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- EMDB-12637: Cryo-EM structure of human integrin alpha5beta1 in the half-bent ... -

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Basic information

Entry
Database: EMDB / ID: EMD-12637
TitleCryo-EM structure of human integrin alpha5beta1 in the half-bent conformation
Map data
Sample
  • Complex: Dimeric complex of integrin a5b1
    • Protein or peptide: Integrin alpha-5
    • Protein or peptide: Integrin beta-1
  • Ligand: CALCIUM ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: MAGNESIUM ION
Function / homology
Function and homology information


integrin alpha8-beta1 complex / integrin alpha3-beta1 complex / integrin alpha5-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 / regulation of inward rectifier potassium channel activity / regulation of collagen catabolic process ...integrin alpha8-beta1 complex / integrin alpha3-beta1 complex / integrin alpha5-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 / regulation of inward rectifier potassium channel activity / regulation of collagen catabolic process / integrin alpha9-beta1 complex / integrin alpha4-beta1 complex / cell-cell adhesion mediated by integrin / C-X3-C chemokine binding / cardiac cell fate specification / integrin binding involved in cell-matrix adhesion / integrin alpha1-beta1 complex / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / regulation of synapse pruning / reactive gliosis / formation of radial glial scaffolds / cerebellar climbing fiber to Purkinje cell synapse / Other semaphorin interactions / Formation of the ureteric bud / CD40 signaling pathway / positive regulation of vascular endothelial growth factor signaling pathway / calcium-independent cell-matrix adhesion / integrin alphav-beta1 complex / positive regulation of fibroblast growth factor receptor signaling pathway / Fibronectin matrix formation / basement membrane organization / myelin sheath abaxonal region / alphav-beta3 integrin-vitronectin complex / CHL1 interactions / cardiac muscle cell myoblast differentiation / Laminin interactions / RUNX2 regulates genes involved in cell migration / MET interacts with TNS proteins / germ cell migration / leukocyte tethering or rolling / cardiac muscle cell differentiation / cell projection organization / Platelet Adhesion to exposed collagen / vascular endothelial growth factor receptor 2 binding / myoblast fusion / Elastic fibre formation / mesodermal cell differentiation / cell-substrate junction assembly / platelet-derived growth factor receptor binding / axon extension / positive regulation of fibroblast migration / positive regulation of vascular endothelial growth factor receptor signaling pathway / cell migration involved in sprouting angiogenesis / wound healing, spreading of epidermal cells / regulation of spontaneous synaptic transmission / heterotypic cell-cell adhesion / myoblast differentiation / integrin complex / positive regulation of cell-substrate adhesion / dendrite morphogenesis / Basigin interactions / Molecules associated with elastic fibres / muscle organ development / negative regulation of Rho protein signal transduction / lamellipodium assembly / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / MET activates PTK2 signaling / cell adhesion mediated by integrin / negative regulation of vasoconstriction / leukocyte cell-cell adhesion / Syndecan interactions / epidermal growth factor receptor binding / positive regulation of wound healing / maintenance of blood-brain barrier / sarcomere organization / positive regulation of neuroblast proliferation / cell-substrate adhesion / positive regulation of sprouting angiogenesis / endodermal cell differentiation / TGF-beta receptor signaling activates SMADs / homophilic cell adhesion via plasma membrane adhesion molecules / establishment of mitotic spindle orientation / glial cell projection / cleavage furrow / fibronectin binding / cellular response to low-density lipoprotein particle stimulus / negative regulation of anoikis / intercalated disc / RHOG GTPase cycle / negative regulation of neuron differentiation / ECM proteoglycans / neuroblast proliferation / RAC2 GTPase cycle / RAC3 GTPase cycle / Integrin cell surface interactions / cellular defense response / coreceptor activity / phagocytosis
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 alpha Ig-like domain 3 / Integrin beta tail domain / 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 alpha Ig-like domain 3 / Integrin beta tail domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain cysteine-rich domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / EGF-like domain, extracellular / EGF-like domain / Integrin alpha-2 / Integrin alpha Ig-like domain 1 / : / Integrin alpha Ig-like domain 2 / Integrin alpha chain / Integrin alpha beta-propellor / Integrin alpha chain, C-terminal cytoplasmic region, conserved site / Integrins alpha chain signature. / FG-GAP repeat profile. / Integrin alpha (beta-propellor repeats). / FG-GAP repeat / FG-GAP repeat / Integrin alpha, N-terminal / 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
Integrin beta-1 / Integrin alpha-5
Similarity search - Component
Biological speciesHomo sapiens (human) / Human (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsSchumacher S / Dedden D / Vazquez Nunez R / Matoba K / Takagi J / Biertumpfel C / Mizuno N
Funding support Germany, European Union, United States, 6 items
OrganizationGrant numberCountry
Max Planck Society Germany
Other privateBoehringer Ingelheim Foundation Plus 3 Program Germany
European Research Council (ERC)ERC-CoG 724209European Union
European Molecular Biology Organization (EMBO)Young Investigator ProgramEuropean Union
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) United States
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS) United States
CitationJournal: Sci Adv / Year: 2021
Title: Structural insights into integrin αβ opening by fibronectin ligand.
Authors: Stephanie Schumacher / Dirk Dedden / Roberto Vazquez Nunez / Kyoko Matoba / Junichi Takagi / Christian Biertümpfel / Naoko Mizuno /
Abstract: Integrin αβ is a major fibronectin receptor critical for cell migration. Upon complex formation, fibronectin and αβ undergo conformational changes. While this is key for cell-tissue connections, ...Integrin αβ is a major fibronectin receptor critical for cell migration. Upon complex formation, fibronectin and αβ undergo conformational changes. While this is key for cell-tissue connections, its mechanism is unknown. Here, we report cryo-electron microscopy structures of native human αβ with fibronectin to 3.1-angstrom resolution, and in its resting state to 4.6-angstrom resolution. The αβ-fibronectin complex revealed simultaneous interactions at the arginine-glycine-aspartate loop, the synergy site, and a newly identified binding site proximal to adjacent to metal ion-dependent adhesion site, inducing the translocation of helix α1 to secure integrin opening. Resting αβ adopts an incompletely bent conformation, challenging the model of integrin sharp bending inhibiting ligand binding. Our biochemical and structural analyses showed that affinity of αβ for fibronectin is increased with manganese ions (Mn) while adopting the half-bent conformation, indicating that ligand-binding affinity does not depend on conformation, and αβ opening is induced by ligand-binding.
History
DepositionMar 18, 2021-
Header (metadata) releaseAug 25, 2021-
Map releaseAug 25, 2021-
UpdateAug 25, 2021-
Current statusAug 25, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0115
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0115
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7nxd
  • Surface level: 0.0115
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12637.png

Downloads & links

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Map

FileDownload / File: emd_12637.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.85 Å
Density
Contour LevelBy AUTHOR: 0.0115 / Movie #1: 0.0115
Minimum - Maximum-0.01388735 - 0.035758696
Average (Standard dev.)0.0002291981 (±0.0016280232)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.850.850.85
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z272.000272.000272.000
α/β/γ90.00090.00090.000
start NX/NY/NZ383838
NX/NY/NZ225225225
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0140.0360.000

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Supplemental data

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Mask #1

Fileemd_12637_msk_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Additional map: focused EM map headpiece

Fileemd_12637_additional_1.map
Annotationfocused EM map headpiece
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: focused EM map legs

Fileemd_12637_additional_2.map
Annotationfocused EM map legs
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_12637_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_12637_half_map_2.map
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Sample components

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Entire : Dimeric complex of integrin a5b1

EntireName: Dimeric complex of integrin a5b1
Components
  • Complex: Dimeric complex of integrin a5b1
    • Protein or peptide: Integrin alpha-5
    • Protein or peptide: Integrin beta-1
  • Ligand: CALCIUM ION
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Dimeric complex of integrin a5b1

SupramoleculeName: Dimeric complex of integrin a5b1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 200 KDa

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Macromolecule #1: Integrin alpha-5

MacromoleculeName: Integrin alpha-5 / type: protein_or_peptide / ID: 1 / Details: Sequence used from GenBank entry CAA30790 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human) / Tissue: placenta
Molecular weightTheoretical: 110.111555 KDa
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 HVYLGDKNAL NLTFHAQ NV GEGGAYEAEL RVTAPPEAEY SGLVRHPGNF SSLSCDYFAV NQSRLLVCDL GNPMKAGASL WGGLRFTVPH LRDTKKTI Q FDFQILSKNL NNSQSDVVSF RLSVEAQAQV TLNGVSKPEA VLFPVSDWHP RDQPQKEEDL GPAVHHVYEL INQGPSSIS QGVLELSCPQ ALEGQQLLYV TRVTGLNCTT NHPINPKGLE LDPEGSLHHQ QKREAPSRSS ASSGPQILKC PEAECFRLRC ELGPLHQQE SQSLQLHFRV WAKTFLQREH QPFSLQCEAV YKALKMPYRI LPRQLPQKER QVATAVQWTK AEGSYGVPLW I IILAILFG LLLLGLLIYI LYKLGFFKRS LPYGTAMEKA QLKPPATSDA

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Macromolecule #2: Integrin beta-1

MacromoleculeName: Integrin beta-1 / type: protein_or_peptide / ID: 2 / Details: Sequence used from GenBank entry CAA30790 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human (human) / Tissue: placenta
Molecular weightTheoretical: 86.338594 KDa
SequenceString: QTDENRCLKA NAKSCGECIQ AGPNCGWCTN STFLQEGMPT SARCDDLEAL KKKGCPPDDI ENPRGSKDIK KNKNVTNRSK GTAEKLKPE DIHQIQPQQL VLRLRSGEPQ TFTLKFKRAE DYPIDLYYLM DLSYSMKDDL ENVKSLGTDL MNEMRRITSD F RIGFGSFV ...String:
QTDENRCLKA NAKSCGECIQ AGPNCGWCTN STFLQEGMPT SARCDDLEAL KKKGCPPDDI ENPRGSKDIK KNKNVTNRSK GTAEKLKPE DIHQIQPQQL VLRLRSGEPQ TFTLKFKRAE DYPIDLYYLM DLSYSMKDDL ENVKSLGTDL MNEMRRITSD F RIGFGSFV EKTVMPYIST TPAKLRNPCT SEQNCTTPFS 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 CQSEGIPESP KCHEGNGTFE CGACRCNEGR VGRHC ECST DEVNSEDMDA YCRKENSSEI CSNNGECVCG QCVCRKRDNT NEIYSGKFCE CDNFNCDRSN GLICGGNGVC KCRVCE CNP NYTGSACDCS LDTSTCEASN GQICNGRGIC ECGVCKCTDP KFQGQTCEMC QTCLGVCAEH KECVQCRAFN KGEKKDT CT QECSYFNITK VESRDKLPQP VQPDPVSHCK EKDVDDCWFY FTYSVNGNNE VMVHVVENPE CPTGPDIIPI VAGVVAGI V LIGLALLLIW KLLMIIHDRR EFAKFEKEKM NAKWDTGENP IYKSAVTTVV NPKYEGK

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Macromolecule #7: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 7 / Number of copies: 7 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #9: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 9 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

Concentration0.15 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMTristris(hydroxymethyl)aminomethane
150.0 mMNaClsodium chloride
1.0 mMMgCl2manganese chloride
1.0 mMCaCl2calcium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: GloQube 20 mA
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsIntegrin a5b1 was assembled into MSPE3D1 nanodiscs that contained bovine brain lipids (Folch fraction I) at a ratio of 1:29:3460, respectively. The assembly mix was incubated with SM-2 BioBeads to remove DDM detergent from solubilized lipids and then purified by size-exclusion chromatography using a Superose 6 3.2/300 column.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #0 - Number grids imaged: 1 / #0 - Number real images: 1829 / #0 - Average exposure time: 7.39 sec. / #0 - Average electron dose: 65.8 e/Å2
#0 - Details: movie: 20 frames/image dose per frame: 3.13 e-/A2
#1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / #1 - Number grids imaged: 1 / #1 - Number real images: 989 / #1 - Average exposure time: 2.5 sec. / #1 - Average electron dose: 82.3 e/Å2
#1 - Details: movie: 50 frames/image dose per frame: 1.65 e-/A2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.62 mm / Nominal defocus max: 3.2 µm / Nominal defocus min: -0.5 µm / Nominal magnification: 105000
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

Image recording ID1
Detailsinitial image processing automatically by FOCUS pipeline: gain normalization, motion correction and dose-weighting in MotionCor2 CTF estimation by GCTF
Particle selectionNumber selected: 496356
Details: 1424 particles were manually picked and used to obtain 2D classes with distinct features as templates for Gautomatch
CTF correctionSoftware - Name: Gctf
Startup modelType of model: OTHER
Details: 30 A-low pass filtered model from previous data analysis: 502 particles were manually picked from 2600 micrographs and used for 2D classification to generate a template for gautomatch, which ...Details: 30 A-low pass filtered model from previous data analysis: 502 particles were manually picked from 2600 micrographs and used for 2D classification to generate a template for gautomatch, which picked 103534 particles. After 2D classification an initial model was obtained in Cryosparc. Further 3D classification and refinement in Relion used 23332 particles yielded a 3D map that was used as a starting model for the high-resolution data set.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 98750
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 8 / Avg.num./class: 30000 / Software - Name: RELION (ver. 3.0) / Details: 255514 particle after initial sorting
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

4wk0

chain_id: A

4wk0

chain_id: B

3vi3

chain_id: A

3vi3

chain_id: B

3fcs

chain_id: A

3fcs

chain_id: B
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7nxd:
Cryo-EM structure of human integrin alpha5beta1 in the half-bent conformation

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