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- EMDB-17270: Rat alpha5beta1 integrin, leg piece -

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Basic information

Entry
Database: EMDB / ID: EMD-17270
TitleRat alpha5beta1 integrin, leg piece
Map dataLocal filtered and sharpened map
Sample
  • Complex: Alpha5beta1 integrin from Rattus norvegicus
    • Protein or peptide: Alpha5beta1 integrin, leg piece
Keywordsintegrin / glycoprotein / membrane protein / CELL ADHESION
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 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: Nat Commun / Year: 2025
Title: Spatial N-glycan rearrangement on αβ integrin nucleates galectin-3 oligomers to determine endocytic fate.
Authors: Massiullah Shafaq-Zadah / Estelle Dransart / Ilyes Hamitouche / Christian Wunder / Valérie Chambon / Cesar A Valades-Cruz / Ludovic Leconte / Nirod Kumar Sarangi / Jack Robinson / Siau-Kun ...Authors: Massiullah Shafaq-Zadah / Estelle Dransart / Ilyes Hamitouche / Christian Wunder / Valérie Chambon / Cesar A Valades-Cruz / Ludovic Leconte / Nirod Kumar Sarangi / Jack Robinson / Siau-Kun Bai / Raju Regmi / Aurélie Di Cicco / Agnès Hovasse / Richard Bartels / Ulf J Nilsson / Sarah Cianférani-Sanglier / Hakon Leffler / Tia E Keyes / Daniel Lévy / Stefan Raunser / Daniel Roderer / Ludger Johannes /
Abstract: Membrane glycoproteins frequently adopt different conformations when altering between active and inactive states. Here, we discover a molecular switch that exploits dynamic spatial rearrangements of ...Membrane glycoproteins frequently adopt different conformations when altering between active and inactive states. Here, we discover a molecular switch that exploits dynamic spatial rearrangements of N-glycans during such conformational transitions to control protein function. For the conformationally switchable cell adhesion glycoprotein αβ integrin, we find that only the bent-closed state arranges N-glycans to nucleate the formation of up to tetrameric oligomers of the glycan-binding protein galectin-3. We propose a structural model of how these galectin-3 oligomers are built and how they clamp the bent-closed state to select it for endocytic uptake and subsequent retrograde trafficking to the Golgi for polarized distribution in cells. Our findings reveal the dynamic regulation of the glycan landscape at the cell surface to achieve oligomerization of galectin-3. Galectin-3 oligomers are thereby identified as functional decoders of defined spatial patterns of N-glycans on specifically the bent-closed conformational state of αβ integrin and possibly other integrin family members.
History
DepositionMay 3, 2023-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateNov 26, 2025-
Current statusNov 26, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17270.png

Downloads & links

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Map

FileDownload / File: emd_17270.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocal filtered and sharpened map
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: 0.3
Minimum - Maximum-1.6506306 - 1.9330271
Average (Standard dev.)0.001334773 (±0.026375715)
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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Additional map: Map before signal subtraction

Fileemd_17270_additional_1.map
AnnotationMap before signal subtraction
Projections & Slices
AxesZYX

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Half map: Half map A, Cryosparc local refinement

Fileemd_17270_half_map_1.map
AnnotationHalf map A, Cryosparc local refinement
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B, Cryosparc local refinement

Fileemd_17270_half_map_2.map
AnnotationHalf map B, Cryosparc local refinement
Projections & Slices
AxesZYX

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Slices (1/2)
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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: Alpha5beta1 integrin, leg piece

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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: all / Details: Purified from rat liver and desialated
Source (natural)Organism: Rattus norvegicus (Norway rat) / Organ: Liver

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Macromolecule #1: Alpha5beta1 integrin, leg piece

MacromoleculeName: Alpha5beta1 integrin, leg piece / type: protein_or_peptide / ID: 1 / Details: heterodimer of alpha5beta1 integrin, leg piece / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat) / Organ: Liver
SequenceString: LDCGEDNICV PDLQLAVYGE KKHVYLGDKN ALNLTFLAQN LGEGGAYEAE LRVTAPLEAE YSGLVRHPGN FSSLSCDYFA VNQSRQLVCD LGNPMKAGTS IWGGLRFTVP HLQDTKKTIQ FDFQILSKNL NNSQSNMVSF PLSVEAQAQV SLNGVSKPEA VIFPVSDWNP ...String:
LDCGEDNICV PDLQLAVYGE KKHVYLGDKN ALNLTFLAQN LGEGGAYEAE LRVTAPLEAE YSGLVRHPGN FSSLSCDYFA VNQSRQLVCD LGNPMKAGTS IWGGLRFTVP HLQDTKKTIQ FDFQILSKNL NNSQSNMVSF PLSVEAQAQV SLNGVSKPEA VIFPVSDWNP QDQPQKEGDL GPAVHHVYEL INQGPSSISQ GVLEISCPQA LEGQQLLYVT KVTGLNNCTS NYTPNSQGLE LDPEVSPHHL QRREAPGRSS TTSGTQVLKC PEAKCFRLRC EFGPLHRQES RSLQLHFRVW AKTFLQQEYQ PFSLQCEALY EALKMPYQIL PRQLPQKKLQ VATAVQWTKA TDEVNSEDM DAYCRKENSS EICSNNGECV CGQCVCRKRE NTNEIYSGKF CECDNFNCDR SNGLICGGNG VCRCRVCECY PNYTGSACDC SLDTVPCVAT NGQICNGRGI CECGACKCTD PKFQGPTCET CQTCLGVCAE HKECVQCRAF NKGEKKDTCA QECSHFNLTK VESREKLPQP VQVDPVTHCK EKDIDDCWFY FTYSVNSKGE AHVHVVE

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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
CTF correctionSoftware - Name: cryoSPARC (ver. 3.3) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: Initial model generated in CryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.03) / Details: Local refinement after signal subtraction / Number images used: 277162
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: RIGID BODY FIT

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