HEADER MEMBRANE PROTEIN 13-MAR-17 5NF8 TITLE SOLUTION STRUCTURE OF DETERGENT-SOLUBILIZED RCF1, A YEAST TITLE 2 MITOCHONDRIAL INNER MEMBRANE PROTEIN INVOLVED IN RESPIRATORY COMPLEX TITLE 3 III/IV SUPERCOMPLEX FORMATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: RESPIRATORY SUPERCOMPLEX FACTOR 1, MITOCHONDRIAL; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ALTERED INHERITANCE OF MITOCHONDRIA PROTEIN 31; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: RCF1, AIM31, SCRG_01865; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 83333 KEYWDS HOMODIMER, SOLUTION STRUCTURE, CHARGED DIMER INTERFACE, MEMBRANE KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR S.ZHOU,P.PETTERSSON,J.SJOHOLM,D.SJOSTRAND,M.HOGBOM,P.BRZEZINSKI, AUTHOR 2 L.MALER,P.ADELROTH REVDAT 5 14-JUN-23 5NF8 1 REMARK REVDAT 4 08-MAY-19 5NF8 1 REMARK REVDAT 3 28-MAR-18 5NF8 1 JRNL REVDAT 2 14-MAR-18 5NF8 1 JRNL REVDAT 1 28-FEB-18 5NF8 0 JRNL AUTH S.ZHOU,P.PETTERSSON,J.HUANG,J.SJOHOLM,D.SJOSTRAND,R.POMES, JRNL AUTH 2 M.HOGBOM,P.BRZEZINSKI,L.MALER,P.ADELROTH JRNL TITL SOLUTION NMR STRUCTURE OF YEAST RCF1, A PROTEIN INVOLVED IN JRNL TITL 2 RESPIRATORY SUPERCOMPLEX FORMATION. JRNL REF PROC. NATL. ACAD. SCI. V. 115 3048 2018 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 29507228 JRNL DOI 10.1073/PNAS.1712061115 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 5NF8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1200003874. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 323; 323; 323; 323; 323; 323 REMARK 210 PH : 5.0; 5.0; 5.0; 5.0; 5.0; 5.0 REMARK 210 IONIC STRENGTH : 0; 0; 0; 0; 0; 0 REMARK 210 PRESSURE : 1 PA; 1 PA; 1 PA; 1 PA; 1 PA; 1 REMARK 210 PA REMARK 210 SAMPLE CONTENTS : 0.4 MM [U-15N] RCF1, 90% H2O/10% REMARK 210 D2O; 0.4 MM [U-13C; U-15N; U-2H] REMARK 210 RCF1, 90% H2O/10% D2O; 0.4 MM [U- REMARK 210 13C; U-15N] RCF1, 90% H2O/10% REMARK 210 D2O; 0.4 MM [U-13C; U-15N; 50% U- REMARK 210 2H] RCF1, 90% H2O/10% D2O; 0.4 REMARK 210 MM [U-15N; U-2H; 99%-1HD, 13CD- REMARK 210 IL; 99%-1HG, 13CG-V] RCF1, 90% REMARK 210 H2O/10% D2O; 0.4 MM [U-50% 13C; REMARK 210 U-50% 15N; U-50% 12C; U-50% 14N] REMARK 210 RCF1, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCACB; 3D REMARK 210 HN(COCA)CB; 3D HNCO; 3D HN(CA)CO; REMARK 210 3D HN(CO)CA; 3D N-NOESY-HSQC; REMARK 210 3D HCCH-TOCSY; 3D CC(CO)NH; 3D REMARK 210 H(CCO)NH; 2D 1H-13C HSQC; 3D C- REMARK 210 NOESY-HSQC; 3D F1-13C/15N- REMARK 210 FILTERED, F3-15N-EDITED-NOESY- REMARK 210 HSQC; 3D F1-13C/15N-FILTERED, F3- REMARK 210 13C-EDITED-NOESY-HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III 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: 1860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 8.0 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 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 1-15 REMARK 465 RES C SSSEQI REMARK 465 GLU A 160 REMARK 465 PHE A 161 REMARK 465 ARG A 162 REMARK 465 VAL A 163 REMARK 465 PRO A 164 REMARK 465 GLY A 165 REMARK 465 SER A 166 REMARK 465 HIS A 167 REMARK 465 HIS A 168 REMARK 465 HIS A 169 REMARK 465 HIS A 170 REMARK 465 HIS A 171 REMARK 465 HIS A 172 REMARK 465 HIS A 173 REMARK 465 HIS A 174 REMARK 465 GLU B 160 REMARK 465 PHE B 161 REMARK 465 ARG B 162 REMARK 465 VAL B 163 REMARK 465 PRO B 164 REMARK 465 GLY B 165 REMARK 465 SER B 166 REMARK 465 HIS B 167 REMARK 465 HIS B 168 REMARK 465 HIS B 169 REMARK 465 HIS B 170 REMARK 465 HIS B 171 REMARK 465 HIS B 172 REMARK 465 HIS B 173 REMARK 465 HIS B 174 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 LYS A 159 O REMARK 470 LYS B 159 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 MET A 4 76.26 -151.70 REMARK 500 1 PRO A 5 104.20 -58.46 REMARK 500 1 SER A 7 116.72 74.53 REMARK 500 1 GLN A 31 70.82 58.98 REMARK 500 1 LYS A 59 -77.49 -138.98 REMARK 500 1 TYR A 62 142.38 68.83 REMARK 500 1 GLU A 129 -70.39 -74.80 REMARK 500 1 LEU A 130 159.35 177.02 REMARK 500 1 SER B 2 -58.41 -127.98 REMARK 500 1 PRO B 5 98.89 -41.18 REMARK 500 1 VAL B 10 46.00 38.70 REMARK 500 1 GLU B 12 59.56 -96.84 REMARK 500 1 VAL B 34 -61.56 -90.82 REMARK 500 1 GLN B 61 -84.37 -153.46 REMARK 500 1 ARG B 116 103.95 -59.34 REMARK 500 1 GLU B 129 -72.44 -96.75 REMARK 500 1 LEU B 130 150.24 159.01 REMARK 500 1 MET B 133 84.13 54.20 REMARK 500 2 PHE A 8 61.96 -156.32 REMARK 500 2 ARG A 13 31.82 -95.70 REMARK 500 2 GLN A 61 111.12 -163.46 REMARK 500 2 TYR A 62 103.72 65.50 REMARK 500 2 SER A 88 57.45 -148.00 REMARK 500 2 GLN A 112 -169.40 -119.61 REMARK 500 2 LEU A 114 -101.81 63.48 REMARK 500 2 GLU A 115 132.48 -176.94 REMARK 500 2 GLU A 129 -70.91 -80.33 REMARK 500 2 LEU A 130 -173.13 -177.02 REMARK 500 2 MET A 133 64.50 -101.39 REMARK 500 2 PRO B 5 98.19 -49.70 REMARK 500 2 GLU B 12 58.02 -97.00 REMARK 500 2 LYS B 59 -158.00 -102.78 REMARK 500 2 ALA B 60 -39.79 -157.62 REMARK 500 2 GLN B 61 -63.98 -165.97 REMARK 500 2 ALA B 131 74.05 -102.42 REMARK 500 3 SER A 2 -74.07 -134.82 REMARK 500 3 ARG A 3 89.57 57.30 REMARK 500 3 SER A 6 -95.22 67.58 REMARK 500 3 VAL A 10 108.51 -59.65 REMARK 500 3 GLN A 61 77.98 -171.15 REMARK 500 3 TYR A 63 -63.58 -157.42 REMARK 500 3 THR A 87 53.49 -143.06 REMARK 500 3 ARG A 116 36.21 -142.85 REMARK 500 3 ALA A 131 44.76 -154.69 REMARK 500 3 ALA B 60 39.10 -164.10 REMARK 500 3 GLN B 61 -70.16 -153.60 REMARK 500 4 PRO A 5 41.78 -85.55 REMARK 500 4 SER A 7 55.68 -98.00 REMARK 500 4 GLU A 12 57.50 -98.39 REMARK 500 4 LYS A 59 96.59 62.69 REMARK 500 REMARK 500 THIS ENTRY HAS 254 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34115 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF DETERGENT-SOLUBILIZED RCF1, A YEAST REMARK 900 MITOCHONDRIAL INNER MEMBRANE PROTEIN INVOLVED IN RESPIRATORY REMARK 900 COMPLEX III/IV SUPERCOMPLEX FORMATION DBREF 5NF8 A 1 159 UNP B3LLM2 RCF1_YEAS1 1 159 DBREF 5NF8 B 1 159 UNP B3LLM2 RCF1_YEAS1 1 159 SEQADV 5NF8 GLU A 160 UNP B3LLM2 EXPRESSION TAG SEQADV 5NF8 PHE A 161 UNP B3LLM2 EXPRESSION TAG SEQADV 5NF8 ARG A 162 UNP B3LLM2 EXPRESSION TAG SEQADV 5NF8 VAL A 163 UNP B3LLM2 EXPRESSION TAG SEQADV 5NF8 PRO A 164 UNP B3LLM2 EXPRESSION TAG SEQADV 5NF8 GLY A 165 UNP B3LLM2 EXPRESSION TAG SEQADV 5NF8 SER A 166 UNP B3LLM2 EXPRESSION TAG SEQADV 5NF8 HIS A 167 UNP B3LLM2 EXPRESSION TAG SEQADV 5NF8 HIS A 168 UNP B3LLM2 EXPRESSION TAG SEQADV 5NF8 HIS A 169 UNP B3LLM2 EXPRESSION TAG SEQADV 5NF8 HIS A 170 UNP B3LLM2 EXPRESSION TAG SEQADV 5NF8 HIS A 171 UNP B3LLM2 EXPRESSION TAG SEQADV 5NF8 HIS A 172 UNP B3LLM2 EXPRESSION TAG SEQADV 5NF8 HIS A 173 UNP B3LLM2 EXPRESSION TAG SEQADV 5NF8 HIS A 174 UNP B3LLM2 EXPRESSION TAG SEQADV 5NF8 GLU B 160 UNP B3LLM2 EXPRESSION TAG SEQADV 5NF8 PHE B 161 UNP B3LLM2 EXPRESSION TAG SEQADV 5NF8 ARG B 162 UNP B3LLM2 EXPRESSION TAG SEQADV 5NF8 VAL B 163 UNP B3LLM2 EXPRESSION TAG SEQADV 5NF8 PRO B 164 UNP B3LLM2 EXPRESSION TAG SEQADV 5NF8 GLY B 165 UNP B3LLM2 EXPRESSION TAG SEQADV 5NF8 SER B 166 UNP B3LLM2 EXPRESSION TAG SEQADV 5NF8 HIS B 167 UNP B3LLM2 EXPRESSION TAG SEQADV 5NF8 HIS B 168 UNP B3LLM2 EXPRESSION TAG SEQADV 5NF8 HIS B 169 UNP B3LLM2 EXPRESSION TAG SEQADV 5NF8 HIS B 170 UNP B3LLM2 EXPRESSION TAG SEQADV 5NF8 HIS B 171 UNP B3LLM2 EXPRESSION TAG SEQADV 5NF8 HIS B 172 UNP B3LLM2 EXPRESSION TAG SEQADV 5NF8 HIS B 173 UNP B3LLM2 EXPRESSION TAG SEQADV 5NF8 HIS B 174 UNP B3LLM2 EXPRESSION TAG SEQRES 1 A 174 MET SER ARG MET PRO SER SER PHE ASP VAL THR GLU ARG SEQRES 2 A 174 ASP LEU ASP ASP MET THR PHE GLY GLU ARG ILE ILE TYR SEQRES 3 A 174 HIS CYS LYS LYS GLN PRO LEU VAL PRO ILE GLY CYS LEU SEQRES 4 A 174 LEU THR THR GLY ALA VAL ILE LEU ALA ALA GLN ASN VAL SEQRES 5 A 174 ARG LEU GLY ASN LYS TRP LYS ALA GLN TYR TYR PHE ARG SEQRES 6 A 174 TRP ARG VAL GLY LEU GLN ALA ALA THR LEU VAL ALA LEU SEQRES 7 A 174 VAL ALA GLY SER PHE ILE TYR GLY THR SER GLY LYS GLU SEQRES 8 A 174 LEU LYS ALA LYS GLU GLU GLN LEU LYS GLU LYS ALA LYS SEQRES 9 A 174 MET ARG GLU LYS LEU TRP ILE GLN GLU LEU GLU ARG ARG SEQRES 10 A 174 GLU GLU GLU THR GLU ALA ARG ARG LYS ARG ALA GLU LEU SEQRES 11 A 174 ALA ARG MET LYS THR LEU GLU ASN GLU GLU GLU ILE LYS SEQRES 12 A 174 ASN LEU GLU LYS GLU LEU SER ASP LEU GLU ASN LYS LEU SEQRES 13 A 174 GLY LYS LYS GLU PHE ARG VAL PRO GLY SER HIS HIS HIS SEQRES 14 A 174 HIS HIS HIS HIS HIS SEQRES 1 B 174 MET SER ARG MET PRO SER SER PHE ASP VAL THR GLU ARG SEQRES 2 B 174 ASP LEU ASP ASP MET THR PHE GLY GLU ARG ILE ILE TYR SEQRES 3 B 174 HIS CYS LYS LYS GLN PRO LEU VAL PRO ILE GLY CYS LEU SEQRES 4 B 174 LEU THR THR GLY ALA VAL ILE LEU ALA ALA GLN ASN VAL SEQRES 5 B 174 ARG LEU GLY ASN LYS TRP LYS ALA GLN TYR TYR PHE ARG SEQRES 6 B 174 TRP ARG VAL GLY LEU GLN ALA ALA THR LEU VAL ALA LEU SEQRES 7 B 174 VAL ALA GLY SER PHE ILE TYR GLY THR SER GLY LYS GLU SEQRES 8 B 174 LEU LYS ALA LYS GLU GLU GLN LEU LYS GLU LYS ALA LYS SEQRES 9 B 174 MET ARG GLU LYS LEU TRP ILE GLN GLU LEU GLU ARG ARG SEQRES 10 B 174 GLU GLU GLU THR GLU ALA ARG ARG LYS ARG ALA GLU LEU SEQRES 11 B 174 ALA ARG MET LYS THR LEU GLU ASN GLU GLU GLU ILE LYS SEQRES 12 B 174 ASN LEU GLU LYS GLU LEU SER ASP LEU GLU ASN LYS LEU SEQRES 13 B 174 GLY LYS LYS GLU PHE ARG VAL PRO GLY SER HIS HIS HIS SEQRES 14 B 174 HIS HIS HIS HIS HIS HELIX 1 AA1 ARG A 13 ILE A 24 1 12 HELIX 2 AA2 ILE A 24 LYS A 30 1 7 HELIX 3 AA3 LEU A 33 LYS A 57 1 25 HELIX 4 AA4 TYR A 62 GLY A 86 1 25 HELIX 5 AA5 SER A 88 GLU A 107 1 20 HELIX 6 AA6 ARG A 116 ALA A 128 1 13 HELIX 7 AA7 MET A 133 GLY A 157 1 25 HELIX 8 AA8 ARG B 13 GLN B 31 1 19 HELIX 9 AA9 VAL B 34 TRP B 58 1 25 HELIX 10 AB1 TYR B 63 GLY B 86 1 24 HELIX 11 AB2 GLY B 89 GLU B 107 1 19 HELIX 12 AB3 ARG B 116 LEU B 130 1 15 HELIX 13 AB4 MET B 133 GLY B 157 1 25 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