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- EMDB-49184: Cryo-EM structure of the alpha5beta1 integrin headpiece with OS29... -

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Basic information

Entry
Database: EMDB / ID: EMD-49184
TitleCryo-EM structure of the alpha5beta1 integrin headpiece with OS2966 Fab
Map datastructure of the alpha5beta1 integrin headpiece with OS2966 Fab
Sample
  • Complex: Human integrin alpha5beta1 headpiece in complex with the Fab fragment of OS2966
    • Protein or peptide: Integrin beta-1
    • Protein or peptide: Human Integrin alpha 5
    • Protein or peptide: IgG heavy chain
    • Protein or peptide: IgG light chain
KeywordsIntegrin antibody / IMMUNE SYSTEM
Function / homology
Function and homology information


integrin alpha8-beta1 complex / 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 ...integrin alpha8-beta1 complex / 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 binding involved in cell-matrix adhesion / integrin alpha4-beta1 complex / cell-cell adhesion mediated by integrin / integrin alpha1-beta1 complex / collagen binding involved in cell-matrix adhesion / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / integrin alpha2-beta1 complex / reactive gliosis / formation of radial glial scaffolds / Other semaphorin interactions / cerebellar climbing fiber to Purkinje cell synapse / Formation of the ureteric bud / myelin sheath abaxonal region / positive regulation of fibroblast growth factor receptor signaling pathway / CD40 signaling pathway / Fibronectin matrix formation / calcium-independent cell-matrix adhesion / regulation of synapse pruning / integrin alphav-beta1 complex / basement membrane organization / CHL1 interactions / cardiac muscle cell myoblast differentiation / MET interacts with TNS proteins / Laminin interactions / leukocyte tethering or rolling / cardiac muscle cell differentiation / germ cell migration / Platelet Adhesion to exposed collagen / cell projection organization / central nervous system neuron differentiation / myoblast fusion / positive regulation of vascular endothelial growth factor signaling pathway / Elastic fibre formation / mesodermal cell differentiation / axon extension / myoblast differentiation / cell migration involved in sprouting angiogenesis / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / integrin complex / wound healing, spreading of epidermal cells / regulation of spontaneous synaptic transmission / heterotypic cell-cell adhesion / positive regulation of fibroblast migration / lamellipodium assembly / sarcomere organization / Molecules associated with elastic fibres / MET activates PTK2 signaling / Basigin interactions / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / negative regulation of vasoconstriction / leukocyte cell-cell adhesion / maintenance of blood-brain barrier / cell adhesion mediated by integrin / muscle organ development / Syndecan interactions / positive regulation of wound healing / dendrite morphogenesis / positive regulation of neuroblast proliferation / negative regulation of Rho protein signal transduction / cell-substrate adhesion / response to muscle activity / homophilic cell adhesion via plasma membrane adhesion molecules / TGF-beta receptor signaling activates SMADs / establishment of mitotic spindle orientation / cleavage furrow / fibronectin binding / negative regulation of anoikis / cellular response to low-density lipoprotein particle stimulus / RHOG GTPase cycle / intercalated disc / glial cell projection / neuroblast proliferation / RAC2 GTPase cycle / negative regulation of neuron differentiation / RAC3 GTPase cycle / ECM proteoglycans / Integrin cell surface interactions / phagocytosis / cellular defense response / coreceptor activity / laminin binding / cell adhesion molecule binding / ruffle / positive regulation of GTPase activity / RAC1 GTPase cycle / extracellular matrix organization / B cell differentiation / protein tyrosine kinase 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 EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail ...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 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 domain superfamily / 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
Biological speciesHEk293 (human) / Homo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.54 Å
AuthorsWang L / Zhang C
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R35GM128641 United States
CitationJournal: To Be Published
Title: ITGB1 regulates triple-negative breast cancer development by modulating the tumor microenvironment
Authors: Song N / Chen S / Wang L / Dang J / Cao X / Singh S / Yang L / Wang J / Rosen ST / Wang Y / Chen CD / Zhang C / Feng M
History
DepositionFeb 11, 2025-
Header (metadata) releaseJul 23, 2025-
Map releaseJul 23, 2025-
UpdateJul 23, 2025-
Current statusJul 23, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49184.png

Downloads & links

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Map

FileDownload / File: emd_49184.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of the alpha5beta1 integrin headpiece with OS2966 Fab
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 416 pix.
= 299.52 Å		0.72 Å/pix.
x 416 pix.
= 299.52 Å		0.72 Å/pix.
x 416 pix.
= 299.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.3256329 - 0.5856905
Average (Standard dev.)-0.000046561272 (±0.007864274)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 299.52002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_49184_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_49184_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 : Human integrin alpha5beta1 headpiece in complex with the Fab frag...

EntireName: Human integrin alpha5beta1 headpiece in complex with the Fab fragment of OS2966
Components
  • Complex: Human integrin alpha5beta1 headpiece in complex with the Fab fragment of OS2966
    • Protein or peptide: Integrin beta-1
    • Protein or peptide: Human Integrin alpha 5
    • Protein or peptide: IgG heavy chain
    • Protein or peptide: IgG light chain

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Supramolecule #1: Human integrin alpha5beta1 headpiece in complex with the Fab frag...

SupramoleculeName: Human integrin alpha5beta1 headpiece in complex with the Fab fragment of OS2966
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: HEk293 (human)

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Macromolecule #1: Integrin beta-1

MacromoleculeName: Integrin beta-1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.586992 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QTDENRCLKA NAKSCGECIQ AGPNCGWCTN STFLQEGMPT SARCDDLEAL KKKGCPPDDI ENPRGSKDIK KNKNVTNRSK GTAEKLKPE DITQIQPQQL VLRLRSGEPQ TFTLKFKRAE DYPIDLYYLM DLSYSMKDDL ENVKSLGTDL MNEMRRITSD F RIGFGSFV ...String:
QTDENRCLKA NAKSCGECIQ AGPNCGWCTN STFLQEGMPT SARCDDLEAL KKKGCPPDDI ENPRGSKDIK KNKNVTNRSK GTAEKLKPE DITQIQPQQL VLRLRSGEPQ TFTLKFKRAE DYPIDLYYLM DLSYSMKDDL ENVKSLGTDL MNEMRRITSD F RIGFGSFV EKTVMPYIST TPAKLRNPCT SEQNCTSPFS YKNVLSLTNK GEVFNELVGK QRISGNLDSP EGGFDAIMQV AV CGSLIGW RNVTRLLVFS TDAGFHFAGD GKLGGIVLPN DGQCHLENNM YTMSHYYDYP SIAHLVQKLS ENNIQTIFAV TEE FQPVYK ELKNLIPKSA VGTLSANSSN VIQLIIDAYN SLSSEVILEN GKLSEGVTIS YKSYCKNGVN GTGENGRKCS NISI GDEVQ FEISITSNKC PKKDSDSFKI RPLGFTEEVE VILQYICECE GGLENLYFQG GKNAQCKKKL QALKKKNAQL KWKLQ ALKK KLAQGGHHHH HHHH

UniProtKB: Integrin beta-1

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Macromolecule #2: Human Integrin alpha 5

MacromoleculeName: Human Integrin alpha 5 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 74.917812 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: FNLDAEAPAV LSGPPGSFFG FSVEFYRPGT DGVSVLVGAP KANTSQPGVL QGGAVYLCPW GASPTQCTPI EFDSKGSRLL ESSLSSSEG EEPVEYKSLQ WFGATVRAHG SSILACAPLY SWRTEKEPLS DPVGTCYLST DNFTRILEYA PCRSDFSWAA G QGYCQGGF ...String:
FNLDAEAPAV LSGPPGSFFG FSVEFYRPGT DGVSVLVGAP KANTSQPGVL QGGAVYLCPW GASPTQCTPI EFDSKGSRLL ESSLSSSEG EEPVEYKSLQ WFGATVRAHG SSILACAPLY SWRTEKEPLS DPVGTCYLST DNFTRILEYA PCRSDFSWAA G QGYCQGGF SAEFTKTGRV VLGGPGSYFW QGQILSATQE QIAESYYPEY LINLVQGQLQ TRQASSIYDD SYLGYSVAVG EF SGDDTED FVAGVPKGNL TYGYVTILNG SDIRSLYNFS GEQMASYFGY AVAATDVNGD GLDDLLVGAP LLMDRTPDGR PQE VGRVYV YLQHPAGIEP TPTLTLTGHD EFGRFGSSLT PLGDLDQDGY NDVAIGAPFG GETQQGVVFV FPGGPGGLGS KPSQ VLQPL WAASHTPDFF GSALRGGRDL DGNGYPDLIV GSFGVDKAVV YRGRPIVSAS ASLTIFPAMF NPEERSCSLE GNPVA CINL SFCLNASGKH VADSIGFTVE LQLDWQKQKG GVRRALFLAS RQATLTQTLL IQNGAREDCR EMKIYLRNES EFRDKL SPI HIALNFSLDP QAPVDSHGLR PALHYQSKSR IEDKAQILLD CGEDNICVPD LQLEVFGEQN GGLENLYFQG GENAQCE KE LQALEKENAQ LEWELQALEK ELAQWSHPQF EKGGGSGGGS GGSAWSHPQF EK

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Macromolecule #3: IgG heavy chain

MacromoleculeName: IgG heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.866797 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLQQSGPE VGRPGSSVKI SCKASGYTFT GYILSWVKQS PGQGLEWIGW VDPEYGSTDS AEKFKKRATL TADISSNTAY IQLSSLTSE DTATYFCTRY YDGYYRRWFA YWGQGTLVTV SSASTKGPSV FPLAPCSRST SESTAALGCL VKDYFPEPVT V SWNSGALT ...String:
EVQLQQSGPE VGRPGSSVKI SCKASGYTFT GYILSWVKQS PGQGLEWIGW VDPEYGSTDS AEKFKKRATL TADISSNTAY IQLSSLTSE DTATYFCTRY YDGYYRRWFA YWGQGTLVTV SSASTKGPSV FPLAPCSRST SESTAALGCL VKDYFPEPVT V SWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TKTYICNVNH KPSNTKVDKK VEPKYGPPCP PC

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Macromolecule #4: IgG light chain

MacromoleculeName: IgG light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.208771 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPAS LSASLGDIVS IECLASEGIS NNLAWHQQKP GKSPQLLIYG AHSLHDGVPS RFSGSGSGTQ YSLKISGMQP EDEGVYYCQ QGYKYPITFG GGTKLELKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQMTQSPAS LSASLGDIVS IECLASEGIS NNLAWHQQKP GKSPQLLIYG AHSLHDGVPS RFSGSGSGTQ YSLKISGMQP EDEGVYYCQ QGYKYPITFG GGTKLELKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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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 R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k 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: 2.0 µm / Nominal defocus min: 1.0 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: PDB ENTRY
PDB model - PDB ID:

3vi3

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.54 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1918745
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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