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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-23294 | |||||||||
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Title | Trimeric human Arginase 1 in complex with mAb5 | |||||||||
![]() | Full map of 2x3hArg:3Mab5 | |||||||||
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Function / homology | ![]() 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 / urea cycle / negative regulation of type II interferon-mediated signaling pathway / 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 / urea cycle / negative regulation of type II interferon-mediated signaling pathway / 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 | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.05 Å | |||||||||
![]() | Gomez-Llorente Y / Scapin G / Palte RL | |||||||||
![]() | ![]() 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
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 117.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 21.9 KB 21.9 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.7 KB | Display | ![]() |
Images | ![]() | 76.6 KB | ||
Masks | ![]() | 125 MB | ![]() | |
Others | ![]() ![]() | 116 MB 116 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 842.6 KB | Display | ![]() |
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Full document | ![]() | 842.2 KB | Display | |
Data in XML | ![]() | 18.4 KB | Display | |
Data in CIF | ![]() | 23.5 KB | Display | |
Arichive directory | ![]() ![]() | 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 ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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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
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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. | ||||||||||||
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Density Histograms |
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File | emd_23294_half_map_2.map | ||||||||||||
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Annotation | Half map A. | ||||||||||||
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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: ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Supramolecule #3: mAb5
Supramolecule | Name: mAb5 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
-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: ![]() |
Molecular weight | Theoretical: 34.779879 KDa |
Recombinant expression | Organism: ![]() ![]() |
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: ![]() |
Molecular weight | Theoretical: 49.036074 KDa |
Recombinant expression | Organism: ![]() ![]() |
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: ![]() |
Molecular weight | Theoretical: 23.381787 KDa |
Recombinant expression | Organism: ![]() ![]() |
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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![]() | single particle reconstruction |
Aggregation state | particle |
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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 |
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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: ![]() |
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 |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
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Output model | ![]() PDB-7ley: |