HEADER MEMBRANE PROTEIN 15-JUL-24 9CMH TITLE CRYO-EM STRUCTURE OF HUMAN CLAUDIN-4 COMPLEX WITH CLOSTRIDIUM TITLE 2 PERFRINGENS ENTEROTOXIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CLAUDIN-4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CLOSTRIDIUM PERFRINGENS ENTEROTOXIN RECEPTOR,CPE-R,CPE- COMPND 5 RECEPTOR,WILLIAMS-BEUREN SYNDROME CHROMOSOMAL REGION 8 PROTEIN; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: HEAT-LABILE ENTEROTOXIN B CHAIN; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CLDN4, CPER, CPETR1, WBSCR8; SOURCE 6 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 7 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: CLOSTRIDIUM PERFRINGENS; SOURCE 11 ORGANISM_TAXID: 1502; SOURCE 12 GENE: CPE; SOURCE 13 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 14 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 7111 KEYWDS CLAUDIN, ENTEROTOXIN, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR A.J.VECCHIO REVDAT 4 27-NOV-24 9CMH 1 JRNL REVDAT 3 30-OCT-24 9CMH 1 JRNL REVDAT 2 23-OCT-24 9CMH 1 REMARK REVDAT 1 24-JUL-24 9CMH 0 JRNL AUTH S.S.RATHNAYAKE,S.K.ERRAMILLI,A.A.KOSSIAKOFF,A.J.VECCHIO JRNL TITL CRYO-EM STRUCTURES OF CLOSTRIDIUM PERFRINGENS ENTEROTOXIN JRNL TITL 2 BOUND TO ITS HUMAN RECEPTOR, CLAUDIN-4. JRNL REF STRUCTURE V. 32 1936 2024 JRNL REFN ISSN 0969-2126 JRNL PMID 39383874 JRNL DOI 10.1016/J.STR.2024.09.015 REMARK 2 REMARK 2 RESOLUTION. 4.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, SERIALEM, CRYOSPARC, UCSF REMARK 3 CHIMERA, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC, PHENIX REMARK 3 RECONSTRUCTION SCHEMA : FOURIER SPACE REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : 7KP4 REMARK 3 REFINEMENT SPACE : REAL REMARK 3 REFINEMENT PROTOCOL : FLEXIBLE FIT REMARK 3 REFINEMENT TARGET : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE : NULL REMARK 3 REMARK 3 FITTING PROCEDURE : NULL REMARK 3 REMARK 3 EM IMAGE RECONSTRUCTION STATISTICS REMARK 3 NOMINAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 ACTUAL PIXEL SIZE (ANGSTROMS) : NULL REMARK 3 EFFECTIVE RESOLUTION (ANGSTROMS) : 4.000 REMARK 3 NUMBER OF PARTICLES : 44683 REMARK 3 CTF CORRECTION METHOD : NONE REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9CMH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-JUL-24. REMARK 100 THE DEPOSITION ID IS D_1000285947. REMARK 245 REMARK 245 EXPERIMENTAL DETAILS REMARK 245 RECONSTRUCTION METHOD : SINGLE PARTICLE REMARK 245 SPECIMEN TYPE : NULL REMARK 245 REMARK 245 ELECTRON MICROSCOPE SAMPLE REMARK 245 SAMPLE TYPE : PARTICLE REMARK 245 PARTICLE TYPE : POINT REMARK 245 NAME OF SAMPLE : HUMAN CLAUDIN-4 COMPLEX WITH REMARK 245 CLOSTRIDIUM PERFRINGENS REMARK 245 ENTEROTOXIN REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 8.00 REMARK 245 SAMPLE SUPPORT DETAILS : GLOW-DISCHARGED FOR 60 SECONDS REMARK 245 AT 15 MA USING A PELCO EASIGLOW REMARK 245 (TED PELLA INC) INSTRUMENT. REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.40 REMARK 245 SAMPLE DETAILS : 2-PROTEIN COMPLEX REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : 7100 REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : FEI TITAN KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 BIOCONTINUUM (6K X REMARK 245 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2500.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : NULL REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 6000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 129000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 300 REMARK 245 IMAGING DETAILS : NULL REMARK 247 REMARK 247 ELECTRON MICROSCOPY REMARK 247 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM ELECTRON REMARK 247 MICROSCOPY DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE REMARK 247 THAT CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES REMARK 247 ON THESE RECORDS ARE MEANINGLESS EXCEPT FOR THE CALCULATION REMARK 247 OF THE STRUCTURE FACTORS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 SER A 3 REMARK 465 MET A 4 REMARK 465 CYS A 185 REMARK 465 PRO A 186 REMARK 465 PRO A 187 REMARK 465 ARG A 188 REMARK 465 THR A 189 REMARK 465 ASP A 190 REMARK 465 LYS A 191 REMARK 465 PRO A 192 REMARK 465 TYR A 193 REMARK 465 SER A 194 REMARK 465 ALA A 195 REMARK 465 LYS A 196 REMARK 465 TYR A 197 REMARK 465 SER A 198 REMARK 465 ALA A 199 REMARK 465 ALA A 200 REMARK 465 ARG A 201 REMARK 465 SER A 202 REMARK 465 ALA A 203 REMARK 465 ALA A 204 REMARK 465 ALA A 205 REMARK 465 SER A 206 REMARK 465 ASN A 207 REMARK 465 TYR A 208 REMARK 465 VAL A 209 REMARK 465 THR B 26 REMARK 465 PRO B 27 REMARK 465 ILE B 28 REMARK 465 ASN B 29 REMARK 465 ILE B 30 REMARK 465 THR B 31 REMARK 465 ASN B 32 REMARK 465 SER B 33 REMARK 465 ASN B 34 REMARK 465 LEU B 321 REMARK 465 VAL B 322 REMARK 465 PRO B 323 REMARK 465 ARG B 324 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OG SER B 60 OH TYR B 129 2.09 REMARK 500 O TYR B 232 OH TYR B 306 2.11 REMARK 500 NE2 GLN B 140 OD1 ASP B 152 2.16 REMARK 500 O ASP B 39 OH TYR B 264 2.16 REMARK 500 OG1 THR B 135 O THR B 159 2.17 REMARK 500 OH TYR B 133 O LEU B 179 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 38 -136.70 52.52 REMARK 500 GLU A 48 73.94 -100.46 REMARK 500 PRO A 74 43.57 -80.61 REMARK 500 GLN A 75 -15.86 70.91 REMARK 500 ASP A 110 112.42 -160.98 REMARK 500 ALA A 153 -13.10 -140.16 REMARK 500 LYS A 157 45.56 -142.76 REMARK 500 TRP B 50 78.83 -101.16 REMARK 500 HIS B 146 13.55 59.87 REMARK 500 PHE B 268 53.03 38.26 REMARK 500 ASN B 269 -4.47 67.93 REMARK 500 VAL B 282 -50.79 -124.75 REMARK 500 GLN B 295 39.59 -98.26 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-45748 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF HUMAN CLAUDIN-4 COMPLEX WITH CLOSTRIDIUM REMARK 900 PERFRINGENS ENTEROTOXIN DBREF 9CMH A 1 209 UNP O14493 CLD4_HUMAN 1 209 DBREF 9CMH B 26 319 UNP P01558 ELTB_CLOPF 26 319 SEQADV 9CMH GLY A -1 UNP O14493 EXPRESSION TAG SEQADV 9CMH SER A 0 UNP O14493 EXPRESSION TAG SEQADV 9CMH GLY B 320 UNP P01558 EXPRESSION TAG SEQADV 9CMH LEU B 321 UNP P01558 EXPRESSION TAG SEQADV 9CMH VAL B 322 UNP P01558 EXPRESSION TAG SEQADV 9CMH PRO B 323 UNP P01558 EXPRESSION TAG SEQADV 9CMH ARG B 324 UNP P01558 EXPRESSION TAG SEQRES 1 A 211 GLY SER MET ALA SER MET GLY LEU GLN VAL MET GLY ILE SEQRES 2 A 211 ALA LEU ALA VAL LEU GLY TRP LEU ALA VAL MET LEU CYS SEQRES 3 A 211 CYS ALA LEU PRO MET TRP ARG VAL THR ALA PHE ILE GLY SEQRES 4 A 211 SER ASN ILE VAL THR SER GLN THR ILE TRP GLU GLY LEU SEQRES 5 A 211 TRP MET ASN CYS VAL VAL GLN SER THR GLY GLN MET GLN SEQRES 6 A 211 CYS LYS VAL TYR ASP SER LEU LEU ALA LEU PRO GLN ASP SEQRES 7 A 211 LEU GLN ALA ALA ARG ALA LEU VAL ILE ILE SER ILE ILE SEQRES 8 A 211 VAL ALA ALA LEU GLY VAL LEU LEU SER VAL VAL GLY GLY SEQRES 9 A 211 LYS CYS THR ASN CYS LEU GLU ASP GLU SER ALA LYS ALA SEQRES 10 A 211 LYS THR MET ILE VAL ALA GLY VAL VAL PHE LEU LEU ALA SEQRES 11 A 211 GLY LEU MET VAL ILE VAL PRO VAL SER TRP THR ALA HIS SEQRES 12 A 211 ASN ILE ILE GLN ASP PHE TYR ASN PRO LEU VAL ALA SER SEQRES 13 A 211 GLY GLN LYS ARG GLU MET GLY ALA SER LEU TYR VAL GLY SEQRES 14 A 211 TRP ALA ALA SER GLY LEU LEU LEU LEU GLY GLY GLY LEU SEQRES 15 A 211 LEU CYS CYS ASN CYS PRO PRO ARG THR ASP LYS PRO TYR SEQRES 16 A 211 SER ALA LYS TYR SER ALA ALA ARG SER ALA ALA ALA SER SEQRES 17 A 211 ASN TYR VAL SEQRES 1 B 299 THR PRO ILE ASN ILE THR ASN SER ASN SER ASN LEU SER SEQRES 2 B 299 ASP GLY LEU TYR VAL ILE ASP LYS GLY ASP GLY TRP ILE SEQRES 3 B 299 LEU GLY GLU PRO SER VAL VAL SER SER GLN ILE LEU ASN SEQRES 4 B 299 PRO ASN GLU THR GLY THR PHE SER GLN SER LEU THR LYS SEQRES 5 B 299 SER LYS GLU VAL SER ILE ASN VAL ASN PHE SER VAL GLY SEQRES 6 B 299 PHE THR SER GLU PHE ILE GLN ALA SER VAL GLU TYR GLY SEQRES 7 B 299 PHE GLY ILE THR ILE GLY GLU GLN ASN THR ILE GLU ARG SEQRES 8 B 299 SER VAL SER THR THR ALA GLY PRO ASN GLU TYR VAL TYR SEQRES 9 B 299 TYR LYS VAL TYR ALA THR TYR ARG LYS TYR GLN ALA ILE SEQRES 10 B 299 ARG ILE SER HIS GLY ASN ILE SER ASP ASP GLY SER ILE SEQRES 11 B 299 TYR LYS LEU THR GLY ILE TRP LEU SER LYS THR SER ALA SEQRES 12 B 299 ASP SER LEU GLY ASN ILE ASP GLN GLY SER LEU ILE GLU SEQRES 13 B 299 THR GLY GLU ARG CYS VAL LEU THR VAL PRO SER THR ASP SEQRES 14 B 299 ILE GLU LYS GLU ILE LEU ASP LEU ALA ALA ALA THR GLU SEQRES 15 B 299 ARG LEU ASN LEU THR ASP ALA LEU ASN SER ASN PRO ALA SEQRES 16 B 299 GLY ASN LEU TYR ASP TRP ARG SER SER ASN SER TYR PRO SEQRES 17 B 299 TRP THR GLN LYS LEU ASN LEU HIS LEU THR ILE THR ALA SEQRES 18 B 299 THR GLY GLN LYS TYR ARG ILE LEU ALA SER LYS ILE VAL SEQRES 19 B 299 ASP PHE ASN ILE TYR SER ASN ASN PHE ASN ASN LEU VAL SEQRES 20 B 299 LYS LEU GLU GLN SER LEU GLY ASP GLY VAL LYS ASP HIS SEQRES 21 B 299 TYR VAL ASP ILE SER LEU ASP ALA GLY GLN TYR VAL LEU SEQRES 22 B 299 VAL MET LYS ALA ASN SER SER TYR SER GLY ASN TYR PRO SEQRES 23 B 299 TYR SER ILE LEU PHE GLN LYS PHE GLY LEU VAL PRO ARG HELIX 1 AA1 GLY A 5 LEU A 27 1 23 HELIX 2 AA2 SER A 69 LEU A 73 5 5 HELIX 3 AA3 LEU A 77 CYS A 104 1 28 HELIX 4 AA4 ASP A 110 ASN A 149 1 40 HELIX 5 AA5 GLY A 161 ASN A 184 1 24 HELIX 6 AA6 THR B 92 PHE B 104 1 13 HELIX 7 AA7 SER B 170 ILE B 174 5 5 HELIX 8 AA8 ASN B 210 ASN B 218 1 9 SHEET 1 AA1 2 TRP A 47 GLU A 48 0 SHEET 2 AA1 2 ASN A 53 CYS A 54 -1 O CYS A 54 N TRP A 47 SHEET 1 AA2 4 VAL B 57 GLN B 61 0 SHEET 2 AA2 4 TYR B 127 ILE B 144 -1 O TYR B 130 N GLN B 61 SHEET 3 AA2 4 GLY B 40 LYS B 46 -1 N TYR B 42 O ILE B 142 SHEET 4 AA2 4 ASP B 194 ILE B 195 -1 O ILE B 195 N ASP B 45 SHEET 1 AA3 5 GLU B 80 ILE B 83 0 SHEET 2 AA3 5 GLY B 153 ALA B 168 -1 O TYR B 156 N GLU B 80 SHEET 3 AA3 5 TYR B 127 ILE B 144 -1 N ARG B 137 O LYS B 157 SHEET 4 AA3 5 GLY B 40 LYS B 46 -1 N TYR B 42 O ILE B 142 SHEET 5 AA3 5 GLU B 198 ILE B 199 -1 O ILE B 199 N LEU B 41 SHEET 1 AA4 2 TRP B 50 ILE B 51 0 SHEET 2 AA4 2 ARG B 185 CYS B 186 -1 O ARG B 185 N ILE B 51 SHEET 1 AA5 2 GLU B 67 PHE B 71 0 SHEET 2 AA5 2 VAL B 118 ALA B 122 -1 O ALA B 122 N GLU B 67 SHEET 1 AA6 5 ARG B 208 LEU B 209 0 SHEET 2 AA6 5 LEU B 238 LEU B 242 1 O HIS B 241 N LEU B 209 SHEET 3 AA6 5 VAL B 297 ALA B 302 -1 O LEU B 298 N LEU B 240 SHEET 4 AA6 5 VAL B 259 ASN B 267 -1 N TYR B 264 O VAL B 297 SHEET 5 AA6 5 ASN B 270 GLU B 275 -1 O VAL B 272 N SER B 265 SHEET 1 AA7 2 ASP B 225 ARG B 227 0 SHEET 2 AA7 2 SER B 313 LEU B 315 -1 O ILE B 314 N TRP B 226 SHEET 1 AA8 2 GLN B 249 LEU B 254 0 SHEET 2 AA8 2 TYR B 286 LEU B 291 -1 O VAL B 287 N ILE B 253 SSBOND 1 CYS A 54 CYS A 64 1555 1555 2.03 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000