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Yorodumi- EMDB-41899: Cryo-EM structure of human claudin-4 complex with Clostridium per... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41899 | |||||||||
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Title | Cryo-EM structure of human claudin-4 complex with Clostridium perfringens enterotoxin C-terminal domain, sFab COP-1, and Nanobody (Loose Mask) | |||||||||
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Sample |
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Keywords | Claudin / Fab / Toxin / Nanobody / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information paracellular transport / positive regulation of metallopeptidase activity / calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules / Tight junction interactions / bicellular tight junction assembly / apicolateral plasma membrane / regulation of cell morphogenesis / tight junction / chloride channel activity / positive regulation of wound healing ...paracellular transport / positive regulation of metallopeptidase activity / calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules / Tight junction interactions / bicellular tight junction assembly / apicolateral plasma membrane / regulation of cell morphogenesis / tight junction / chloride channel activity / positive regulation of wound healing / renal absorption / chloride channel complex / bicellular tight junction / lateral plasma membrane / establishment of skin barrier / basal plasma membrane / response to progesterone / female pregnancy / circadian rhythm / transmembrane signaling receptor activity / cell-cell junction / toxin activity / cell adhesion / positive regulation of cell migration / apical plasma membrane / structural molecule activity / extracellular region / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Clostridium perfringens (bacteria) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.99 Å | |||||||||
Authors | Vecchio AJ | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Commun Biol / Year: 2024 Title: Structural and biophysical insights into targeting of claudin-4 by a synthetic antibody fragment. Authors: Satchal K Erramilli / Pawel K Dominik / Chinemerem P Ogbu / Anthony A Kossiakoff / Alex J Vecchio / Abstract: Claudins are a 27-member family of ~25 kDa membrane proteins that integrate into tight junctions to form molecular barriers at the paracellular spaces between endothelial and epithelial cells. As ...Claudins are a 27-member family of ~25 kDa membrane proteins that integrate into tight junctions to form molecular barriers at the paracellular spaces between endothelial and epithelial cells. As the backbone of tight junction structure and function, claudins are attractive targets for modulating tissue permeability to deliver drugs or treat disease. However, structures of claudins are limited due to their small sizes and physicochemical properties-these traits also make therapy development a challenge. Here we report the development of a synthetic antibody fragment (sFab) that binds human claudin-4 and the determination of a high-resolution structure of it bound to claudin-4/enterotoxin complexes using cryogenic electron microscopy. Structural and biophysical results reveal this sFabs mechanism of select binding to human claudin-4 over other homologous claudins and establish the ability of sFabs to bind hard-to-target claudins to probe tight junction structure and function. The findings provide a framework for tight junction modulation by sFabs for tissue-selective therapies. #1: Journal: bioRxiv / Year: 2023 Title: Cryo-EM structures of a synthetic antibody against 22 kDa claudin-4 reveal its complex with Authors: Erramilli SK / Dominik PK / Ogbu CP / Kossiakoff AA / Vecchio AJ | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41899.map.gz | 52.1 MB | EMDB map data format | |
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Header (meta data) | emd-41899-v30.xml emd-41899.xml | 23.3 KB 23.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41899_fsc.xml | 13.6 KB | Display | FSC data file |
Images | emd_41899.png | 48.8 KB | ||
Masks | emd_41899_msk_1.map | 103 MB | Mask map | |
Filedesc metadata | emd-41899.cif.gz | 7.1 KB | ||
Others | emd_41899_half_map_1.map.gz emd_41899_half_map_2.map.gz | 95.6 MB 95.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41899 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41899 | HTTPS FTP |
-Validation report
Summary document | emd_41899_validation.pdf.gz | 699.2 KB | Display | EMDB validaton report |
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Full document | emd_41899_full_validation.pdf.gz | 698.8 KB | Display | |
Data in XML | emd_41899_validation.xml.gz | 17.8 KB | Display | |
Data in CIF | emd_41899_validation.cif.gz | 23.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41899 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41899 | HTTPS FTP |
-Related structure data
Related structure data | 8u4vMC 8u5bC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_41899.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.068 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_41899_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_41899_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_41899_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human claudin-4 complex with Clostridium perfringens enterotoxin ...
Entire | Name: Human claudin-4 complex with Clostridium perfringens enterotoxin C-terminal domain, sFab COP-1, and Nanobody |
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Components |
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-Supramolecule #1: Human claudin-4 complex with Clostridium perfringens enterotoxin ...
Supramolecule | Name: Human claudin-4 complex with Clostridium perfringens enterotoxin C-terminal domain, sFab COP-1, and Nanobody type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 Details: Assembled complex of 5 proteins (Fab is 2 protein) expressed from insect cells and E coli |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 100 KDa |
-Macromolecule #1: Claudin-4
Macromolecule | Name: Claudin-4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 22.613852 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MASMGLQVMG IALAVLGWLA VMLCCALPMW RVTAFIGSNI VTSQTIWEGL WMNCVVQSTG QMQCKVYDSL LALPQDLQAA RALVIISII VAALGVLLSV VGGKCTNCLE DESAKAKTMI VAGVVFLLAG LMVIVPVSWT AHNIIQDFYN PLVASGQKRE M GASLYVGW ...String: MASMGLQVMG IALAVLGWLA VMLCCALPMW RVTAFIGSNI VTSQTIWEGL WMNCVVQSTG QMQCKVYDSL LALPQDLQAA RALVIISII VAALGVLLSV VGGKCTNCLE DESAKAKTMI VAGVVFLLAG LMVIVPVSWT AHNIIQDFYN PLVASGQKRE M GASLYVGW AASGLLLLGG GLLCCNCPPR TDKPYSAKYS AARSAAASNY VGLVPR UniProtKB: Claudin-4 |
-Macromolecule #2: Heat-labile enterotoxin B chain
Macromolecule | Name: Heat-labile enterotoxin B chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Clostridium perfringens (bacteria) |
Molecular weight | Theoretical: 14.044594 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: GSDEILDLAA ATERLNLTDA LNSNPAGNLY DWRSSNSYPW TQKLNLHLTI TATGQKYRIL ASKIVDFNIY SNNFNNLVKL EQSLGDGVK DHYVDISLDA GQYVLVMKAN SSYSGNYPYS ILFQKF UniProtKB: Heat-labile enterotoxin B chain |
-Macromolecule #3: COP-1 sFab Light Chain
Macromolecule | Name: COP-1 sFab Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.258783 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQSSSSLITF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String: SDIQMTQSPS SLSASVGDRV TITCRASQSV SSAVAWYQQK PGKAPKLLIY SASSLYSGVP SRFSGSRSGT DFTLTISSLQ PEDFATYYC QQSSSSLITF GQGTKVEIKR TVAAPSVFIF PPSDSQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC |
-Macromolecule #4: COP-1 sFab Heavy Chain
Macromolecule | Name: COP-1 sFab Heavy Chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 28.064498 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKKNIAFLLA SMFVFSIATN AYAEISEVQL VESGGGLVQP GGSLRLSCAA SGFNFSSSYI HWVRQAPGKG LEWVASISSS SGSTSYADS VKGRFTISAD TSKNTAYLQM NSLRAEDTAV YYCARWFHPW WWWEYLFRGA IDYWGQGTLV TVSSASTKGP S VFPLAPSS ...String: MKKNIAFLLA SMFVFSIATN AYAEISEVQL VESGGGLVQP GGSLRLSCAA SGFNFSSSYI HWVRQAPGKG LEWVASISSS SGSTSYADS VKGRFTISAD TSKNTAYLQM NSLRAEDTAV YYCARWFHPW WWWEYLFRGA IDYWGQGTLV TVSSASTKGP S VFPLAPSS KSTSGGTAAL GCLVKDYFPE PVTVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NH KPSNTKV DKKVEPKSCD KTHT |
-Macromolecule #5: Anti-fab nanobody
Macromolecule | Name: Anti-fab nanobody / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 13.175438 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: GSVQLQESGG GLVQPGGSLR LSCAASGRTI SRYAMSWFRQ APGKEREFVA VARRSGDGAF YADSVQGRFT VSRDDAKNTV YLQMNSLKP EDTAVYYCAI DSDTFYSGSY DYWGQGTQVT VS |
-Macromolecule #6: Lauryl Maltose Neopentyl Glycol
Macromolecule | Name: Lauryl Maltose Neopentyl Glycol / type: ligand / ID: 6 / Number of copies: 1 / Formula: AV0 |
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Molecular weight | Theoretical: 1.005188 KDa |
Chemical component information | ChemComp-AV0: |
-Macromolecule #7: water
Macromolecule | Name: water / type: ligand / ID: 7 / Number of copies: 3 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 7 mg/mL |
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Buffer | pH: 7.4 / Details: 20 mM Hepes pH 7.4, 100 mM NaCl, and 0.003% LMNG |
Grid | Model: UltrAuFoil / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 5039 / Average electron dose: 60.0 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: 2.1 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |