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Yorodumi- EMDB-45749: Cryo-EM structure of human claudin-4 complex with Clostridium per... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-45749 | |||||||||
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Title | Cryo-EM structure of human claudin-4 complex with Clostridium perfringens enterotoxin, sFab COP-1, and Nanobody | |||||||||
Map data | ||||||||||
Sample |
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Keywords | claudin / Fab / enterotoxin / 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 | synthetic construct (others) / Homo sapiens (human) / Clostridium perfringens (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.83 Å | |||||||||
Authors | Vecchio AJ | |||||||||
Funding support | United States, 2 items
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Citation | Journal: To Be Published Title: Cryo-EM Structures of Clostridium perfringens Enterotoxin Bound to its Human Receptor, Claudin-4 Authors: Vecchio AJ / Kossiakoff AA / Erramilli SK / Rathnayake SS | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_45749.map.gz | 88.8 MB | EMDB map data format | |
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Header (meta data) | emd-45749-v30.xml emd-45749.xml | 23.4 KB 23.4 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_45749_fsc.xml | 11.9 KB | Display | FSC data file |
Images | emd_45749.png | 81.6 KB | ||
Filedesc metadata | emd-45749.cif.gz | 7.3 KB | ||
Others | emd_45749_half_map_1.map.gz emd_45749_half_map_2.map.gz | 165 MB 165 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-45749 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-45749 | HTTPS FTP |
-Validation report
Summary document | emd_45749_validation.pdf.gz | 767.5 KB | Display | EMDB validaton report |
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Full document | emd_45749_full_validation.pdf.gz | 767 KB | Display | |
Data in XML | emd_45749_validation.xml.gz | 20.6 KB | Display | |
Data in CIF | emd_45749_validation.cif.gz | 26.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-45749 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-45749 | HTTPS FTP |
-Related structure data
Related structure data | 9cmiMC 9cmhC 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_45749.map.gz / Format: CCP4 / Size: 178 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: 0.827 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_45749_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_45749_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, 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, sFab COP-1, and Nanobody type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 / Details: 5-protein complex |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 120 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: 22.234332 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: GSMASMGLQV MGIALAVLGW LAVMLCCALP MWRVTAFIGS NIVTSQTIWE GLWMNCVVQS TGQMQCKVYD SLLALPQDLQ AARALVIIS IIVAALGVLL SVVGGKCTNC LEDESAKAKT MIVAGVVFLL AGLMVIVPVS WTAHNIIQDF YNPLVASGQK R EMGASLYV ...String: GSMASMGLQV MGIALAVLGW LAVMLCCALP MWRVTAFIGS NIVTSQTIWE GLWMNCVVQS TGQMQCKVYD SLLALPQDLQ AARALVIIS IIVAALGVLL SVVGGKCTNC LEDESAKAKT MIVAGVVFLL AGLMVIVPVS WTAHNIIQDF YNPLVASGQK R EMGASLYV GWAASGLLLL GGGLLCCNCP PRTDKPYSAK YSAARSAAAS NYV UniProtKB: Claudin-4 |
-Macromolecule #2: Heat-labile enterotoxin B chain
Macromolecule | Name: Heat-labile enterotoxin B chain / type: protein_or_peptide / ID: 2 / Details: Trypsin treated CpE / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Clostridium perfringens (bacteria) |
Molecular weight | Theoretical: 33.000582 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: TPINITNSNS NLSDGLYVID KGDGWILGEP SVVSSQILNP NETGTFSQSL TKSKEVSINV NFSVGFTSEF IQASVEYGFG ITIGEQNTI ERSVSTTAGP NEYVYYKVYA TYRKYQAIRI SHGNISDDGS IYKLTGIWLS KTSADSLGNI DQGSLIETGE R CVLTVPST ...String: TPINITNSNS NLSDGLYVID KGDGWILGEP SVVSSQILNP NETGTFSQSL TKSKEVSINV NFSVGFTSEF IQASVEYGFG ITIGEQNTI ERSVSTTAGP NEYVYYKVYA TYRKYQAIRI SHGNISDDGS IYKLTGIWLS KTSADSLGNI DQGSLIETGE R CVLTVPST DIEKEILDLA AATERLNLTD ALNSNPAGNL YDWRSSNSYP WTQKLNLHLT ITATGQKYRI LASKIVDFNI YS NNFNNLV KLEQSLGDGV KDHYVDISLD AGQYVLVMKA NSSYSGNYPY SILFQKFGLV PR UniProtKB: Heat-labile enterotoxin B chain |
-Macromolecule #3: COP-1 sFab Heavy Chain
Macromolecule | Name: COP-1 sFab Heavy 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: 28.064498 KDa |
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 #4: Anti-Fab Nanobody
Macromolecule | Name: Anti-Fab Nanobody / 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: 13.175438 KDa |
Sequence | String: GSVQLQESGG GLVQPGGSLR LSCAASGRTI SRYAMSWFRQ APGKEREFVA VARRSGDGAF YADSVQGRFT VSRDDAKNTV YLQMNSLKP EDTAVYYCAI DSDTFYSGSY DYWGQGTQVT VS |
-Macromolecule #5: COP-1 sFab Light Chain
Macromolecule | Name: COP-1 sFab Light Chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 25.794859 KDa |
Sequence | String: MKKNIAFLLA SMFVFSIATN AYASDIQMTQ SPSSLSASVG DRVTITCRAS QSVSSAVAWY QQKPGKAPKL LIYSASSLYS GVPSRFSGS RSGTDFTLTI SSLQPEDFAT YYCQQSSSSL ITFGQGTKVE IKRTVAAPSV FIFPPSDSQL KSGTASVVCL L NNFYPREA ...String: MKKNIAFLLA SMFVFSIATN AYASDIQMTQ SPSSLSASVG DRVTITCRAS QSVSSAVAWY QQKPGKAPKL LIYSASSLYS GVPSRFSGS RSGTDFTLTI SSLQPEDFAT YYCQQSSSSL ITFGQGTKVE IKRTVAAPSV FIFPPSDSQL KSGTASVVCL L NNFYPREA KVQWKVDNAL QSGNSQESVT EQDSKDSTYS LSSTLTLSKA DYEKHKVYAC EVTHQGLSSP VTKSFNRGEC |
-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: 2 / 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 | 5.6 mg/mL | ||||||||||||
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Buffer | pH: 7.4 Component:
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: 30 sec. Details: glow-discharged for 30 seconds at 20 W using a Solarus 950 (Gatan) plasma cleaner | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum |
Software | Name: EPU |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 6774 / Average electron dose: 70.0 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: 105000 |
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
Initial model |
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Software | Name: UCSF Chimera | ||||||
Refinement | Space: REAL / Protocol: FLEXIBLE FIT | ||||||
Output model | PDB-9cmi: |