+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41154 | ||||||||||||||||||
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Title | Integrin alpha-v beta-6 in complex with minibinder B6_BP_dslf | ||||||||||||||||||
Map data | Integrin alpha-v beta-6 in complex with minibinder B6_BP_dsulf, locally refined, sharpened | ||||||||||||||||||
Sample |
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Keywords | Complex / heterodimer / signaling / ECM-binding / DE NOVO PROTEIN | ||||||||||||||||||
Function / homology | Function and homology information Langerhans cell differentiation / integrin alphav-beta6 complex / integrin alphav-beta8 complex / hard palate development / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / opsonin binding / integrin alphav-beta1 complex / enamel mineralization ...Langerhans cell differentiation / integrin alphav-beta6 complex / integrin alphav-beta8 complex / hard palate development / transforming growth factor beta production / negative regulation of entry of bacterium into host cell / integrin alphav-beta5 complex / opsonin binding / integrin alphav-beta1 complex / enamel mineralization / Cross-presentation of particulate exogenous antigens (phagosomes) / extracellular matrix protein binding / bronchiole development / Laminin interactions / integrin alphav-beta3 complex / negative regulation of lipoprotein metabolic process / alphav-beta3 integrin-PKCalpha complex / entry into host cell by a symbiont-containing vacuole / alphav-beta3 integrin-HMGB1 complex / phospholipid homeostasis / negative regulation of lipid transport / negative regulation of low-density lipoprotein receptor activity / regulation of phagocytosis / Elastic fibre formation / alphav-beta3 integrin-IGF-1-IGF1R complex / transforming growth factor beta binding / surfactant homeostasis / filopodium membrane / extracellular matrix binding / positive regulation of small GTPase mediated signal transduction / apolipoprotein A-I-mediated signaling pathway / apoptotic cell clearance / wound healing, spreading of epidermal cells / positive regulation of intracellular signal transduction / heterotypic cell-cell adhesion / integrin complex / Molecules associated with elastic fibres / microvillus membrane / cell adhesion mediated by integrin / skin development / negative chemotaxis / Syndecan interactions / lung alveolus development / cell-substrate adhesion / endodermal cell differentiation / positive regulation of osteoblast proliferation / TGF-beta receptor signaling activates SMADs / PECAM1 interactions / lamellipodium membrane / negative regulation of macrophage derived foam cell differentiation / fibronectin binding / negative regulation of lipid storage / ECM proteoglycans / voltage-gated calcium channel activity / Integrin cell surface interactions / vasculogenesis / specific granule membrane / coreceptor activity / phagocytic vesicle / extrinsic apoptotic signaling pathway in absence of ligand / ERK1 and ERK2 cascade / positive regulation of cell adhesion / bone development / substrate adhesion-dependent cell spreading / transforming growth factor beta receptor signaling pathway / cell-matrix adhesion / Signal transduction by L1 / molecular function activator activity / integrin-mediated signaling pathway / negative regulation of extrinsic apoptotic signaling pathway / cellular response to ionizing radiation / calcium ion transmembrane transport / protein kinase C binding / wound healing / response to virus / cell morphogenesis / cell-cell adhesion / VEGFA-VEGFR2 Pathway / ruffle membrane / cell migration / integrin binding / cell junction / virus receptor activity / positive regulation of cytosolic calcium ion concentration / protease binding / angiogenesis / receptor complex / cell adhesion / positive regulation of cell migration / inflammatory response / symbiont entry into host cell / immune response / external side of plasma membrane / focal adhesion / centrosome / Neutrophil degranulation / positive regulation of cell population proliferation / cell surface / extracellular exosome / nucleoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | ||||||||||||||||||
Authors | Campbell MG / Fernandez A / Roy A / Kraft J / Baker D | ||||||||||||||||||
Funding support | United States, 5 items
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Citation | Journal: Nat Commun / Year: 2023 Title: De novo design of highly selective miniprotein inhibitors of integrins αvβ6 and αvβ8. Authors: Anindya Roy / Lei Shi / Ashley Chang / Xianchi Dong / Andres Fernandez / John C Kraft / Jing Li / Viet Q Le / Rebecca Viazzo Winegar / Gerald Maxwell Cherf / Dean Slocum / P Daniel Poulson / ...Authors: Anindya Roy / Lei Shi / Ashley Chang / Xianchi Dong / Andres Fernandez / John C Kraft / Jing Li / Viet Q Le / Rebecca Viazzo Winegar / Gerald Maxwell Cherf / Dean Slocum / P Daniel Poulson / Garrett E Casper / Mary L Vallecillo-Zúniga / Jonard Corpuz Valdoz / Marcos C Miranda / Hua Bai / Yakov Kipnis / Audrey Olshefsky / Tanu Priya / Lauren Carter / Rashmi Ravichandran / Cameron M Chow / Max R Johnson / Suna Cheng / McKaela Smith / Catherine Overed-Sayer / Donna K Finch / David Lowe / Asim K Bera / Gustavo Matute-Bello / Timothy P Birkland / Frank DiMaio / Ganesh Raghu / Jennifer R Cochran / Lance J Stewart / Melody G Campbell / Pam M Van Ry / Timothy Springer / David Baker / Abstract: The RGD (Arg-Gly-Asp)-binding integrins αvβ6 and αvβ8 are clinically validated cancer and fibrosis targets of considerable therapeutic importance. Compounds that can discriminate between ...The RGD (Arg-Gly-Asp)-binding integrins αvβ6 and αvβ8 are clinically validated cancer and fibrosis targets of considerable therapeutic importance. Compounds that can discriminate between homologous αvβ6 and αvβ8 and other RGD integrins, stabilize specific conformational states, and have high thermal stability could have considerable therapeutic utility. Existing small molecule and antibody inhibitors do not have all these properties, and hence new approaches are needed. Here we describe a generalized method for computationally designing RGD-containing miniproteins selective for a single RGD integrin heterodimer and conformational state. We design hyperstable, selective αvβ6 and αvβ8 inhibitors that bind with picomolar affinity. CryoEM structures of the designed inhibitor-integrin complexes are very close to the computational design models, and show that the inhibitors stabilize specific conformational states of the αvβ6 and the αvβ8 integrins. In a lung fibrosis mouse model, the αvβ6 inhibitor potently reduced fibrotic burden and improved overall lung mechanics, demonstrating the therapeutic potential of de novo designed integrin binding proteins with high selectivity. | ||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41154.map.gz | 85.9 MB | EMDB map data format | |
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Header (meta data) | emd-41154-v30.xml emd-41154.xml | 24.3 KB 24.3 KB | Display Display | EMDB header |
Images | emd_41154.png | 98.3 KB | ||
Others | emd_41154_additional_1.map.gz emd_41154_additional_2.map.gz emd_41154_half_map_1.map.gz emd_41154_half_map_2.map.gz | 83.8 MB 83.6 MB 154.2 MB 154.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41154 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41154 | HTTPS FTP |
-Validation report
Summary document | emd_41154_validation.pdf.gz | 990.9 KB | Display | EMDB validaton report |
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Full document | emd_41154_full_validation.pdf.gz | 990.5 KB | Display | |
Data in XML | emd_41154_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | emd_41154_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41154 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41154 | HTTPS FTP |
-Related structure data
Related structure data | 8tcgMC 7lmvC 7lmxC 8tcfC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_41154.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Integrin alpha-v beta-6 in complex with minibinder B6_BP_dsulf, locally refined, sharpened | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.122 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #2
File | emd_41154_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: #1
File | emd_41154_additional_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_41154_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_41154_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Ternary complex of integrin heterodimer (alpha-v beta-6) and the ...
Entire | Name: Ternary complex of integrin heterodimer (alpha-v beta-6) and the de novo minibinder protein B6_BP_dslf |
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Components |
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-Supramolecule #1: Ternary complex of integrin heterodimer (alpha-v beta-6) and the ...
Supramolecule | Name: Ternary complex of integrin heterodimer (alpha-v beta-6) and the de novo minibinder protein B6_BP_dslf type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 Details: Integrin expressed in expiCHO cells, minibinder expressed in e. coli |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Integrin alpha-V heavy chain
Macromolecule | Name: Integrin alpha-V heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 47.898004 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: FNLDVDSPAE YSGPEGSYFG FAVDFFVPSA SSRMFLLVGA PKANTTQPGI VEGGQVLKCD WSSTRRCQPI EFDATGNRDY AKDDPLEFK SHQWFGASVR SKQDKILACA PLYHWRTEMK QEREPVGTCF LQDGTKTVEY APCRSQDIDA DGQGFCQGGF S IDFTKADR ...String: FNLDVDSPAE YSGPEGSYFG FAVDFFVPSA SSRMFLLVGA PKANTTQPGI VEGGQVLKCD WSSTRRCQPI EFDATGNRDY AKDDPLEFK SHQWFGASVR SKQDKILACA PLYHWRTEMK QEREPVGTCF LQDGTKTVEY APCRSQDIDA DGQGFCQGGF S IDFTKADR VLLGGPGSFY WQGQLISDQV AEIVSKYDPN VYSIKYNNQL ATRTAQAIFD DSYLGYSVAV GDFNGDGIDD FV SGVPRAA RTLGMVYIYD GKNMSSLYNF TGEQMAAYFG FSVAATDING DDYADVFIGA PLFMDRGSDG KLQEVGQVSV SLQ RASGDF QTTKLNGFEV FARFGSAIAP LGDLDQDGFN DIAIAAPYGG EDKKGIVYIF NGRSTGLNAV PSQILEGQWA ARSG CPPSF GYSMKGATDI DKNGYPDLIV GAFGVDRAIL YRARP UniProtKB: Integrin alpha-V |
-Macromolecule #2: Integrin beta-6
Macromolecule | Name: Integrin beta-6 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 26.948713 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: DYPVDLYYLM DLSASMDDDL NTIKELGSRL SKEMSKLTSN FRLGFGSFVE KPVSPFVKTT PEEIANPCSS IPYFCLPTFG FKHILPLTN DAERFNEIVK NQKISANIDT PEGGFDAIMQ AAVCKEKIGW RNDSLHLLVF VSDADSHFGM DSKLAGIVCP N DGLCHLDS ...String: DYPVDLYYLM DLSASMDDDL NTIKELGSRL SKEMSKLTSN FRLGFGSFVE KPVSPFVKTT PEEIANPCSS IPYFCLPTFG FKHILPLTN DAERFNEIVK NQKISANIDT PEGGFDAIMQ AAVCKEKIGW RNDSLHLLVF VSDADSHFGM DSKLAGIVCP N DGLCHLDS KNEYSMSTVL EYPTIGQLID KLVQNNVLLI FAVTQEQVHL YENYAKLIPG ATVGLLQKDS GNILQLIISA YE EL UniProtKB: Integrin beta-6 |
-Macromolecule #3: Minibinder B6_BP_dslf
Macromolecule | Name: Minibinder B6_BP_dslf / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 8.415737 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: CVVRFVFRGD LAELMLRAVK DHLKKEGPHW NITSTNNGKE LVVRGIHESD AKRIAKWVEK RFPRVHTETQ CD |
-Macromolecule #5: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 2 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Macromolecule #7: MANGANESE (II) ION
Macromolecule | Name: MANGANESE (II) ION / type: ligand / ID: 7 / Number of copies: 3 / Formula: MN |
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Molecular weight | Theoretical: 54.938 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Material: GOLD |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm |