HEADER STRUCTURAL PROTEIN 14-JUN-20 6ZDB TITLE NMR STRUCTURAL ANALYSIS OF YEAST COX13 REVEALS ITS C-TERMINUS IN TITLE 2 INTERACTION WITH ATP COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOCHROME C OXIDASE SUBUNIT 13, MITOCHONDRIAL; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CYTOCHROME C OXIDASE POLYPEPTIDE VIA; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE S288C; SOURCE 3 ORGANISM_TAXID: 559292; SOURCE 4 GENE: COX13, YGL191W, G1341; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 83333 KEYWDS MEMBRANE PROTEIN, SOLUTION STRUCTURE, ATP/ADP, STRUCTURAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR Z.SHU,P.PONTUS,B.PETER,M.LENA,A.PIA REVDAT 2 15-MAY-24 6ZDB 1 REMARK REVDAT 1 19-MAY-21 6ZDB 0 JRNL AUTH S.ZHOU,P.PETTERSSON,M.L.BJORCK,H.DAWITZ,P.BRZEZINSKI, JRNL AUTH 2 L.MALER,P.ADELROTH JRNL TITL NMR STRUCTURAL ANALYSIS OF THE YEAST CYTOCHROME C OXIDASE JRNL TITL 2 SUBUNIT COX13 AND ITS INTERACTION WITH ATP. JRNL REF BMC BIOL. V. 19 98 2021 JRNL REFN ESSN 1741-7007 JRNL PMID 33971868 JRNL DOI 10.1186/S12915-021-01036-X REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6ZDB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1292109376. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 313.15 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 20 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-15N] CYTOCHROME C REMARK 210 OXIDASE SUBUNIT 13, COX13, 90% REMARK 210 H2O/10% D2O; 0.5 MM [U-13C; U- REMARK 210 15N] CYTOCHROME C OXIDASE REMARK 210 SUBUNIT 13, COX13, 90% H2O/10% REMARK 210 D2O; 0.5 MM 50%[15N, 13C] MIXED REMARK 210 WITH 50% [14N, 12C] CYTOCHROME C REMARK 210 OXIDASE SUBUNIT 13, COX13, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N TROSY HSQC; 3D REMARK 210 BACKBONE EXPERIMENTS; 3D REMARK 210 SIDECHAIN EXPERIMENTS; 3D 15N- REMARK 210 NOESY; 3D 13C-NOESY; 3D 15N- REMARK 210 FILTERED/EDITED-NOESY; 3D 13C- REMARK 210 FILTERED/EDITED-NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, CCPNMR ANALYSIS REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-15 REMARK 470 RES CSSEQI ATOMS REMARK 470 ASP A 129 O 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 ARG A 3 38.14 -162.08 REMARK 500 1 ALA A 10 31.18 -99.37 REMARK 500 1 SER A 11 89.25 -159.97 REMARK 500 1 PRO A 15 109.87 -53.23 REMARK 500 1 LYS A 27 98.75 60.12 REMARK 500 1 ALA A 39 -66.89 -104.65 REMARK 500 1 HIS A 43 151.43 62.03 REMARK 500 1 ASP A 46 38.00 -161.90 REMARK 500 1 GLU A 82 87.15 62.87 REMARK 500 1 HIS A 86 -164.18 -77.84 REMARK 500 1 VAL A 87 -64.61 -155.11 REMARK 500 1 PHE A 107 -67.68 68.75 REMARK 500 1 GLN B 4 101.70 60.44 REMARK 500 1 CYS B 5 32.66 -98.96 REMARK 500 1 ASN B 16 -47.37 -137.96 REMARK 500 1 ALA B 21 124.96 65.64 REMARK 500 1 PHE B 22 46.90 -109.26 REMARK 500 1 PRO B 25 -176.03 -52.26 REMARK 500 1 LYS B 45 158.51 60.72 REMARK 500 1 GLU B 82 -50.50 -144.05 REMARK 500 1 LEU B 84 81.87 60.48 REMARK 500 1 VAL B 87 -66.96 -126.02 REMARK 500 1 PRO B 88 170.04 -59.70 REMARK 500 1 PHE B 107 -75.72 66.33 REMARK 500 1 HIS B 124 112.90 61.19 REMARK 500 2 ARG A 3 107.07 60.21 REMARK 500 2 SER A 12 -176.29 60.94 REMARK 500 2 ALA A 17 -48.42 -143.37 REMARK 500 2 VAL A 28 -43.37 -155.23 REMARK 500 2 GLU A 41 99.80 60.92 REMARK 500 2 GLU A 82 -48.15 -139.93 REMARK 500 2 PHE A 107 -73.34 -169.89 REMARK 500 2 ARG B 3 -55.89 -134.53 REMARK 500 2 CYS B 5 87.87 61.02 REMARK 500 2 ALA B 10 -71.87 -160.38 REMARK 500 2 LEU B 13 87.47 -160.53 REMARK 500 2 ALA B 17 -56.95 -158.76 REMARK 500 2 PRO B 20 94.69 -49.97 REMARK 500 2 LEU B 84 43.91 -94.69 REMARK 500 2 HIS B 86 177.38 -59.87 REMARK 500 2 VAL B 87 79.76 63.86 REMARK 500 2 PHE B 107 -79.74 63.13 REMARK 500 2 HIS B 124 97.74 61.63 REMARK 500 2 ILE B 125 -42.85 -144.22 REMARK 500 2 GLU B 126 -78.40 63.95 REMARK 500 2 ASP B 128 -179.48 60.39 REMARK 500 3 PHE A 2 -65.93 -92.77 REMARK 500 3 ARG A 3 -45.23 -136.97 REMARK 500 3 CYS A 5 -57.79 -156.74 REMARK 500 3 ALA A 6 96.78 -66.85 REMARK 500 REMARK 500 THIS ENTRY HAS 355 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34522 RELATED DB: BMRB REMARK 900 NMR STRUCTURAL ANALYSIS OF YEAST COX13 REVEALS ITS C-TERMINUS IN REMARK 900 INTERACTION WITH ATP DBREF 6ZDB A 1 129 UNP P32799 COX13_YEAST 1 129 DBREF 6ZDB B 1 129 UNP P32799 COX13_YEAST 1 129 SEQRES 1 A 129 MET PHE ARG GLN CYS ALA LYS ARG TYR ALA SER SER LEU SEQRES 2 A 129 PRO PRO ASN ALA LEU LYS PRO ALA PHE GLY PRO PRO ASP SEQRES 3 A 129 LYS VAL ALA ALA GLN LYS PHE LYS GLU SER LEU MET ALA SEQRES 4 A 129 THR GLU LYS HIS ALA LYS ASP THR SER ASN MET TRP VAL SEQRES 5 A 129 LYS ILE SER VAL TRP VAL ALA LEU PRO ALA ILE ALA LEU SEQRES 6 A 129 THR ALA VAL ASN THR TYR PHE VAL GLU LYS GLU HIS ALA SEQRES 7 A 129 GLU HIS ARG GLU HIS LEU LYS HIS VAL PRO ASP SER GLU SEQRES 8 A 129 TRP PRO ARG ASP TYR GLU PHE MET ASN ILE ARG SER LYS SEQRES 9 A 129 PRO PHE PHE TRP GLY ASP GLY ASP LYS THR LEU PHE TRP SEQRES 10 A 129 ASN PRO VAL VAL ASN ARG HIS ILE GLU HIS ASP ASP SEQRES 1 B 129 MET PHE ARG GLN CYS ALA LYS ARG TYR ALA SER SER LEU SEQRES 2 B 129 PRO PRO ASN ALA LEU LYS PRO ALA PHE GLY PRO PRO ASP SEQRES 3 B 129 LYS VAL ALA ALA GLN LYS PHE LYS GLU SER LEU MET ALA SEQRES 4 B 129 THR GLU LYS HIS ALA LYS ASP THR SER ASN MET TRP VAL SEQRES 5 B 129 LYS ILE SER VAL TRP VAL ALA LEU PRO ALA ILE ALA LEU SEQRES 6 B 129 THR ALA VAL ASN THR TYR PHE VAL GLU LYS GLU HIS ALA SEQRES 7 B 129 GLU HIS ARG GLU HIS LEU LYS HIS VAL PRO ASP SER GLU SEQRES 8 B 129 TRP PRO ARG ASP TYR GLU PHE MET ASN ILE ARG SER LYS SEQRES 9 B 129 PRO PHE PHE TRP GLY ASP GLY ASP LYS THR LEU PHE TRP SEQRES 10 B 129 ASN PRO VAL VAL ASN ARG HIS ILE GLU HIS ASP ASP HELIX 1 AA1 VAL A 28 ALA A 39 1 12 HELIX 2 AA2 SER A 48 HIS A 80 1 33 HELIX 3 AA3 TRP A 92 ARG A 102 1 11 HELIX 4 AA4 ARG A 102 PHE A 107 1 6 HELIX 5 AA5 GLY A 111 PHE A 116 1 6 HELIX 6 AA6 PRO A 119 HIS A 124 1 6 HELIX 7 AA7 VAL B 28 THR B 40 1 13 HELIX 8 AA8 ASP B 46 GLU B 74 1 29 HELIX 9 AA9 GLU B 74 HIS B 80 1 7 HELIX 10 AB1 TRP B 92 ARG B 102 1 11 HELIX 11 AB2 ASP B 112 TRP B 117 1 6 HELIX 12 AB3 ASN B 118 HIS B 124 1 7 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