+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40589 | |||||||||||||||||||||
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Title | hPAD4 bound to Activating Fab hA362 | |||||||||||||||||||||
Map data | Sharpened map for human PAD4 bound to activating Fab 362 | |||||||||||||||||||||
Sample |
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Keywords | complex / enzyme / inflammation / calcium binding / IMMUNE SYSTEM | |||||||||||||||||||||
Function / homology | Function and homology information histone H3R2 arginine deiminase activity / histone H3R8 arginine deiminase activity / histone H3R17 arginine deiminase activity / histone arginine deiminase activity / histone H3R26 arginine deiminase activity / protein-arginine deiminase / protein-arginine deiminase activity / stem cell population maintenance / Chromatin modifying enzymes / post-translational protein modification ...histone H3R2 arginine deiminase activity / histone H3R8 arginine deiminase activity / histone H3R17 arginine deiminase activity / histone arginine deiminase activity / histone H3R26 arginine deiminase activity / protein-arginine deiminase / protein-arginine deiminase activity / stem cell population maintenance / Chromatin modifying enzymes / post-translational protein modification / protein modification process / nucleosome assembly / chromatin organization / chromatin remodeling / innate immune response / calcium ion binding / protein-containing complex / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||||||||||||||
Authors | Maker A / Verba KA | |||||||||||||||||||||
Funding support | United States, 6 items
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Citation | Journal: Nat Chem Biol / Year: 2024 Title: Antibody discovery identifies regulatory mechanisms of protein arginine deiminase 4. Authors: Xin Zhou / Sophie Kong / Allison Maker / Soumya G Remesh / Kevin K Leung / Kliment A Verba / James A Wells / Abstract: Unlocking the potential of protein arginine deiminase 4 (PAD4) as a drug target for rheumatoid arthritis requires a deeper understanding of its regulation. In this study, we use unbiased antibody ...Unlocking the potential of protein arginine deiminase 4 (PAD4) as a drug target for rheumatoid arthritis requires a deeper understanding of its regulation. In this study, we use unbiased antibody selections to identify functional antibodies capable of either activating or inhibiting PAD4 activity. Through cryogenic-electron microscopy, we characterized the structures of these antibodies in complex with PAD4 and revealed insights into their mechanisms of action. Rather than steric occlusion of the substrate-binding catalytic pocket, the antibodies modulate PAD4 activity through interactions with allosteric binding sites adjacent to the catalytic pocket. These binding events lead to either alteration of the active site conformation or the enzyme oligomeric state, resulting in modulation of PAD4 activity. Our study uses antibody engineering to reveal new mechanisms for enzyme regulation and highlights the potential of using PAD4 agonist and antagonist antibodies for studying PAD4-dependency in disease models and future therapeutic development. | |||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40589.map.gz | 14.7 MB | EMDB map data format | |
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Header (meta data) | emd-40589-v30.xml emd-40589.xml | 20.3 KB 20.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_40589_fsc.xml | 13.3 KB | Display | FSC data file |
Images | emd_40589.png | 111.8 KB | ||
Masks | emd_40589_msk_1.map | 244.1 MB | Mask map | |
Filedesc metadata | emd-40589.cif.gz | 6.7 KB | ||
Others | emd_40589_half_map_1.map.gz emd_40589_half_map_2.map.gz | 66.4 MB 66.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40589 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40589 | HTTPS FTP |
-Validation report
Summary document | emd_40589_validation.pdf.gz | 715.5 KB | Display | EMDB validaton report |
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Full document | emd_40589_full_validation.pdf.gz | 715.1 KB | Display | |
Data in XML | emd_40589_validation.xml.gz | 21.9 KB | Display | |
Data in CIF | emd_40589_validation.cif.gz | 27.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40589 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40589 | HTTPS FTP |
-Related structure data
Related structure data | 8smkMC 8smlC 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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-Map
File | Download / File: emd_40589.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened map for human PAD4 bound to activating Fab 362 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.835 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_40589_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half map 1 for human PAD4 bound to activating Fab 362
File | emd_40589_half_map_1.map | ||||||||||||
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Annotation | Half map 1 for human PAD4 bound to activating Fab 362 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2 for human PAD4 bound to activating Fab 362
File | emd_40589_half_map_2.map | ||||||||||||
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Annotation | Half map 2 for human PAD4 bound to activating Fab 362 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : hPAD4 bound to Activating Fab hA362
Entire | Name: hPAD4 bound to Activating Fab hA362 |
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Components |
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-Supramolecule #1: hPAD4 bound to Activating Fab hA362
Supramolecule | Name: hPAD4 bound to Activating Fab hA362 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 248 KDa |
-Macromolecule #1: Protein-arginine deiminase type-4
Macromolecule | Name: Protein-arginine deiminase type-4 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: protein-arginine deiminase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 77.902953 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: HHHHHHASGG LNDIFEAQKI EWHEENLYFQ GTSAQGTLIR VTPEQPTHAV CVLGTLTQLD ICSSAPEDCT SFSINASPGV VVDIAHGPP AKKKSTGSST WPLDPGVEVT LTMKAASGST GDQKVQISYY GPKTPPVKAL LYLTGVEISL CADITRTGKV K PTRAVKDQ ...String: HHHHHHASGG LNDIFEAQKI EWHEENLYFQ GTSAQGTLIR VTPEQPTHAV CVLGTLTQLD ICSSAPEDCT SFSINASPGV VVDIAHGPP AKKKSTGSST WPLDPGVEVT LTMKAASGST GDQKVQISYY GPKTPPVKAL LYLTGVEISL CADITRTGKV K PTRAVKDQ RTWTWGPCGQ GAILLVNCDR DNLESSAMDC EDDEVLDSED LQDMSLMTLS TKTPKDFFTN HTLVLHVARS EM DKVRVFQ ATRGKLSSKC SVVLGPKWPS HYLMVPGGKH NMDFYVEALA FPDTDFPGLI TLTISLLDTS NLELPEAVVF QDS VVFRVA PWIMTPNTQP PQEVYACSIF ENEDFLKSVT TLAMKAKCKL TICPEEENMD DQWMQDEMEI GYIQAPHKTL PVVF DSPRN RGLKEFPIKR VMGPDFGYVT RGPQTGGISG LDSFGNLEVS PPVTVRGKEY PLGRILFGDS CYPSNDSRQM HQALQ DFLS AQQVQAPVKL YSDWLSVGHV DEFLSFVPAP DRKGFRLLLA SPRSCYKLFQ EQQNEGHGEA LLFEGIKKKK QQKIKN ILS NKTLREHNSF VERCIDWNRE LLKRELGLAE SDIIDIPQLF KLKEFSKAEA FFPNMVNMLV LGKHLGIPKP FGPVING RC CLEEKVCSLL EPLGLQCTFI NDFFTYHIRH GEVHCGTNVR RKPFSFKWWN MVP UniProtKB: Protein-arginine deiminase type-4 |
-Macromolecule #2: Activating Fab 362 heavy chain
Macromolecule | Name: Activating Fab 362 heavy chain / 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: 24.363195 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: EVQLVESGGG LVQPGGSLRL SCAASGFNVS YYSIHWVRQA PGKGLEWVAS ISPYYGSTYY ADSVKGRFTI SADTSKNTAY LQMNSLRAE DTAVYYCARH PYRKGYSGLD YWGQGTLVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT ...String: EVQLVESGGG LVQPGGSLRL SCAASGFNVS YYSIHWVRQA PGKGLEWVAS ISPYYGSTYY ADSVKGRFTI SADTSKNTAY LQMNSLRAE DTAVYYCARH PYRKGYSGLD YWGQGTLVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKK VEPKSCDKTH T |
-Macromolecule #3: Activating Fab 362 light chain
Macromolecule | Name: Activating Fab 362 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.405016 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: DIQMTQSPSS LSASVGDRVT ITCRASQSVS SAVAWYQQKP GKAPKLLIYS ASSLYSGVPS RFSGSRSGTD FTLTISSLQP EDFATYYCQ QSSYLPLFTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String: DIQMTQSPSS LSASVGDRVT ITCRASQSVS SAVAWYQQKP GKAPKLLIYS ASSLYSGVPS RFSGSRSGTD FTLTISSLQP EDFATYYCQ QSSYLPLFTF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC |
-Macromolecule #4: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 8 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 Component:
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Grid | Model: Quantifoil / Material: GOLD / Mesh: 300 | |||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 72.0 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: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT |
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Output model | PDB-8smk: |