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Yorodumi- EMDB-40047: Structure of human ENPP1 in complex with variable heavy domain VH27.2 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40047 | |||||||||
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Title | Structure of human ENPP1 in complex with variable heavy domain VH27.2 | |||||||||
Map data | From cryosparc non-uniform refinement and local resolution filter | |||||||||
Sample |
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Keywords | phosphodiesterase / inhibitor / IMMUNE SYSTEM | |||||||||
Function / homology | Function and homology information GTP diphosphatase activity / cyclic-GMP-AMP hydrolase activity / negative regulation of hh target transcription factor activity / inorganic diphosphate transport / Vitamin B2 (riboflavin) metabolism / UTP diphosphatase activity / phosphodiesterase I / 3'-phosphoadenosine 5'-phosphosulfate binding / dinucleotide phosphatase activity / Vitamin B5 (pantothenate) metabolism ...GTP diphosphatase activity / cyclic-GMP-AMP hydrolase activity / negative regulation of hh target transcription factor activity / inorganic diphosphate transport / Vitamin B2 (riboflavin) metabolism / UTP diphosphatase activity / phosphodiesterase I / 3'-phosphoadenosine 5'-phosphosulfate binding / dinucleotide phosphatase activity / Vitamin B5 (pantothenate) metabolism / nucleotide diphosphatase / nucleoside triphosphate catabolic process / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / nucleic acid metabolic process / negative regulation of protein autophosphorylation / nucleoside triphosphate diphosphatase activity / intracellular phosphate ion homeostasis / sequestering of triglyceride / ATP diphosphatase activity / negative regulation of glycogen biosynthetic process / negative regulation of bone mineralization / phosphate ion homeostasis / melanocyte differentiation / phosphodiesterase I activity / scavenger receptor activity / negative regulation of glucose import / regulation of bone mineralization / phosphate-containing compound metabolic process / exonuclease activity / polysaccharide binding / response to ATP / negative regulation of fat cell differentiation / bone mineralization / phosphatase activity / : / 3',5'-cyclic-AMP phosphodiesterase activity / immunoglobulin complex, circulating / immunoglobulin receptor binding / ATP metabolic process / negative regulation of insulin receptor signaling pathway / complement activation, classical pathway / generation of precursor metabolites and energy / antigen binding / insulin receptor binding / negative regulation of cell growth / cellular response to insulin stimulus / gene expression / antibacterial humoral response / basolateral plasma membrane / nucleic acid binding / blood microparticle / immune response / lysosomal membrane / calcium ion binding / cell surface / protein homodimerization activity / extracellular space / extracellular exosome / zinc ion binding / ATP binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Carozza JA / Wang H / Solomon PE / Wells JA / Li L | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Nat Chem Biol / Year: 2024 Title: Discovery of VH domains that allosterically inhibit ENPP1. Authors: Paige E Solomon / Colton J Bracken / Jacqueline A Carozza / Haoqing Wang / Elizabeth P Young / Alon Wellner / Chang C Liu / E Alejandro Sweet-Cordero / Lingyin Li / James A Wells / Abstract: Ectodomain phosphatase/phosphodiesterase-1 (ENPP1) is overexpressed on cancer cells and functions as an innate immune checkpoint by hydrolyzing extracellular cyclic guanosine monophosphate adenosine ...Ectodomain phosphatase/phosphodiesterase-1 (ENPP1) is overexpressed on cancer cells and functions as an innate immune checkpoint by hydrolyzing extracellular cyclic guanosine monophosphate adenosine monophosphate (cGAMP). Biologic inhibitors have not yet been reported and could have substantial therapeutic advantages over current small molecules because they can be recombinantly engineered into multifunctional formats and immunotherapies. Here we used phage and yeast display coupled with in cellulo evolution to generate variable heavy (VH) single-domain antibodies against ENPP1 and discovered a VH domain that allosterically inhibited the hydrolysis of cGAMP and adenosine triphosphate (ATP). We solved a 3.2 Å-resolution cryo-electron microscopy structure for the VH inhibitor complexed with ENPP1 that confirmed its new allosteric binding pose. Finally, we engineered the VH domain into multispecific formats and immunotherapies, including a bispecific fusion with an anti-PD-L1 checkpoint inhibitor that showed potent cellular activity. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40047.map.gz | 5.1 MB | EMDB map data format | |
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Header (meta data) | emd-40047-v30.xml emd-40047.xml | 17.8 KB 17.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_40047_fsc.xml | 11.9 KB | Display | FSC data file |
Images | emd_40047.png | 93.1 KB | ||
Filedesc metadata | emd-40047.cif.gz | 6.4 KB | ||
Others | emd_40047_half_map_1.map.gz emd_40047_half_map_2.map.gz | 165.1 MB 165.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40047 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40047 | HTTPS FTP |
-Related structure data
Related structure data | 8ghrMC 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_40047.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | From cryosparc non-uniform refinement and local resolution filter | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.8677 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map A from non-uniform refinement
File | emd_40047_half_map_1.map | ||||||||||||
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Annotation | half map A from non-uniform refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map B from non-uniform refinement
File | emd_40047_half_map_2.map | ||||||||||||
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Annotation | half map B from non-uniform refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : ENPP1-VH27 complex
Entire | Name: ENPP1-VH27 complex |
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Components |
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-Supramolecule #1: ENPP1-VH27 complex
Supramolecule | Name: ENPP1-VH27 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Ectonucleotide pyrophosphatase/phosphodiesterase family member 1,...
Macromolecule | Name: Ectonucleotide pyrophosphatase/phosphodiesterase family member 1, secreted form, Immunoglobulin gamma-1 heavy chain fusion type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 115.488617 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: GEKSWVEEPC ESINEPQCPA GFETPPTLLF SLDGFRAEYL HTWGGLLPVI SKLKKCGTYT KNMRPVYPTK AFPNHYSIVT GLYPESHGI IDNKMYDPKM NASFSLKSKE KFNPEWYKGE PIWVTAKYQG LKSGTFFWPG SDVEINGIFP DIYKMYNGSV P FEERILAV ...String: GEKSWVEEPC ESINEPQCPA GFETPPTLLF SLDGFRAEYL HTWGGLLPVI SKLKKCGTYT KNMRPVYPTK AFPNHYSIVT GLYPESHGI IDNKMYDPKM NASFSLKSKE KFNPEWYKGE PIWVTAKYQG LKSGTFFWPG SDVEINGIFP DIYKMYNGSV P FEERILAV LQWLQLPKDE RPHFYTLYLE EPDSSGHSYG PVSSEVIKAL QRVDGMVGML MDGLKELNLH RCLNLILISD HG MEQGSCK KYIYLNKYLG DVKNIKVIYG PAARLRPSDV PDKYYSFNYE GIARNLSCRE PNQHFKPYLK HFLPKRLHFA KSD RIEPLT FYLDPQWQLA LNPSERKYCG SGFHGSDNVF SNMQALFVGY GPGFKHGIEA DTFENIEVYN LMCDLLNLTP APNN GTHGS LNHLLKNPVY TPKHPKEVHP LVQCPFTRNP RDNLGCSCNP SILPIEDFQT QFNLTVAEEK IIKHETLPYG RPRVL QKEN TICLLSQHQF MSGYSQDILM PLWTSYTVDR NDSFSTEDFS NCLYQDFRIP LSPVHKCSFY KNNTKVSYGF LSPPQL NKN SSGIYSEALL TTNIVPMYQS FQVIWRYFHD TLLRKYAEER NGVNVVSGPV FDFDYDGRCD SLENLRQKRR VIRNQEI LI PTHFFIVLTS CKDTSQTPLH CENLDTLAFI LPHRTDNSES CVHGKHDSSW VEELLMLHRA RITDVEHITG LSFYQQRK E PVSDILKLKT HLPTFSQEDT SSGGGGENLY FQSSGGGSGG GEPKSCDKTH TCPPCPAPEL LGGPSVFLFP PKPKDTLMI SRTPEVTCVV VDVSHEDPEV KFNWYVDGVE VHNAKTKPRE EQYNSTYRVV SVLTVLHQDW LNGKEYKCKV SNKALPAPIE KTISKAKGQ PREPQVYTLP PSRDELTKNQ VSLTCLVKGF YPSDIAVEWE SNGQPENNYK TTPPVLDSDG SFFLYSKLTV D KSRWQQGN VFSCSVMHEA LHNHYTQKSL SLSPGKGGGG SGLNDIFEAQ KIEWHEG UniProtKB: Ectonucleotide pyrophosphatase/phosphodiesterase family member 1, Immunoglobulin gamma-1 heavy chain |
-Macromolecule #2: VH27
Macromolecule | Name: VH27 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 13.564035 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EVQLVESGGG LVQPGGSLRL SCAASGFDIY YSYYIGWVRR APGKGEELVA RISPSYGSTS YADSVKGRFT ISADISKNTA YLQMNSLRV EDTAVYYCAR FAYPWYVADD ALDYWGQGTL VTVSS |
-Macromolecule #4: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 4 / Number of copies: 4 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #5: ADENOSINE MONOPHOSPHATE
Macromolecule | Name: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: AMP |
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Molecular weight | Theoretical: 347.221 Da |
Chemical component information | ChemComp-AMP: |
-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: 4 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Macromolecule #7: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #8: water
Macromolecule | Name: water / type: ligand / ID: 8 / Number of copies: 6 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 7.4 / Details: phosphate buffered saline |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 57.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.7000000000000001 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |