+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23294 | |||||||||
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Title | Trimeric human Arginase 1 in complex with mAb5 | |||||||||
Map data | Full map of 2x3hArg:3Mab5 | |||||||||
Sample |
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Function / homology | Function and homology information positive regulation of neutrophil mediated killing of fungus / Urea cycle / negative regulation of T-helper 2 cell cytokine production / arginase / arginase activity / arginine catabolic process to ornithine / negative regulation of type II interferon-mediated signaling pathway / urea cycle / defense response to protozoan / negative regulation of activated T cell proliferation ...positive regulation of neutrophil mediated killing of fungus / Urea cycle / negative regulation of T-helper 2 cell cytokine production / arginase / arginase activity / arginine catabolic process to ornithine / negative regulation of type II interferon-mediated signaling pathway / urea cycle / defense response to protozoan / negative regulation of activated T cell proliferation / arginine catabolic process / negative regulation of T cell proliferation / specific granule lumen / azurophil granule lumen / manganese ion binding / adaptive immune response / innate immune response / Neutrophil degranulation / extracellular space / extracellular region / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.05 Å | |||||||||
Authors | Gomez-Llorente Y / Scapin G / Palte RL | |||||||||
Citation | Journal: Commun Biol / Year: 2021 Title: Cryo-EM structures of inhibitory antibodies complexed with arginase 1 provide insight into mechanism of action. Authors: Rachel L Palte / Veronica Juan / Yacob Gomez-Llorente / Marc Andre Bailly / Kalyan Chakravarthy / Xun Chen / Daniel Cipriano / Ghassan N Fayad / Laurence Fayadat-Dilman / Symon Gathiaka / ...Authors: Rachel L Palte / Veronica Juan / Yacob Gomez-Llorente / Marc Andre Bailly / Kalyan Chakravarthy / Xun Chen / Daniel Cipriano / Ghassan N Fayad / Laurence Fayadat-Dilman / Symon Gathiaka / Heiko Greb / Brian Hall / Mas Handa / Mark Hsieh / Esther Kofman / Heping Lin / J Richard Miller / Nhung Nguyen / Jennifer O'Neil / Hussam Shaheen / Eric Sterner / Corey Strickland / Angie Sun / Shane Taremi / Giovanna Scapin / Abstract: Human Arginase 1 (hArg1) is a metalloenzyme that catalyzes the hydrolysis of L-arginine to L-ornithine and urea, and modulates T-cell-mediated immune response. Arginase-targeted therapies have been ...Human Arginase 1 (hArg1) is a metalloenzyme that catalyzes the hydrolysis of L-arginine to L-ornithine and urea, and modulates T-cell-mediated immune response. Arginase-targeted therapies have been pursued across several disease areas including immunology, oncology, nervous system dysfunction, and cardiovascular dysfunction and diseases. Currently, all published hArg1 inhibitors are small molecules usually less than 350 Da in size. Here we report the cryo-electron microscopy structures of potent and inhibitory anti-hArg antibodies bound to hArg1 which form distinct macromolecular complexes that are greater than 650 kDa. With local resolutions of 3.5 Å or better we unambiguously mapped epitopes and paratopes for all five antibodies and determined that the antibodies act through orthosteric and allosteric mechanisms. These hArg1:antibody complexes present an alternative mechanism to inhibit hArg1 activity and highlight the ability to utilize antibodies as probes in the discovery and development of peptide and small molecule inhibitors for enzymes in general. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_23294.map.gz | 117.9 MB | EMDB map data format | |
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Header (meta data) | emd-23294-v30.xml emd-23294.xml | 21.9 KB 21.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_23294_fsc.xml | 14.7 KB | Display | FSC data file |
Images | emd_23294.png | 76.6 KB | ||
Masks | emd_23294_msk_1.map | 125 MB | Mask map | |
Others | emd_23294_half_map_1.map.gz emd_23294_half_map_2.map.gz | 116 MB 116 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23294 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23294 | HTTPS FTP |
-Validation report
Summary document | emd_23294_validation.pdf.gz | 842.6 KB | Display | EMDB validaton report |
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Full document | emd_23294_full_validation.pdf.gz | 842.2 KB | Display | |
Data in XML | emd_23294_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | emd_23294_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23294 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23294 | HTTPS FTP |
-Related structure data
Related structure data | 7leyMC 7lexC 7lezC 7lf0C 7lf1C 7lf2C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_23294.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Full map of 2x3hArg:3Mab5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_23294_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half map B.
File | emd_23294_half_map_1.map | ||||||||||||
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Annotation | Half map B. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A.
File | emd_23294_half_map_2.map | ||||||||||||
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Annotation | Half map A. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Trimeric human arginase in complex with mAb5
Entire | Name: Trimeric human arginase in complex with mAb5 |
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Components |
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-Supramolecule #1: Trimeric human arginase in complex with mAb5
Supramolecule | Name: Trimeric human arginase in complex with mAb5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 Details: 2 trimers of human arginase, bound to 3 mAb5 molecules |
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Molecular weight | Experimental: 427 KDa |
-Supramolecule #2: Arginase-1
Supramolecule | Name: Arginase-1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: 'BL21-Gold(DE3)pLysS AG' |
-Supramolecule #3: mAb5
Supramolecule | Name: mAb5 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
-Macromolecule #1: Arginase-1
Macromolecule | Name: Arginase-1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: arginase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 34.779879 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSAKSRTIGI IGAPFSKGQP RGGVEEGPTV LRKAGLLEKL KEQECDVKDY GDLPFADIPN DSPFQIVKNP RSVGKASEQL AGKVAEVKK NGRISLVLGG DHSLAIGSIS GHARVHPDLG VIWVDAHTDI NTPLTTTSGN LHGQPVSFLL KELKGKIPDV P GFSWVTPC ...String: MSAKSRTIGI IGAPFSKGQP RGGVEEGPTV LRKAGLLEKL KEQECDVKDY GDLPFADIPN DSPFQIVKNP RSVGKASEQL AGKVAEVKK NGRISLVLGG DHSLAIGSIS GHARVHPDLG VIWVDAHTDI NTPLTTTSGN LHGQPVSFLL KELKGKIPDV P GFSWVTPC ISAKDIVYIG LRDVDPGEHY ILKTLGIKYF SMTEVDRLGI GKVMEETLSY LLGRKKRPIH LSFDVDGLDP SF TPATGTP VVGGLTYREG LYITEEIYKT GLLSGLDIME VNPSLGKTPE EVTRTVNTAV AITLACFGLA REGNHKPIDY LNP PK |
-Macromolecule #2: mAb5 heavy chain
Macromolecule | Name: mAb5 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 49.036074 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: EVQLVESGGG VVRPGGSLRL SCAASGFTFD DYGMTWVRQA PGKGLEWVSG INWNGGSTGY ADSVKGRFTI SRDNAKNSLY LQMNSLRAE DTALYHCARD RRRGSYGSDA FDIWGQGTMV TVSSAKTTPP SVYPLAPGSA AQTNSMVTLG CLVKGYFPEP V TVTWNSGS ...String: EVQLVESGGG VVRPGGSLRL SCAASGFTFD DYGMTWVRQA PGKGLEWVSG INWNGGSTGY ADSVKGRFTI SRDNAKNSLY LQMNSLRAE DTALYHCARD RRRGSYGSDA FDIWGQGTMV TVSSAKTTPP SVYPLAPGSA AQTNSMVTLG CLVKGYFPEP V TVTWNSGS LSSGVHTFPA VLESDLYTLS SSVTVPSSPR PSETVTCNVA HPASSTKVDK KIVPRDCGCK PCICTVPEVS SV FIFPPKP KDVLTITLTP KVTCVVVDIS KDDPEVQFSW FVDDVEVHTA QTQPREEQFN STFRSVSELP IMHQDWLNGK EFK CRVNSA AFPAPIEKTI SKTKGRPKAP QVYTIPPPKE QMAKDKVSLT CMITDFFPED ITVEWQWNGQ PAENYKNTQP IMNT NGSYF VYSKLNVQKS NWEAGNTFTC SVLHEGLHNH HTEKSLSHSP GK |
-Macromolecule #3: mAb5 light chain
Macromolecule | Name: mAb5 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.381787 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: DIQMTQSPSS LSASVGDRVT ITCRASQGIS NYLAWYQQKP GKVPQLLISA ASTLQSGVPS RFSGSGSGTD FTLTISSLQP EDVATYYCQ KYNSAPRTFG QGTKVEIKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS ...String: DIQMTQSPSS LSASVGDRVT ITCRASQGIS NYLAWYQQKP GKVPQLLISA ASTLQSGVPS RFSGSGSGTD FTLTISSLQP EDVATYYCQ KYNSAPRTFG QGTKVEIKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS KDSTYSMSST LTLTKDEYER HNSYTCEATH KTSTSPIVKS FNRNEC |
-Macromolecule #4: MANGANESE (II) ION
Macromolecule | Name: MANGANESE (II) ION / type: ligand / ID: 4 / Number of copies: 6 / 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 | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Number grids imaged: 1 / Number real images: 1197 / Average exposure time: 6.0 sec. / Average electron dose: 44.3 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | PDB-7ley: |