HEADER TRANSPORT PROTEIN 20-NOV-24 9KOM TITLE CRYO-EM STRUCTURE OF HUMAN PANNEXIN-3 PROTOMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: PANNEXIN-3; COMPND 3 CHAIN: A; COMPND 4 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: PANX3; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: EXPI293F; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PCDNA3.4 KEYWDS PANNEXIN, INNEXIN, TRANSPORT PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR T.TSUYAMA,K.YOKOYAMA REVDAT 1 15-JAN-25 9KOM 0 JRNL AUTH T.TSUYAMA,R.TERAMURA,K.MITSUOKA,J.I.KISHIKAWA,K.YOKOYAMA JRNL TITL CRYO-EM STRUCTURE OF THE HUMAN PANNEXIN-3 CHANNEL. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 745 51227 2025 JRNL REFN ESSN 1090-2104 JRNL PMID 39721314 JRNL DOI 10.1016/J.BBRC.2024.151227 REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, SERIALEM, CTFFIND, REMARK 3 CRYOSPARC, COOT, PHENIX, CRYOSPARC, REMARK 3 CRYOSPARC, CRYOSPARC REMARK 3 RECONSTRUCTION SCHEMA : FOURIER SPACE REMARK 3 REMARK 3 EM MAP-MODEL FITTING AND REFINEMENT REMARK 3 PDB ENTRY : NULL REMARK 3 REFINEMENT SPACE : NULL REMARK 3 REFINEMENT PROTOCOL : AB INITIO MODEL 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) : 3.200 REMARK 3 NUMBER OF PARTICLES : 393863 REMARK 3 CTF CORRECTION METHOD : PHASE FLIPPING AND AMPLITUDE REMARK 3 CORRECTION REMARK 3 REMARK 3 EM RECONSTRUCTION MAGNIFICATION CALIBRATION: NULL REMARK 3 REMARK 3 OTHER DETAILS: NULL REMARK 4 REMARK 4 9KOM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-NOV-24. REMARK 100 THE DEPOSITION ID IS D_1300053913. 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 : PANNEXIN-3 PROTOMER REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 2.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : NULL REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 8.00 REMARK 245 SAMPLE DETAILS : NULL REMARK 245 REMARK 245 DATA ACQUISITION REMARK 245 DATE OF EXPERIMENT : NULL REMARK 245 NUMBER OF MICROGRAPHS-IMAGES : NULL REMARK 245 TEMPERATURE (KELVIN) : NULL REMARK 245 MICROSCOPE MODEL : TFS KRIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 1000.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2200.00 REMARK 245 MINIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 MAXIMUM TILT ANGLE (DEGREES) : NULL REMARK 245 NOMINAL CS : 2.70 REMARK 245 IMAGING MODE : BRIGHT FIELD REMARK 245 ELECTRON DOSE (ELECTRONS NM**-2) : 5000.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : NULL 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 MET A 1 REMARK 465 SER A 2 REMARK 465 LEU A 3 REMARK 465 ALA A 4 REMARK 465 HIS A 5 REMARK 465 THR A 6 REMARK 465 ALA A 7 REMARK 465 ALA A 8 REMARK 465 GLU A 9 REMARK 465 TYR A 10 REMARK 465 MET A 11 REMARK 465 LEU A 12 REMARK 465 SER A 13 REMARK 465 ASP A 14 REMARK 465 ALA A 15 REMARK 465 LEU A 16 REMARK 465 LEU A 17 REMARK 465 PRO A 18 REMARK 465 ASP A 19 REMARK 465 ARG A 20 REMARK 465 ARG A 21 REMARK 465 GLY A 22 REMARK 465 PRO A 23 REMARK 465 ARG A 24 REMARK 465 LEU A 25 REMARK 465 LYS A 26 REMARK 465 GLN A 93 REMARK 465 ASP A 94 REMARK 465 GLY A 95 REMARK 465 PRO A 96 REMARK 465 GLY A 97 REMARK 465 GLN A 98 REMARK 465 ASP A 99 REMARK 465 LYS A 100 REMARK 465 MET A 101 REMARK 465 MET A 161 REMARK 465 LEU A 162 REMARK 465 LYS A 163 REMARK 465 ILE A 164 REMARK 465 ARG A 165 REMARK 465 GLN A 166 REMARK 465 LYS A 167 REMARK 465 SER A 168 REMARK 465 SER A 169 REMARK 465 ASP A 170 REMARK 465 PRO A 171 REMARK 465 TYR A 172 REMARK 465 VAL A 173 REMARK 465 PHE A 174 REMARK 465 TRP A 175 REMARK 465 ASN A 176 REMARK 465 GLU A 177 REMARK 465 LEU A 178 REMARK 465 GLU A 179 REMARK 465 LYS A 180 REMARK 465 ALA A 181 REMARK 465 ARG A 182 REMARK 465 LEU A 301 REMARK 465 LEU A 302 REMARK 465 SER A 303 REMARK 465 VAL A 304 REMARK 465 TYR A 305 REMARK 465 GLU A 306 REMARK 465 MET A 307 REMARK 465 LEU A 308 REMARK 465 LEU A 349 REMARK 465 CYS A 350 REMARK 465 VAL A 351 REMARK 465 LEU A 352 REMARK 465 LYS A 353 REMARK 465 ASP A 354 REMARK 465 THR A 355 REMARK 465 THR A 356 REMARK 465 THR A 357 REMARK 465 GLN A 358 REMARK 465 LYS A 359 REMARK 465 HIS A 360 REMARK 465 ASN A 361 REMARK 465 ILE A 362 REMARK 465 ASP A 363 REMARK 465 THR A 364 REMARK 465 VAL A 365 REMARK 465 VAL A 366 REMARK 465 LEU A 375 REMARK 465 GLU A 376 REMARK 465 PRO A 377 REMARK 465 SER A 378 REMARK 465 LYS A 379 REMARK 465 PRO A 380 REMARK 465 LYS A 381 REMARK 465 HIS A 382 REMARK 465 LEU A 383 REMARK 465 THR A 384 REMARK 465 ASN A 385 REMARK 465 SER A 386 REMARK 465 ALA A 387 REMARK 465 CYS A 388 REMARK 465 ASP A 389 REMARK 465 GLU A 390 REMARK 465 HIS A 391 REMARK 465 PRO A 392 REMARK 465 GLY A 393 REMARK 465 SER A 394 REMARK 465 GLY A 395 REMARK 465 GLY A 396 REMARK 465 SER A 397 REMARK 465 GLY A 398 REMARK 465 HIS A 399 REMARK 465 HIS A 400 REMARK 465 HIS A 401 REMARK 465 HIS A 402 REMARK 465 HIS A 403 REMARK 465 HIS A 404 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 183 CG CD CE NZ REMARK 470 GLU A 184 CG CD OE1 OE2 REMARK 470 ARG A 185 CG CD NE CZ NH1 NH2 REMARK 470 TYR A 186 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 PHE A 187 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 188 CG CD OE1 OE2 REMARK 470 PHE A 343 CG CD1 CD2 CE1 CE2 CZ REMARK 470 SER A 344 OG REMARK 470 TRP A 345 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 345 CZ3 CH2 REMARK 470 LEU A 346 CG CD1 CD2 REMARK 470 SER A 347 OG REMARK 470 VAL A 348 CG1 CG2 REMARK 470 ASP A 367 CG OD1 OD2 REMARK 470 PHE A 368 CG CD1 CD2 CE1 CE2 CZ REMARK 470 MET A 369 CG SD CE REMARK 470 THR A 370 OG1 CG2 REMARK 470 LEU A 371 CG CD1 CD2 REMARK 470 LEU A 372 CG CD1 CD2 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 ASN A 71 36.81 -98.27 REMARK 500 SER A 73 -137.26 58.26 REMARK 500 ALA A 109 32.19 -98.39 REMARK 500 GLU A 184 54.90 -91.10 REMARK 500 HIS A 203 33.85 -140.75 REMARK 500 LEU A 319 -178.16 -172.50 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-62478 RELATED DB: EMDB REMARK 900 CRYO-EM STRUCTURE OF HUMAN PANNEXIN-3 PROTOMER DBREF 9KOM A 1 392 UNP Q96QZ0 PANX3_HUMAN 1 392 SEQADV 9KOM GLY A 393 UNP Q96QZ0 EXPRESSION TAG SEQADV 9KOM SER A 394 UNP Q96QZ0 EXPRESSION TAG SEQADV 9KOM GLY A 395 UNP Q96QZ0 EXPRESSION TAG SEQADV 9KOM GLY A 396 UNP Q96QZ0 EXPRESSION TAG SEQADV 9KOM SER A 397 UNP Q96QZ0 EXPRESSION TAG SEQADV 9KOM GLY A 398 UNP Q96QZ0 EXPRESSION TAG SEQADV 9KOM HIS A 399 UNP Q96QZ0 EXPRESSION TAG SEQADV 9KOM HIS A 400 UNP Q96QZ0 EXPRESSION TAG SEQADV 9KOM HIS A 401 UNP Q96QZ0 EXPRESSION TAG SEQADV 9KOM HIS A 402 UNP Q96QZ0 EXPRESSION TAG SEQADV 9KOM HIS A 403 UNP Q96QZ0 EXPRESSION TAG SEQADV 9KOM HIS A 404 UNP Q96QZ0 EXPRESSION TAG SEQRES 1 A 404 MET SER LEU ALA HIS THR ALA ALA GLU TYR MET LEU SER SEQRES 2 A 404 ASP ALA LEU LEU PRO ASP ARG ARG GLY PRO ARG LEU LYS SEQRES 3 A 404 GLY LEU ARG LEU GLU LEU PRO LEU ASP ARG ILE VAL LYS SEQRES 4 A 404 PHE VAL ALA VAL GLY SER PRO LEU LEU LEU MET SER LEU SEQRES 5 A 404 ALA PHE ALA GLN GLU PHE SER SER GLY SER PRO ILE SER SEQRES 6 A 404 CYS PHE SER PRO SER ASN PHE SER ILE ARG GLN ALA ALA SEQRES 7 A 404 TYR VAL ASP SER SER CYS TRP ASP SER LEU LEU HIS HIS SEQRES 8 A 404 LYS GLN ASP GLY PRO GLY GLN ASP LYS MET LYS SER LEU SEQRES 9 A 404 TRP PRO HIS LYS ALA LEU PRO TYR SER LEU LEU ALA LEU SEQRES 10 A 404 ALA LEU LEU MET TYR LEU PRO VAL LEU LEU TRP GLN TYR SEQRES 11 A 404 ALA ALA VAL PRO ALA LEU SER SER ASP LEU LEU PHE ILE SEQRES 12 A 404 ILE SER GLU LEU ASP LYS SER TYR ASN ARG SER ILE ARG SEQRES 13 A 404 LEU VAL GLN HIS MET LEU LYS ILE ARG GLN LYS SER SER SEQRES 14 A 404 ASP PRO TYR VAL PHE TRP ASN GLU LEU GLU LYS ALA ARG SEQRES 15 A 404 LYS GLU ARG TYR PHE GLU PHE PRO LEU LEU GLU ARG TYR SEQRES 16 A 404 LEU ALA CYS LYS GLN ARG SER HIS SER LEU VAL ALA THR SEQRES 17 A 404 TYR LEU LEU ARG ASN SER LEU LEU LEU ILE PHE THR SER SEQRES 18 A 404 ALA THR TYR LEU TYR LEU GLY HIS PHE HIS LEU ASP VAL SEQRES 19 A 404 PHE PHE GLN GLU GLU PHE SER CYS SER ILE LYS THR GLY SEQRES 20 A 404 LEU LEU SER ASP GLU THR HIS VAL PRO ASN LEU ILE THR SEQRES 21 A 404 CYS ARG LEU THR SER LEU SER ILE PHE GLN ILE VAL SER SEQRES 22 A 404 LEU SER SER VAL ALA ILE TYR THR ILE LEU VAL PRO VAL SEQRES 23 A 404 ILE ILE TYR ASN LEU THR ARG LEU CYS ARG TRP ASP LYS SEQRES 24 A 404 ARG LEU LEU SER VAL TYR GLU MET LEU PRO ALA PHE ASP SEQRES 25 A 404 LEU LEU SER ARG LYS MET LEU GLY CYS PRO ILE ASN ASP SEQRES 26 A 404 LEU ASN VAL ILE LEU LEU PHE LEU ARG ALA ASN ILE SER SEQRES 27 A 404 GLU LEU ILE SER PHE SER TRP LEU SER VAL LEU CYS VAL SEQRES 28 A 404 LEU LYS ASP THR THR THR GLN LYS HIS ASN ILE ASP THR SEQRES 29 A 404 VAL VAL ASP PHE MET THR LEU LEU ALA GLY LEU GLU PRO SEQRES 30 A 404 SER LYS PRO LYS HIS LEU THR ASN SER ALA CYS ASP GLU SEQRES 31 A 404 HIS PRO GLY SER GLY GLY SER GLY HIS HIS HIS HIS HIS SEQRES 32 A 404 HIS HELIX 1 AA1 LEU A 32 GLY A 61 1 30 HELIX 2 AA2 ILE A 74 LEU A 88 1 15 HELIX 3 AA3 LEU A 104 ALA A 109 1 6 HELIX 4 AA4 ALA A 109 ALA A 132 1 24 HELIX 5 AA5 ALA A 132 GLN A 159 1 28 HELIX 6 AA6 PRO A 190 ARG A 201 1 12 HELIX 7 AA7 LEU A 205 HIS A 231 1 27 HELIX 8 AA8 LEU A 232 PHE A 235 5 4 HELIX 9 AA9 SER A 265 LEU A 294 1 30 HELIX 10 AB1 ALA A 310 LYS A 317 1 8 HELIX 11 AB2 ASP A 325 ASN A 336 1 12 HELIX 12 AB3 PHE A 368 GLY A 374 1 7 SHEET 1 AA1 3 ILE A 64 CYS A 66 0 SHEET 2 AA1 3 ILE A 259 LEU A 263 -1 O ARG A 262 N SER A 65 SHEET 3 AA1 3 GLU A 239 CYS A 242 -1 N CYS A 242 O ILE A 259 SSBOND 1 CYS A 66 CYS A 261 1555 1555 2.03 SSBOND 2 CYS A 84 CYS A 242 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 TER 2269 GLY A 374 CONECT 298 1614 CONECT 436 1473 CONECT 1473 436 CONECT 1614 298 MASTER 267 0 0 12 3 0 0 6 2268 1 4 32 END