HEADER MEMBRANE PROTEIN 07-JUL-25 9PFZ TITLE ARCHITECTURE OF HUMAN VOLTAGE DEPENDENT ANION CHANNEL 1 IN NANODISCS COMPND MOL_ID: 1; COMPND 2 MOLECULE: NON-SELECTIVE VOLTAGE-GATED ION CHANNEL VDAC1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: OUTER MITOCHONDRIAL MEMBRANE PROTEIN PORIN 1,PLASMALEMMAL COMPND 5 PORIN,PORIN 31HL,PORIN 31HM,VOLTAGE-DEPENDENT ANION-SELECTIVE CHANNEL COMPND 6 PROTEIN 1,VDAC-1,HVDAC1; COMPND 7 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: VDAC1, VDAC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS BETA-BARREL, MITOCHONDRIAL OUTER MEMBRANE PROTEIN, LIPID BILAYER KEYWDS 2 NANODISC, MEMBRANE PROTEIN EXPDTA ELECTRON MICROSCOPY AUTHOR S.M.MODARESI,M.DEGEN,S.HILLER REVDAT 1 27-MAY-26 9PFZ 0 JRNL AUTH S.M.MODARESI,L.ZHANG,A.A.SAEI,M.DEGEN,M.KHAVANI,H.GHARIBI, JRNL AUTH 2 A.VEGVARI,Z.YE,J.ZHANG,E.PAVLOV,E.A.JONAS,K.D.TEW,S.HILLER, JRNL AUTH 3 D.M.TOWNSEND,E.N.MALDONADO JRNL TITL SMALL MOLECULE INHIBITION OF VDAC1 REROUTES MITOCHONDRIAL JRNL TITL 2 METABOLITE FLUX. JRNL REF MOL.CELLS 00369 2026 JRNL REFN ISSN 1016-8478 JRNL PMID 42134653 JRNL DOI 10.1016/J.MOCELL.2026.100369 REMARK 2 REMARK 2 RESOLUTION. 5.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 SOFTWARE PACKAGES : CRYOSPARC, CRYOSPARC, UCSF CHIMERAX, REMARK 3 CRYOSPARC, CRYOSPARC, CRYOSPARC, REMARK 3 CRYOSPARC, UCSF CHIMERAX REMARK 3 RECONSTRUCTION SCHEMA : NULL 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) : 5.400 REMARK 3 NUMBER OF PARTICLES : 202865 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 9PFZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JUL-25. REMARK 100 THE DEPOSITION ID IS D_1000297764. 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 : VDAC1 REMARK 245 SAMPLE CONCENTRATION (MG ML-1) : 2.00 REMARK 245 SAMPLE SUPPORT DETAILS : NULL REMARK 245 SAMPLE VITRIFICATION DETAILS : 3.0 UL SAMPLE, BLOT TIME 3SEC, REMARK 245 BLOTFORCE 1, BLOT TOTAL 1, REMARK 245 SAMPLE BUFFER : NULL REMARK 245 PH : 7.00 REMARK 245 SAMPLE DETAILS : RECOMBINANT HUMAN VDAC1 REMARK 245 RECONSTITUTED IN LIPID BILAYER NANODISCS 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 GLACIOS REMARK 245 DETECTOR TYPE : GATAN K3 (6K X 4K) REMARK 245 MINIMUM DEFOCUS (NM) : 600.00 REMARK 245 MAXIMUM DEFOCUS (NM) : 2000.00 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) : 5400.00 REMARK 245 ILLUMINATION MODE : FLOOD BEAM REMARK 245 NOMINAL MAGNIFICATION : 45000 REMARK 245 CALIBRATED MAGNIFICATION : NULL REMARK 245 SOURCE : FIELD EMISSION GUN REMARK 245 ACCELERATION VOLTAGE (KV) : 200 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 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 ASP A 89 -3.42 61.56 REMARK 500 HIS A 122 -6.84 62.86 REMARK 500 PHE A 131 47.52 -107.02 REMARK 500 THR A 188 -11.83 -141.15 REMARK 500 ASN A 267 43.03 -87.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: EMD-71616 RELATED DB: EMDB REMARK 900 ARCHITECTURE OF HUMAN VOLTAGE DEPENDENT ANION CHANNEL 1 IN NANODISCS DBREF 9PFZ A 1 283 UNP P21796 VDAC1_HUMAN 1 283 SEQRES 1 A 283 MET ALA VAL PRO PRO THR TYR ALA ASP LEU GLY LYS SER SEQRES 2 A 283 ALA ARG ASP VAL PHE THR LYS GLY TYR GLY PHE GLY LEU SEQRES 3 A 283 ILE LYS LEU ASP LEU LYS THR LYS SER GLU ASN GLY LEU SEQRES 4 A 283 GLU PHE THR SER SER GLY SER ALA ASN THR GLU THR THR SEQRES 5 A 283 LYS VAL THR GLY SER LEU GLU THR LYS TYR ARG TRP THR SEQRES 6 A 283 GLU TYR GLY LEU THR PHE THR GLU LYS TRP ASN THR ASP SEQRES 7 A 283 ASN THR LEU GLY THR GLU ILE THR VAL GLU ASP GLN LEU SEQRES 8 A 283 ALA ARG GLY LEU LYS LEU THR PHE ASP SER SER PHE SER SEQRES 9 A 283 PRO ASN THR GLY LYS LYS ASN ALA LYS ILE LYS THR GLY SEQRES 10 A 283 TYR LYS ARG GLU HIS ILE ASN LEU GLY CYS ASP MET ASP SEQRES 11 A 283 PHE ASP ILE ALA GLY PRO SER ILE ARG GLY ALA LEU VAL SEQRES 12 A 283 LEU GLY TYR GLU GLY TRP LEU ALA GLY TYR GLN MET ASN SEQRES 13 A 283 PHE GLU THR ALA LYS SER ARG VAL THR GLN SER ASN PHE SEQRES 14 A 283 ALA VAL GLY TYR LYS THR ASP GLU PHE GLN LEU HIS THR SEQRES 15 A 283 ASN VAL ASN ASP GLY THR GLU PHE GLY GLY SER ILE TYR SEQRES 16 A 283 GLN LYS VAL ASN LYS LYS LEU GLU THR ALA VAL ASN LEU SEQRES 17 A 283 ALA TRP THR ALA GLY ASN SER ASN THR ARG PHE GLY ILE SEQRES 18 A 283 ALA ALA LYS TYR GLN ILE ASP PRO ASP ALA CYS PHE SER SEQRES 19 A 283 ALA LYS VAL ASN ASN SER SER LEU ILE GLY LEU GLY TYR SEQRES 20 A 283 THR GLN THR LEU LYS PRO GLY ILE LYS LEU THR LEU SER SEQRES 21 A 283 ALA LEU LEU ASP GLY LYS ASN VAL ASN ALA GLY GLY HIS SEQRES 22 A 283 LYS LEU GLY LEU GLY LEU GLU PHE GLN ALA HELIX 1 AA1 THR A 6 LEU A 10 5 5 HELIX 2 AA2 GLY A 11 LYS A 20 1 10 HELIX 3 AA3 THR A 65 TYR A 67 5 3 HELIX 4 AA4 ASN A 267 GLY A 271 5 5 SHEET 1 AA120 LEU A 26 SER A 35 0 SHEET 2 AA120 LEU A 39 ASN A 48 -1 O PHE A 41 N THR A 33 SHEET 3 AA120 VAL A 54 TRP A 64 -1 O LYS A 61 N GLU A 40 SHEET 4 AA120 LEU A 69 ASN A 76 -1 O GLU A 73 N THR A 60 SHEET 5 AA120 LEU A 81 GLU A 88 -1 O THR A 86 N THR A 70 SHEET 6 AA120 LEU A 95 PHE A 103 -1 O PHE A 99 N ILE A 85 SHEET 7 AA120 LYS A 110 ARG A 120 -1 O LYS A 113 N ASP A 100 SHEET 8 AA120 ILE A 123 ASP A 130 -1 O MET A 129 N ILE A 114 SHEET 9 AA120 SER A 137 TYR A 146 -1 O ARG A 139 N ASP A 128 SHEET 10 AA120 TRP A 149 GLU A 158 -1 O ALA A 151 N LEU A 144 SHEET 11 AA120 VAL A 164 LYS A 174 -1 O ASN A 168 N GLN A 154 SHEET 12 AA120 PHE A 178 ASN A 185 -1 O VAL A 184 N PHE A 169 SHEET 13 AA120 GLU A 189 LYS A 197 -1 O GLU A 189 N ASN A 185 SHEET 14 AA120 LEU A 202 THR A 211 -1 O TRP A 210 N PHE A 190 SHEET 15 AA120 THR A 217 GLN A 226 -1 O ARG A 218 N ALA A 209 SHEET 16 AA120 ALA A 231 ASN A 238 -1 O PHE A 233 N TYR A 225 SHEET 17 AA120 LEU A 242 LYS A 252 -1 O THR A 248 N CYS A 232 SHEET 18 AA120 ILE A 255 ASP A 264 -1 O LEU A 263 N ILE A 243 SHEET 19 AA120 LYS A 274 ALA A 283 -1 O GLU A 280 N LYS A 256 SHEET 20 AA120 LEU A 26 SER A 35 1 N LEU A 26 O LEU A 277 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 MASTER 123 0 0 4 20 0 0 6 2171 1 0 22 END