+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40590 | |||||||||||||||||||||
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Title | hPAD4 bound to inhibitory Fab hI365 | |||||||||||||||||||||
Map data | Relion sharpened map of PAD4 bound to inhibitory fab 365 | |||||||||||||||||||||
Sample |
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Keywords | complex / deiminase / enzyme / arginine / inflammation / calcium binding / Fab / IMMUNE SYSTEM / HYDROLASE-IMMUNE SYSTEM complex | |||||||||||||||||||||
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: 3.3 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_40590.map.gz | 24.7 MB | EMDB map data format | |
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Header (meta data) | emd-40590-v30.xml emd-40590.xml | 20 KB 20 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_40590_fsc.xml | 17 KB | Display | FSC data file |
Images | emd_40590.png | 112.8 KB | ||
Masks | emd_40590_msk_1.map | 512 MB | Mask map | |
Filedesc metadata | emd-40590.cif.gz | 6.5 KB | ||
Others | emd_40590_half_map_1.map.gz emd_40590_half_map_2.map.gz | 96.5 MB 96.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40590 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40590 | HTTPS FTP |
-Related structure data
Related structure data | 8smlMC 8smkC 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_40590.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Relion sharpened map of PAD4 bound to inhibitory fab 365 | ||||||||||||||||||||
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_40590_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: Half map 1 of PAD4 bound to inhibitory fab 365
File | emd_40590_half_map_1.map | ||||||||||||
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Annotation | Half map 1 of PAD4 bound to inhibitory fab 365 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2 of PAD4 bound to inhibitory fab 365
File | emd_40590_half_map_2.map | ||||||||||||
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Annotation | Half map 2 of PAD4 bound to inhibitory fab 365 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : hPAD4 bound to inhibitory Fab hI365
Entire | Name: hPAD4 bound to inhibitory Fab hI365 |
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Components |
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-Supramolecule #1: hPAD4 bound to inhibitory Fab hI365
Supramolecule | Name: hPAD4 bound to inhibitory Fab hI365 / 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: Fab hI365 light chain
Macromolecule | Name: Fab hI365 light 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: 23.157678 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: DIQMTQSPSS LSASVGDRVT ITCRASQSVS SAVAWYQQKP GKAPKLLIYS ASSLYSGVPS RFSGSRSGTD FTLTISSLQP EDFATYYCQ QSSSSLVTFG QGTKVEIKRT VAAPSVFIFP PSDSQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String: DIQMTQSPSS LSASVGDRVT ITCRASQSVS SAVAWYQQKP GKAPKLLIYS ASSLYSGVPS RFSGSRSGTD FTLTISSLQP EDFATYYCQ QSSSSLVTFG QGTKVEIKRT VAAPSVFIFP PSDSQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC |
-Macromolecule #3: Fab hI365 heavy chain
Macromolecule | Name: Fab hI365 heavy 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: 24.615482 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: EVQLVESGGG LVQPGGSLRL SCAASGFNFY YSIHWVRQAP GKGLEWVASI SPYSGYTSYA DSVKGRFTIS ADTSKNTAYL QMNSLRAED TAVYYCARKH PGSYPFWGWA LDYWGQGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String: EVQLVESGGG LVQPGGSLRL SCAASGFNFY YSIHWVRQAP GKGLEWVASI SPYSGYTSYA DSVKGRFTIS ADTSKNTAYL QMNSLRAED TAVYYCARKH PGSYPFWGWA LDYWGQGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSCDK THT |
-Macromolecule #4: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 6 / 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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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-8sml: |