitamin D / cardiac muscle cell differentiation / germ cell migration / cell projection organization / regulation of G protein-coupled receptor signaling pathway / glycinergic synapse / myoblast fusion / positive regulation of vascular endothelial growth factor signaling pathway / mesodermal cell differentiation / cell-substrate junction assembly / axon extension / myoblast differentiation / cell migration involved in sprouting angiogenesis / positive regulation of fibroblast migration / positive regulation of cell-substrate adhesion / wound healing, spreading of epidermal cells / integrin complex / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / heterotypic cell-cell adhesion / regulation of spontaneous synaptic transmission / epidermal growth factor receptor binding / lamellipodium assembly / dendrite morphogenesis / sarcomere organization / positive regulation of peptidyl-tyrosine phosphorylation / negative regulation of vasoconstriction / leukocyte cell-cell adhesion / cell adhesion mediated by integrin / positive regulation of wound healing / muscle organ development / response to muscle activity / positive regulation of neuroblast proliferation / negative regulation of Rho protein signal transduction / positive regulation of sprouting angiogenesis / cell-substrate adhesion / endodermal cell differentiation / alpha-actinin binding / positive regulation of endocytosis / establishment of mitotic spindle orientation / fibronectin binding
Similarity search - Function
Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain / : / Integrin alpha Ig-like domain 3 / Integrin beta subunit, tail / Integrin beta tail domain superfamily ...Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / Integrin beta tail domain / : / Integrin alpha Ig-like domain 3 / 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 chain, C-terminal cytoplasmic region, conserved site / : / Integrin alpha Ig-like domain 2 / Integrins alpha chain signature. / 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.
Similarity search - Domain/homology
Integrin subunit alpha 5 / Integrin beta-1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsRoderer D / Dransart E / Shafaq-Zadah M / Bartels R / Johannes L
Funding support France, 1 items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: To Be Published
Title: Dynamic N-glycan rearrangement nucleates galectin-3 oligomers to determine endocytic fate
Authors: Shafaq-Zadah M / Dransart E / Wunder C / Chambon V / Valades-Cruz CA / Leconte L / Sarangi NK / Robinson J / Bai S-K / Regmi R / Di Cicco A / Hovasse A / Bartels R / Nilsson UJ / Cianferani- ...Authors: Shafaq-Zadah M / Dransart E / Wunder C / Chambon V / Valades-Cruz CA / 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
DepositionMay 3, 2023-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateNov 27, 2024-
Current statusNov 27, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17269.png

Downloads & links

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Map

FileDownload / File: emd_17269.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of alpha5beta1 integrin headpiece
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 266.24 Å		0.83 Å/pix.
x 320 pix.
= 266.24 Å		0.83 Å/pix.
x 320 pix.
= 266.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.085
Minimum - Maximum-0.00173627 - 2.05627
Average (Standard dev.)0.0011465721 (±0.024609797)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17269_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Non-sharpened map

Fileemd_17269_additional_1.map
AnnotationNon-sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B, Cryosparc local refinement

Fileemd_17269_half_map_1.map
AnnotationHalf map B, Cryosparc local refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A, Cryosparc local refinement

Fileemd_17269_half_map_2.map
AnnotationHalf map A, Cryosparc local refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Alpha5beta1 integrin from Rattus norvegicus

EntireName: Alpha5beta1 integrin from Rattus norvegicus
Components
  • Complex: Alpha5beta1 integrin from Rattus norvegicus
    • Protein or peptide: Integrin subunit alpha 5
    • Protein or peptide: Integrin beta-1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Alpha5beta1 integrin from Rattus norvegicus

SupramoleculeName: Alpha5beta1 integrin from Rattus norvegicus / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: Purified from rat liver and desialated
Source (natural)Organism: Rattus norvegicus (Norway rat) / Organ: Liver

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Macromolecule #1: Integrin subunit alpha 5

MacromoleculeName: Integrin subunit alpha 5 / type: protein_or_peptide / ID: 1 / Details: headpiece, residues 94 - 691 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat) / Organ: Liver / Tissue: Liver
Molecular weightTheoretical: 119.567656 KDa
SequenceString: MPPRQPTRRP GGGPSRELGK LLPALSHSPL GGLGSGSGSV APGQGRTGAM GSWTPRSPRS PLHAVLLRWG PRRLPPLLPL LLLLWPPPL QVGGFNLDAE APAVLSGPPG SLFGFSVEFY RPGRDGVSVL VGAPKANTSQ PGVLQGGAVY VCPWGTSPIQ C STIQFDSK ...String:
MPPRQPTRRP GGGPSRELGK LLPALSHSPL GGLGSGSGSV APGQGRTGAM GSWTPRSPRS PLHAVLLRWG PRRLPPLLPL LLLLWPPPL QVGGFNLDAE APAVLSGPPG SLFGFSVEFY RPGRDGVSVL VGAPKANTSQ PGVLQGGAVY VCPWGTSPIQ C STIQFDSK GSRILESSLY SEEPVEYKSL QWFGATVRAH GSSILACAPL YSWRTEKDPQ NDPVGTCYLS TENFTRILEY AP CRSDFGS AAGQGYCQGG FSAEFTKTGR VVLGGPGSYF WQGQILSATQ EQISESYYPQ YLINPVQGQL QTRQASSVYD DSY LGYSVA VGEFSGDDTE DFVAGVPKGN LTYGYVTVLN GSDIHSLYNV SGEQMASYFG YAVAATDTNG DGLDDLLVGA PLLM ERTAD GRPQEVGRVY IYLQHPEGIE PTPSLTLTGQ DEFGRFGSSL TPLGDLDQDG YNDVAIGAPF GGEAQQGVVF IFPGG PGGL NTKPSQVLQP LWAAGHTPDF FGSALRGGRD LDGNGYPDLI VGSFGVDKAL VYRGRPIISA SASLTIFPSM FNPEER SCS LEGNPVSCIN LSFCLNASGK HVPNSIGFEV ELQLDWQKQK GGVRRALFLA SKQATLTQTL LIQNGAREDC REMKIYL RN ESEFRDKLSP IHIALNFSLD PKAPMDSHGL RPVLHYQSKS RIEDKAQILL DCGEDNICVP DLQLAVYGEK KHVYLGDK N ALNLTFLAQN LGEGGAYEAE LRVTAPLEAE YSGLVRHPGN FSSLSCDYFA VNQSRQLVCD LGNPMKAGTS IWGGLRFTV PHLQDTKKTI QFDFQILSKN LNNSQSNMVS FPLSVEAQAQ VSLNGVSKPE AVIFPVSDWN PQDQPQKEGD LGPAVHHVYE LINQGPSSI SQGVLEISCP QALEGQQLLY VTKVTGLNNC TSNYTPNSQG LELDPEVSPH HLQRREAPGR SSTTSGTQVL K CPEAKCFR LRCEFGPLHR QESRSLQLHF RVWAKTFLQQ EYQPFSLQCE ALYEALKMPY QILPRQLPQK KLQVATAVQW TK AEGSNGV PLWIIILAIL FGLLLLGLLI YVLYKLGFFK RSLPYGTAME KAQLKPPATS DA

UniProtKB: Integrin subunit alpha 5

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Macromolecule #2: Integrin beta-1

MacromoleculeName: Integrin beta-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat) / Organ: Liver / Tissue: Liver
Molecular weightTheoretical: 88.594602 KDa
SequenceString: MNLQLVFWIG LISLICSVFG QTDKNRCLKA NAKSCGECIQ AGPNCGWCTN TTFLQEGMPT SARCDDLEAL KKKGCHPSDI ENPRGSQTI KKNKNVTNRS KGMAEKLRPE DITQIQPQQL LLKLRSGEPQ KFTLKFKRAE DYPIDLYYLM DLSYSMKDDL E NVKSLGTD ...String:
MNLQLVFWIG LISLICSVFG QTDKNRCLKA NAKSCGECIQ AGPNCGWCTN TTFLQEGMPT SARCDDLEAL KKKGCHPSDI ENPRGSQTI KKNKNVTNRS KGMAEKLRPE DITQIQPQQL LLKLRSGEPQ KFTLKFKRAE DYPIDLYYLM DLSYSMKDDL E NVKSLGTD LMNEMRRITS DFRIGFGSFV EKTVMPYIST TPAKLRNPCT SEQNCTSPFS YKNVLSLTDR GEFFNELVGQ QR ISGNLDS PEGGFDAIMQ VAVCGSLIGW RNVTRLLVFS TDAGFHFAGD GKLGGIVLPN DGQCHLENNV YTMSHYYDYP SAI HLVQKL SENNIQTIFA VTEEFQPVYK ELKNLIPKSA VGTLSGNSSN VIQLIIDAYN SLSSEVILEN SKLPDGVTIN YKSY CKNGV NGTGENGRKC SNISIGDEVQ FEISITANKC PNKESENQLK LNPLGFTEEV EVVLQFICKC NCQSHGIPAS PKCHE GNGT FECGACRCNE GRVGRHCECS TDEVNSEDMD AYCRKENSSE ICSNNGECVC GQCVCRKREN TNEIYSGKFC ECDNFN CDR SNGLICGGNG VCRCRVCECY PNYTGSACDC SLDTVPCVAT NGQICNGRGI CECGACKCTD PKFQGPTCET CQTCLGV CA EHKECVQCRA FNKGEKKDTC AQECSHFNLT KVESREKLPQ PVQVDPVTHC KEKDIDDCWF YFTYSVNSKG EAHVHVVE T PDCPTGPDII PIVAGVVAGI VLIGLALLLI WKLLMIIHDR REFAKFEKEK MNAKWDTGEN PIYKSAVTTV VNPKYEGK

UniProtKB: Integrin beta-1

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 8 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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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

Concentration0.25 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV
DetailsVitrified immeadiately after elution from NiNTA beads

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DetailsPreliminary grid screening was performed manually.
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average electron dose: 42.0 e/Å2
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: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 96000
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: 1444502
Startup modelType of model: NONE / Details: Initial model generated in CryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.03) / Number images used: 101740
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.03)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Modeller / Chain - Initial model type: in silico model / Details: Homology model generated from PDB 7NXD
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 144 / Target criteria: Cross-correlation
Output model

PDB-8oxz:
Rat alpha5beta1 integrin, headpiece

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