+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-23298 | |||||||||
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Title | Trimeric human Arginase 1 in complex with mAb4 | |||||||||
Map data | Full map for the complex 2x3hARG:3Mab4, | |||||||||
Sample |
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Keywords | Arginase / Metalloenzyme / IMMUNE SYSTEM / HYDROLASE-IMMUNE SYSTEM complex | |||||||||
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 / 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 / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.72 Å | |||||||||
Authors | Gomez-Llorente Y / Scapin G | |||||||||
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_23298.map.gz | 118 MB | EMDB map data format | |
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Header (meta data) | emd-23298-v30.xml emd-23298.xml | 23.3 KB 23.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_23298_fsc.xml | 14.7 KB | Display | FSC data file |
Images | emd_23298.png | 48.3 KB | ||
Masks | emd_23298_msk_1.map | 125 MB | Mask map | |
Filedesc metadata | emd-23298.cif.gz | 6.7 KB | ||
Others | emd_23298_additional_1.map.gz emd_23298_half_map_1.map.gz emd_23298_half_map_2.map.gz | 117.9 MB 115.8 MB 115.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-23298 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23298 | HTTPS FTP |
-Validation report
Summary document | emd_23298_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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Full document | emd_23298_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | emd_23298_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | emd_23298_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23298 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23298 | HTTPS FTP |
-Related structure data
Related structure data | 7lf2MC 7lexC 7leyC 7lezC 7lf0C 7lf1C 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_23298.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Full map for the complex 2x3hARG:3Mab4, | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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_23298_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Map focused on one of the hARG trimer:Mab halves to gain resolution.
File | emd_23298_additional_1.map | ||||||||||||
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Annotation | Map focused on one of the hARG trimer:Mab halves to gain resolution. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map B.
File | emd_23298_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_23298_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 mAb4
Entire | Name: Trimeric human arginase in complex with mAb4 |
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Components |
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-Supramolecule #1: Trimeric human arginase in complex with mAb4
Supramolecule | Name: Trimeric human arginase in complex with mAb4 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 Details: 2 trimers of human arginase bound to the Fab regions of 3 mAb4 molecules. |
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Molecular weight | Theoretical: 427 KDa |
-Supramolecule #2: Trimeric human arginase
Supramolecule | Name: Trimeric human arginase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: Monoclonal antibody mAb4
Supramolecule | Name: Monoclonal antibody mAb4 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Arginase-1
Macromolecule | Name: Arginase-1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / 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 UniProtKB: Arginase-1 |
-Macromolecule #2: mAb4 monoclonal antibody heavy chain
Macromolecule | Name: mAb4 monoclonal antibody heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 48.877801 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: EVQLVQSGAE VKKPGASVKV SCKASGYTFT DYYMNWVRQA PGQGLEWIGV ISPYNGGTTY NQKFKGKATL TVDKSTSTAY MELSSLRSE DTAVYYCVYD LYYFDYWGQG TLVTVSSAST KGPSVFPLAP CSRSTSESTA ALGCLVKDYF PEPVTVSWNS G ALTSGVHT ...String: EVQLVQSGAE VKKPGASVKV SCKASGYTFT DYYMNWVRQA PGQGLEWIGV ISPYNGGTTY NQKFKGKATL TVDKSTSTAY MELSSLRSE DTAVYYCVYD LYYFDYWGQG TLVTVSSAST KGPSVFPLAP CSRSTSESTA ALGCLVKDYF PEPVTVSWNS G ALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTKTYT CNVDHKPSNT KVDKRVESKY GPPCPPCPAP EFLGGPSVFL FP PKPKDTL MISRTPEVTC VVVDVSQEDP EVQFNWYVDG VEVHNAKTKP REEQFNSTYR VVSVLTVLHQ DWLNGKEYKC KVS NKGLPS SIEKTISKAK GQPREPQVYT LPPSQEEMTK NQVSLTCLVK GFYPSDIAVE WESNGQPENN YKTTPPVLDS DGSF FLYSR LTVDKSRWQE GNVFSCSVMH EALHNHYTQK SLSLSLGK |
-Macromolecule #3: mAb4 monoclonal antibody light chain
Macromolecule | Name: mAb4 monoclonal antibody light chain / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.471062 KDa |
Recombinant expression | Organism: Cricetulus griseus (Chinese hamster) |
Sequence | String: EIVLTQSPAT LSLSPGERAT LSCRASQRIS NDLHWYQQKP GQAPRLLIKY ASQSISGIPS RFSGSGSGTD FTLTISSLEP EDFAVYYCQ QSNSWPRTFG GGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String: EIVLTQSPAT LSLSPGERAT LSCRASQRIS NDLHWYQQKP GQAPRLLIKY ASQSISGIPS RFSGSGSGTD FTLTISSLEP EDFAVYYCQ QSNSWPRTFG GGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC |
-Macromolecule #4: MANGANESE (II) ION
Macromolecule | Name: MANGANESE (II) ION / type: ligand / ID: 4 / Number of copies: 12 / 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 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec. |
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-7lf2: |