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- EMDB-51029: Complex of nanodisc-embedded alpha5beta1 integrin with Gal3 tetramer -

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Basic information

Entry
Database: EMDB / ID: EMD-51029
TitleComplex of nanodisc-embedded alpha5beta1 integrin with Gal3 tetramer
Map dataMain map of complex of Gal3 tetramer bound to nanodisc-embedded alpha5beta1 integrin, non-sharpened
Sample
  • Complex: Alpha5beta1 integrin heterodimer in complex with four Galectin-3
    • Complex: Alpha5beta1 integrin heterodimer
      • Protein or peptide: alpha5 integrin, Rattus norvegicus
      • Protein or peptide: beta1 integrin, Rattus norvegicus
    • Complex: Galectin-3
      • Protein or peptide: Galectin-3, human
Keywordsintegrin / clathrin-independent endocytosis / galectin / glycoprotein / ENDOCYTOSIS
Biological speciesRattus norvegicus (Norway rat) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.6 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
DepositionJul 14, 2024-
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_51029.png

Downloads & links

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Map

FileDownload / File: emd_51029.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map of complex of Gal3 tetramer bound to nanodisc-embedded alpha5beta1 integrin, non-sharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.65 Å/pix.
x 128 pix.
= 339.2 Å		2.65 Å/pix.
x 128 pix.
= 339.2 Å		2.65 Å/pix.
x 128 pix.
= 339.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.046
Minimum - Maximum-0.2754451 - 0.6668132
Average (Standard dev.)0.0018142709 (±0.02836072)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 339.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51029_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A of complex of Gal3 tetramer...

Fileemd_51029_half_map_1.map
AnnotationHalf map A of complex of Gal3 tetramer bound to nanodisc-embedded alpha5beta1 integrin
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of complex of Gal3 tetramer...

Fileemd_51029_half_map_2.map
AnnotationHalf map B of complex of Gal3 tetramer bound to nanodisc-embedded alpha5beta1 integrin
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 heterodimer in complex with four Galectin-3

EntireName: Alpha5beta1 integrin heterodimer in complex with four Galectin-3
Components
  • Complex: Alpha5beta1 integrin heterodimer in complex with four Galectin-3
    • Complex: Alpha5beta1 integrin heterodimer
      • Protein or peptide: alpha5 integrin, Rattus norvegicus
      • Protein or peptide: beta1 integrin, Rattus norvegicus
    • Complex: Galectin-3
      • Protein or peptide: Galectin-3, human

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Supramolecule #1: Alpha5beta1 integrin heterodimer in complex with four Galectin-3

SupramoleculeName: Alpha5beta1 integrin heterodimer in complex with four 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: alpha5 integrin, Rattus norvegicus

MacromoleculeName: alpha5 integrin, Rattus norvegicus / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
SequenceString: MGSWTPRSPR SPLHAVLLRW GPRRLPPLLP LLLLLWPPPL QVGGFNLDAE APAVLSGPPG SLFGFSVEF YRPGRDGVSV LVGAPKANTS QPGVLQGGAV YVCPWGTSPI QCSTIQFDSK G SRILESSL YSEEPVEYKS LQWFGATVRA HGSSILACAP LYSWRTEKDP ...String:
MGSWTPRSPR SPLHAVLLRW GPRRLPPLLP LLLLLWPPPL QVGGFNLDAE APAVLSGPPG SLFGFSVEF YRPGRDGVSV LVGAPKANTS QPGVLQGGAV YVCPWGTSPI QCSTIQFDSK G SRILESSL YSEEPVEYKS LQWFGATVRA HGSSILACAP LYSWRTEKDP QNDPVGTCYL ST ENFTRIL EYAPCRSDFG SAAGQGYCQG GFSAEFTKTG RVVLGGPGSY FWQGQILSAT QEQ ISESYY PQYLINPVQG QLQTRQASSV YDDSYLGYSV AVGEFSGDDT EDFVAGVPKG NLTY GYVTV LNGSDIHSLY NVSGEQMASY FGYAVAATDT NGDGLDDLLV GAPLLMERTA DGRPQ EVGR VYIYLQHPEG IEPTPSLTLT GQDEFGRFGS SLTPLGDLDQ DGYNDVAIGA PFGGEA QQG VVFIFPGGPG GLNTKPSQVL QPLWAAGHTP DFFGSALRGG RDLDGNGYPD LIVGSFG VD KALVYRGRPI ISASASLTIF PSMFNPEERS CSLEGNPVSC INLSFCLNAS GKHVPNSI G FEVELQLDWQ KQKGGVRRAL FLASKQATLT QTLLIQNGAR EDCREMKIYL RNESEFRDK LSPIHIALNF SLDPKAPMDS HGLRPVLHYQ SKSRIEDKAQ ILLDCGEDNI CVPDLQLAVY GEKKHVYLG DKNALNLTFL AQNLGEGGAY EAELRVTAPL EAEYSGLVRH PGNFSSLSCD Y FAVNQSRQ LVCDLGNPMK AGTSIWGGLR FTVPHLQDTK KTIQFDFQIL SKNLNNSQSN MV SFPLSVE AQAQVSLNGV SKPEAVIFPV SDWNPQDQPQ KEGDLGPAVH HVYELINQGP SSI SQGVLE ISCPQALEGQ QLLYVTKVTG LNNCTSNYTP NSQGLELDPE VSPHHLQRRE APGR SSTTS GTQVLKCPEA KCFRLRCEFG PLHRQESRSL QLHFRVWAKT FLQEYQPFSL QCEAL YEAL KMPYQILPRQ LPQKKLQVAT AVQWTKAEGS NGVPLWIIIL AILFGLLLLG LLIYVL YKL GFFKPNPPLS SNPPNLFKLC C

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Macromolecule #2: beta1 integrin, Rattus norvegicus

MacromoleculeName: beta1 integrin, Rattus norvegicus / 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

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Macromolecule #3: Galectin-3, human

MacromoleculeName: Galectin-3, human / type: protein_or_peptide / ID: 3 / Details: 4 copies in density / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: ADNFSLHDAL SGSGNPNPQG WPGAWGNQPA GAGGYPGASY PGAYPGQAPP GAYPGQAPP GAYPGAPGAY PGAPAPGVYP GPPSGPGAYP SSGQPSATGA YPATGPYGAP AGPLIVPYNL PLPGGVVPR MLITILGTVK PNANRIALDF QRGNDVAFHF NPRFNENNRR ...String:
ADNFSLHDAL SGSGNPNPQG WPGAWGNQPA GAGGYPGASY PGAYPGQAPP GAYPGQAPP GAYPGAPGAY PGAPAPGVYP GPPSGPGAYP SSGQPSATGA YPATGPYGAP AGPLIVPYNL PLPGGVVPR MLITILGTVK PNANRIALDF QRGNDVAFHF NPRFNENNRR VIVCNTKLDN N WGREERQS VFPFESGKPF KIQVLVEPDH FKVAVNDAHL LQYNHRVKKL NEISKLGISG DI DLTSASY TMI

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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

Concentration0.20 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV / Details: blot force 0, blotting time 3.
DetailsNanodisc-embedded protein complex. Vitrification immediately after elution from NiNTA beads to minimize dissociation.

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Electron microscopy

MicroscopeFEI TITAN 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: 22022 / Average exposure time: 1.7 sec. / Average electron dose: 80.0 e/Å2
Details: Three data sets with 7188, 5139 and 9696 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: 2.6 µm / Nominal defocus min: 1.3 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: 6093261
Details: template-based particle picking after initial round of 2D classification
CTF correctionSoftware - Name: cryoSPARC (ver. 4.2.1) / 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: 7.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1)
Details: 3D variability analysis after the last 3D classification
Number images used: 41848
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 4.2.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

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

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