HEADER PROTEIN BINDING 22-NOV-11 2LM4 TITLE SOLUTION NMR STRUCTURE OF MITOCHONDRIAL SUCCINATE DEHYDROGENASE TITLE 2 ASSEMBLY FACTOR 2 FROM SACCHAROMYCES CEREVISIAE, NORTHEAST STRUCTURAL TITLE 3 GENOMICS CONSORTIUM TARGET YT682A COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUCCINATE DEHYDROGENASE ASSEMBLY FACTOR 2, MITOCHONDRIAL; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 55-152; COMPND 5 SYNONYM: SDH ASSEMBLY FACTOR 2, EARLY MEIOTIC INDUCTION PROTEIN 5, COMPND 6 SUCCINATE DEHYDROGENASE SUBUNIT 5, MITOCHONDRIAL; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 STRAIN: ATCC 204508 / S288C; SOURCE 6 GENE: EMI5, SDH5, YOL071W; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PMGK; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET15_NESG KEYWDS STRUCTURAL GENOMICS, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), KEYWDS 2 PSI-BIOLOGY, PROTEIN STRUCTURE INITIATIVE, PROTEIN BINDING, KEYWDS 3 MITOCHONDRIAL PROTEIN PARTNERSHIP, MPP EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.ELETSKY,D.R.WINGE,H.LEE,D.LEE,E.KOHAN,K.HAMILTON,T.B.ACTON,R.XIAO, AUTHOR 2 J.K.EVERETT,J.H.PRESTEGARD,G.T.MONTELIONE,T.SZYPERSKI,NORTHEAST AUTHOR 3 STRUCTURAL GENOMICS CONSORTIUM (NESG),MITOCHONDRIAL PROTEIN AUTHOR 4 PARTNERSHIP (MPP) REVDAT 4 14-JUN-23 2LM4 1 REMARK SEQADV REVDAT 3 30-JAN-13 2LM4 1 JRNL REVDAT 2 05-DEC-12 2LM4 1 JRNL REVDAT 1 04-JAN-12 2LM4 0 JRNL AUTH A.ELETSKY,M.Y.JEONG,H.KIM,H.W.LEE,R.XIAO,D.J.PAGLIARINI, JRNL AUTH 2 J.H.PRESTEGARD,D.R.WINGE,G.T.MONTELIONE,T.SZYPERSKI JRNL TITL SOLUTION NMR STRUCTURE OF YEAST SUCCINATE DEHYDROGENASE JRNL TITL 2 FLAVINYLATION FACTOR SDH5 REVEALS A PUTATIVE SDH1 BINDING JRNL TITL 3 SITE. JRNL REF BIOCHEMISTRY V. 51 8475 2012 JRNL REFN ISSN 0006-2960 JRNL PMID 23062074 JRNL DOI 10.1021/BI301171U REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2, CNS REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 (CNS), BRUNGER, ADAMS, CLORE, GROS, NILGES AND REMARK 3 READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURE DETERMINATION WAS PERFORMED REMARK 3 BY RUNNING CYANA AND ASDP IN PARALLEL USING NOE-BASED REMARK 3 CONSTRAINTS AND PHI AND PSI DIHEDRAL ANGLE CONSTRAINTS FROM REMARK 3 TALOS+. CONSENSUS PEAK ASSIGNMENTS WERE SELECTED AND USED IN REMARK 3 ITERATIVE REFINEMENT WITH CYANA, WITH RDC CONSTRAINTS ADDED AT REMARK 3 LATER STAGES. THE 20 CONFORMERS OUT OF 100 WITH THE LOWEST REMARK 3 TARGET FUNCTION WERE FURTHER REFINED BY SIMULATED ANNEALING IN REMARK 3 EXPLICIT WATER BATH USING THE PROGRAM CNS WITH PARAM19 FORCE REMARK 3 FIELD REMARK 4 REMARK 4 2LM4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-NOV-11. REMARK 100 THE DEPOSITION ID IS D_1000102550. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.0 MM [U-100% 13C; U-100% 15N] REMARK 210 YT682A, 20 MM MES, 100 MM SODIUM REMARK 210 CHLORIDE, 5 MM CALCIUM CHLORIDE, REMARK 210 10 MM DTT, 0.02 % SODIUM AZIDE, REMARK 210 50 UM DSS, 95% H2O/5% D2O; 1.1 REMARK 210 MM [5% 13C; U-100% 15N] YT682A, REMARK 210 20 MM MES, 100 MM SODIUM REMARK 210 CHLORIDE, 5 MM CALCIUM CHLORIDE, REMARK 210 10 MM DTT, 0.02 % SODIUM AZIDE, REMARK 210 50 UM DSS, 95% H2O/5% D2O; 0.7 REMARK 210 MM [5% 13C; U-100% 15N] YT682A, REMARK 210 20 MM MES, 100 MM SODIUM REMARK 210 CHLORIDE, 5 MM CALCIUM CHLORIDE, REMARK 210 10 MM DTT, 0.02 % SODIUM AZIDE, REMARK 210 50 UM DSS, 4 % C12E5 PEG, 4 % REMARK 210 HEXANOL, 90% H2O/10% D2O; 1.1 MM REMARK 210 [5% 13C; U-100% 15N] YT682A, 20 REMARK 210 MM MES, 100 MM SODIUM CHLORIDE, REMARK 210 5 MM CALCIUM CHLORIDE, 10 MM DTT, REMARK 210 0.02 % SODIUM AZIDE, 50 UM DSS, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C CT REMARK 210 -HSQC ALIPHATIC; 3D HNCO; 3D REMARK 210 CBCA(CO)NH; 3D HNCACB; 3D REMARK 210 HBHA(CO)NH; 3D SIMUTANEOUS 13C- REMARK 210 AROMATIC,13C-ALIPHATIC,15N REMARK 210 EDITED 1H-1H NOESY; 3D HN(CA)CO; REMARK 210 2D 1H-13C CT-HSQC AROMATIC; 3D REMARK 210 HCCH-TOCSY; 3D (H)CCH-COSY REMARK 210 ALIPHATIC; 3D (H)CCH-COSY REMARK 210 AROMATIC; 1D 15N T1; 1D 15N T2; REMARK 210 2D 1H-13C CT-HSQC METHYL; 2D J- REMARK 210 RESOLVED 1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 3.0, ASDP 1.0, AUTOASSIGN REMARK 210 2.3.0, NMRPIPE, XEASY 1.3.13, REMARK 210 PROSA 6.4, VNMRJ 2.2D, TALOS+, REMARK 210 CARA 1.8.4 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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 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 1 ASN A 104 -77.27 -90.02 REMARK 500 1 LYS A 105 -80.85 45.65 REMARK 500 2 HIS A 4 79.52 -154.71 REMARK 500 2 ASN A 16 -162.15 59.91 REMARK 500 2 LYS A 78 84.69 -67.42 REMARK 500 2 THR A 82 -32.34 -162.83 REMARK 500 3 SER A 9 179.75 62.17 REMARK 500 3 LYS A 107 84.67 43.40 REMARK 500 4 HIS A 5 80.50 54.79 REMARK 500 4 SER A 9 -68.70 -136.39 REMARK 500 4 LYS A 13 95.48 64.01 REMARK 500 4 THR A 15 -79.02 -151.71 REMARK 500 4 ASN A 16 -65.89 -138.93 REMARK 500 5 GLU A 17 79.45 55.84 REMARK 500 5 LYS A 105 87.95 -68.84 REMARK 500 6 LYS A 78 70.91 55.07 REMARK 500 7 HIS A 3 -81.86 -79.47 REMARK 500 7 HIS A 6 -78.43 -131.94 REMARK 500 7 HIS A 7 -79.56 -141.77 REMARK 500 7 HIS A 8 -163.54 58.54 REMARK 500 7 SER A 9 -173.56 67.85 REMARK 500 7 MET A 11 178.48 63.05 REMARK 500 7 PHE A 80 -79.13 65.28 REMARK 500 7 LYS A 81 -74.82 51.41 REMARK 500 8 HIS A 4 -7.35 -144.92 REMARK 500 8 SER A 9 -166.19 59.95 REMARK 500 8 ARG A 14 82.79 56.27 REMARK 500 8 GLU A 106 -74.80 -146.04 REMARK 500 9 HIS A 8 11.69 -162.24 REMARK 500 9 ILE A 12 75.79 -100.82 REMARK 500 9 ASN A 16 164.29 72.60 REMARK 500 9 LYS A 107 103.77 60.48 REMARK 500 10 SER A 9 -87.93 -68.67 REMARK 500 10 LYS A 13 99.95 -69.67 REMARK 500 10 GLU A 17 91.68 63.35 REMARK 500 10 ASN A 79 48.59 -94.43 REMARK 500 11 HIS A 5 96.85 -62.98 REMARK 500 11 HIS A 7 -37.39 -132.92 REMARK 500 11 MET A 11 104.73 -55.80 REMARK 500 11 ILE A 12 128.92 63.22 REMARK 500 11 ASN A 79 -72.75 -65.51 REMARK 500 12 HIS A 7 -55.75 -133.06 REMARK 500 12 LYS A 78 39.68 -96.14 REMARK 500 12 ASN A 79 51.22 -110.68 REMARK 500 12 GLU A 106 -81.11 -127.41 REMARK 500 12 LYS A 107 36.66 -162.92 REMARK 500 13 HIS A 5 50.41 -151.03 REMARK 500 13 HIS A 10 95.93 65.13 REMARK 500 13 ILE A 12 95.55 -67.01 REMARK 500 13 ASN A 79 -71.73 -67.37 REMARK 500 REMARK 500 THIS ENTRY HAS 83 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: YT682A RELATED DB: TARGETDB REMARK 900 RELATED ID: 18098 RELATED DB: BMRB DBREF 2LM4 A 12 109 UNP Q08230 SDHF2_YEAST 55 152 SEQADV 2LM4 MET A 1 UNP Q08230 EXPRESSION TAG SEQADV 2LM4 GLY A 2 UNP Q08230 EXPRESSION TAG SEQADV 2LM4 HIS A 3 UNP Q08230 EXPRESSION TAG SEQADV 2LM4 HIS A 4 UNP Q08230 EXPRESSION TAG SEQADV 2LM4 HIS A 5 UNP Q08230 EXPRESSION TAG SEQADV 2LM4 HIS A 6 UNP Q08230 EXPRESSION TAG SEQADV 2LM4 HIS A 7 UNP Q08230 EXPRESSION TAG SEQADV 2LM4 HIS A 8 UNP Q08230 EXPRESSION TAG SEQADV 2LM4 SER A 9 UNP Q08230 EXPRESSION TAG SEQADV 2LM4 HIS A 10 UNP Q08230 EXPRESSION TAG SEQADV 2LM4 MET A 11 UNP Q08230 EXPRESSION TAG SEQRES 1 A 109 MET GLY HIS HIS HIS HIS HIS HIS SER HIS MET ILE LYS SEQRES 2 A 109 ARG THR ASN GLU PRO LEU ASP LYS LYS ARG ALA ARG LEU SEQRES 3 A 109 ILE TYR GLN SER ARG LYS ARG GLY ILE LEU GLU THR ASP SEQRES 4 A 109 LEU LEU LEU SER GLY PHE ALA ALA LYS TYR LEU LYS LYS SEQRES 5 A 109 MET ASN GLU GLU GLU LEU GLU GLU TYR ASP SER LEU LEU SEQRES 6 A 109 ASN GLU LEU ASP TRP ASP ILE TYR TYR TRP ALA THR LYS SEQRES 7 A 109 ASN PHE LYS THR SER PRO LEU PRO ASP LYS TRP ALA ASN SEQRES 8 A 109 SER LYS LEU LEU LYS GLN LEU GLN GLU PHE SER GLU ASN SEQRES 9 A 109 LYS GLU LYS GLU ILE HELIX 1 1 PRO A 18 ARG A 31 1 14 HELIX 2 2 ILE A 35 MET A 53 1 19 HELIX 3 3 ASN A 54 ASN A 66 1 13 HELIX 4 4 LEU A 68 THR A 77 1 10 HELIX 5 5 PRO A 86 ASN A 91 1 6 HELIX 6 6 SER A 92 LYS A 105 1 14 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