HEADER TRANSPORT PROTEIN 22-NOV-19 6TIR TITLE NOE BASED MODEL OF HVDAC-1 BOUND TO BETA-NADH IN DETERGENT MICELLES COMPND MOL_ID: 1; COMPND 2 MOLECULE: VOLTAGE-DEPENDENT ANION-SELECTIVE CHANNEL PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HVDAC1,OUTER MITOCHONDRIAL MEMBRANE PROTEIN PORIN 1, COMPND 5 PLASMALEMMAL PORIN,PORIN 31HL,PORIN 31HM; COMPND 6 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; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BETA-BARREL MEMBRANE PROTEIN COMPLEX, TRANSPORT PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR R.BOEHM,S.HILLER,G.WAGNER REVDAT 3 12-FEB-20 6TIR 1 JRNL REVDAT 2 01-JAN-20 6TIR 1 JRNL REVDAT 1 04-DEC-19 6TIR 0 JRNL AUTH R.BOHM,G.F.AMODEO,S.MURLIDARAN,S.CHAVALI,G.WAGNER, JRNL AUTH 2 M.WINTERHALTER,G.BRANNIGAN,S.HILLER JRNL TITL THE STRUCTURAL BASIS FOR LOW CONDUCTANCE IN THE MEMBRANE JRNL TITL 2 PROTEIN VDAC UPON BETA-NADH BINDING AND VOLTAGE GATING. JRNL REF STRUCTURE V. 28 206 2020 JRNL REFN ISSN 0969-2126 JRNL PMID 31862297 JRNL DOI 10.1016/J.STR.2019.11.015 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA, CYANA REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), REMARK 3 GUNTERT, MUMENTHALER AND WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6TIR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1292105533. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303.15 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 25 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-99%-2H, 15N; 99% REMARK 210 -1HDELTA-IL; 99%-1HGAMMA-V] REMARK 210 HUMAN VDAC-1, 45 MM BETA-NADH, REMARK 210 150 MM [U-99% 2H] LDAO, 90% H2O/ REMARK 210 10% D2O; 0.5 MM [U-99%-2H, 15N; REMARK 210 99%-1H,13C-DELTA-IL; 99%-1H, REMARK 210 13CGAMMA-V] HUMAN VDAC-1, 45 MM REMARK 210 BETA-NADH, 150 MM [U-99% 2H] REMARK 210 LDAO, 90% H2O/10% D2O; 0.5 MM U- REMARK 210 99%-2H,15N,13C HUMAN VDAC-1, 150 REMARK 210 MM [U-99% 2H] LDAO, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 15N RESOLVED NOESY; 3D 13C REMARK 210 RESOLVED NOESY; 3D HNCA; 3D HNCO; REMARK 210 3D HNCACB REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA, XEASY REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-10 REMARK 465 RES C SSSEQI REMARK 465 HIS A 286 REMARK 465 HIS A 287 REMARK 465 HIS A 288 REMARK 465 HIS A 289 REMARK 465 HIS A 290 REMARK 465 HIS A 291 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 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 1 VAL A 3 82.58 60.47 REMARK 500 1 TYR A 22 97.96 -59.89 REMARK 500 1 GLU A 36 49.46 -89.42 REMARK 500 1 THR A 65 136.35 66.34 REMARK 500 1 THR A 107 -41.53 -136.96 REMARK 500 1 GLU A 147 96.12 -50.31 REMARK 500 1 LYS A 161 -167.51 -126.11 REMARK 500 1 ASP A 176 -73.82 -39.79 REMARK 500 1 ASP A 186 -176.40 72.40 REMARK 500 1 LYS A 200 -170.42 -69.63 REMARK 500 1 SER A 215 36.93 -97.38 REMARK 500 1 ASP A 228 -56.89 170.70 REMARK 500 1 PRO A 229 -156.42 -69.81 REMARK 500 1 LEU A 251 -74.71 -111.36 REMARK 500 1 PRO A 253 67.08 -69.75 REMARK 500 1 ASN A 267 19.91 -168.44 REMARK 500 1 PHE A 281 -157.99 168.73 REMARK 500 2 PRO A 5 95.55 -69.76 REMARK 500 2 THR A 19 78.34 51.90 REMARK 500 2 ASN A 37 23.12 -159.28 REMARK 500 2 GLU A 50 40.13 39.90 REMARK 500 2 TYR A 67 -53.70 179.58 REMARK 500 2 ASN A 79 -154.00 -78.88 REMARK 500 2 ASN A 106 99.06 -56.20 REMARK 500 2 GLU A 147 96.34 -50.44 REMARK 500 2 LYS A 161 -168.76 -125.79 REMARK 500 2 ASP A 186 179.46 65.77 REMARK 500 2 LEU A 202 -168.49 -79.19 REMARK 500 2 LEU A 251 -73.33 -78.58 REMARK 500 2 LYS A 252 -60.66 179.29 REMARK 500 2 PRO A 253 -86.40 -69.77 REMARK 500 2 PHE A 281 -150.75 172.08 REMARK 500 3 VAL A 3 75.62 61.18 REMARK 500 3 THR A 19 80.51 65.06 REMARK 500 3 ASN A 37 16.96 -147.67 REMARK 500 3 LYS A 53 99.90 -166.53 REMARK 500 3 THR A 65 163.43 60.68 REMARK 500 3 TYR A 67 43.35 37.81 REMARK 500 3 ASN A 79 38.55 77.16 REMARK 500 3 LEU A 91 -70.12 -96.79 REMARK 500 3 ASN A 106 -74.25 -51.56 REMARK 500 3 GLU A 147 97.99 -57.35 REMARK 500 3 LYS A 161 -167.72 -120.93 REMARK 500 3 ASP A 176 -86.72 -9.50 REMARK 500 3 ASP A 186 176.86 66.20 REMARK 500 3 ASN A 214 36.29 -171.79 REMARK 500 3 ASP A 228 -60.91 172.12 REMARK 500 3 PRO A 229 -157.52 -69.76 REMARK 500 3 LYS A 252 161.46 62.44 REMARK 500 3 PRO A 253 76.84 -69.81 REMARK 500 REMARK 500 THIS ENTRY HAS 188 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAI A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34150 RELATED DB: BMRB REMARK 900 NOE BASED MODEL OF HVDAC-1 BOUND TO BETA-NADH IN DETERGENT MICELLES REMARK 900 RELATED ID: 34458 RELATED DB: BMRB REMARK 900 NOE BASED MODEL OF HVDAC-1 BOUND TO BETA-NADH IN DETERGENT MICELLES DBREF 6TIR A 1 283 UNP P21796 VDAC1_HUMAN 1 283 SEQADV 6TIR LEU A 284 UNP P21796 EXPRESSION TAG SEQADV 6TIR GLU A 285 UNP P21796 EXPRESSION TAG SEQADV 6TIR HIS A 286 UNP P21796 EXPRESSION TAG SEQADV 6TIR HIS A 287 UNP P21796 EXPRESSION TAG SEQADV 6TIR HIS A 288 UNP P21796 EXPRESSION TAG SEQADV 6TIR HIS A 289 UNP P21796 EXPRESSION TAG SEQADV 6TIR HIS A 290 UNP P21796 EXPRESSION TAG SEQADV 6TIR HIS A 291 UNP P21796 EXPRESSION TAG SEQRES 1 A 291 MET ALA VAL PRO PRO THR TYR ALA ASP LEU GLY LYS SER SEQRES 2 A 291 ALA ARG ASP VAL PHE THR LYS GLY TYR GLY PHE GLY LEU SEQRES 3 A 291 ILE LYS LEU ASP LEU LYS THR LYS SER GLU ASN GLY LEU SEQRES 4 A 291 GLU PHE THR SER SER GLY SER ALA ASN THR GLU THR THR SEQRES 5 A 291 LYS VAL THR GLY SER LEU GLU THR LYS TYR ARG TRP THR SEQRES 6 A 291 GLU TYR GLY LEU THR PHE THR GLU LYS TRP ASN THR ASP SEQRES 7 A 291 ASN THR LEU GLY THR GLU ILE THR VAL GLU ASP GLN LEU SEQRES 8 A 291 ALA ARG GLY LEU LYS LEU THR PHE ASP SER SER PHE SER SEQRES 9 A 291 PRO ASN THR GLY LYS LYS ASN ALA LYS ILE LYS THR GLY SEQRES 10 A 291 TYR LYS ARG GLU HIS ILE ASN LEU GLY CYS ASP MET ASP SEQRES 11 A 291 PHE ASP ILE ALA GLY PRO SER ILE ARG GLY ALA LEU VAL SEQRES 12 A 291 LEU GLY TYR GLU GLY TRP LEU ALA GLY TYR GLN MET ASN SEQRES 13 A 291 PHE GLU THR ALA LYS SER ARG VAL THR GLN SER ASN PHE SEQRES 14 A 291 ALA VAL GLY TYR LYS THR ASP GLU PHE GLN LEU HIS THR SEQRES 15 A 291 ASN VAL ASN ASP GLY THR GLU PHE GLY GLY SER ILE TYR SEQRES 16 A 291 GLN LYS VAL ASN LYS LYS LEU GLU THR ALA VAL ASN LEU SEQRES 17 A 291 ALA TRP THR ALA GLY ASN SER ASN THR ARG PHE GLY ILE SEQRES 18 A 291 ALA ALA LYS TYR GLN ILE ASP PRO ASP ALA CYS PHE SER SEQRES 19 A 291 ALA LYS VAL ASN ASN SER SER LEU ILE GLY LEU GLY TYR SEQRES 20 A 291 THR GLN THR LEU LYS PRO GLY ILE LYS LEU THR LEU SER SEQRES 21 A 291 ALA LEU LEU ASP GLY LYS ASN VAL ASN ALA GLY GLY HIS SEQRES 22 A 291 LYS LEU GLY LEU GLY LEU GLU PHE GLN ALA LEU GLU HIS SEQRES 23 A 291 HIS HIS HIS HIS HIS HET NAI A 301 73 HETNAM NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE HETSYN NAI NADH FORMUL 2 NAI C21 H29 N7 O14 P2 HELIX 1 AA1 TYR A 7 LEU A 10 5 4 HELIX 2 AA2 GLY A 11 THR A 19 1 9 SHEET 1 AA120 ILE A 27 LYS A 34 0 SHEET 2 AA120 GLU A 40 ASN A 48 -1 O ALA A 47 N ILE A 27 SHEET 3 AA120 LYS A 53 TRP A 64 -1 O GLU A 59 N THR A 42 SHEET 4 AA120 LEU A 69 ASN A 76 -1 O PHE A 71 N TYR A 62 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 SER A 101 N THR A 83 SHEET 7 AA120 LYS A 110 LYS A 119 -1 O LYS A 115 N THR A 98 SHEET 8 AA120 ILE A 123 PHE A 131 -1 O CYS A 127 N THR A 116 SHEET 9 AA120 SER A 137 GLY A 145 -1 O ALA A 141 N GLY A 126 SHEET 10 AA120 TRP A 149 GLU A 158 -1 O TYR A 153 N LEU A 142 SHEET 11 AA120 ARG A 163 LYS A 174 -1 O GLN A 166 N ASN A 156 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 TYR A 195 N GLN A 179 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 ALA A 235 N ALA A 223 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 GLN A 282 -1 O GLY A 276 N SER A 260 SHEET 20 AA120 ILE A 27 LYS A 34 1 N LYS A 28 O LEU A 279 SITE 1 AC1 10 ARG A 15 PHE A 18 LYS A 20 TYR A 22 SITE 2 AC1 10 ASN A 183 ARG A 218 VAL A 237 ASN A 238 SITE 3 AC1 10 LEU A 242 LEU A 262 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 MODEL 1