HEADER OXIDOREDUCTASE 08-MAY-08 2K3J TITLE THE SOLUTION STRUCTURE OF HUMAN MIA40 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MITOCHONDRIAL INTERMEMBRANE SPACE IMPORT AND ASSEMBLY COMPND 3 PROTEIN 40; COMPND 4 CHAIN: A; COMPND 5 SYNONYM: COILED-COIL-HELIX-COILED-COIL-HELIX DOMAIN-CONTAINING COMPND 6 PROTEIN 4; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 GENE: CHCHD4, MIA40; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: ORIGAMI-PLYSS; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PDEST/HIS-MBP KEYWDS ALPHA-HAIRPIN FOLD, COILED COIL-HELIX-COILED COIL-HELIX DOMAIN, KEYWDS 2 MITOCHONDRIAL OXIDASE, PROTEIN IMPORT AND FOLDING, ALTERNATIVE KEYWDS 3 SPLICING, MITOCHONDRION, PROTEIN TRANSPORT, TRANSLOCATION, KEYWDS 4 TRANSPORT, OXIDOREDUCTASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.CIOFI BAFFONI,I.BERTINI,A.GALLO REVDAT 4 14-JUN-23 2K3J 1 REMARK REVDAT 3 19-FEB-20 2K3J 1 REMARK SEQADV REVDAT 2 17-FEB-09 2K3J 1 JRNL REVDAT 1 10-FEB-09 2K3J 0 JRNL AUTH L.BANCI,I.BERTINI,C.CEFARO,S.CIOFI-BAFFONI,A.GALLO, JRNL AUTH 2 M.MARTINELLI,D.P.SIDERIS,N.KATRAKILI,K.TOKATLIDIS JRNL TITL MIA40 IS AN OXIDOREDUCTASE THAT CATALYZES OXIDATIVE PROTEIN JRNL TITL 2 FOLDING IN MITOCHONDRIA. JRNL REF NAT.STRUCT.MOL.BIOL. V. 16 198 2009 JRNL REFN ISSN 1545-9993 JRNL PMID 19182799 JRNL DOI 10.1038/NSMB.1553 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 2.1, AMBER 8.0 REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), CASE, DARDEN, CHEATHAM, REMARK 3 III, SIMMERLING, WANG, DUKE, LUO, ... AND KOLLM REMARK 3 (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2K3J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-MAY-08. REMARK 100 THE DEPOSITION ID IS D_1000100630. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5-1 MM [U-100% 15N] HUMAN REMARK 210 MIA40, 2 MM DTT, 50 MM POTASSIUM REMARK 210 PHOSPHATE, 0.5 MM EDTA, 90% H2O/ REMARK 210 10% D2O; 0.5-1 MM [U-100% 13C; U- REMARK 210 100% 15N] HUMAN MIA40, 2 MM DTT, REMARK 210 50 MM POTASSIUM PHOSPHATE, 0.5 REMARK 210 MM EDTA, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-1H NOESY; REMARK 210 3D CBCA(CO)NH; 3D HNCO; 3D HNCA; REMARK 210 3D HNCACB; 3D HBHA(CO)NH; 3D REMARK 210 HN(CO)CA; 3D 1H-15N NOESY; 3D 1H- REMARK 210 13C NOESY; 3D HCCH-TOCSY; 2D 1H- REMARK 210 1H TOCSY; 3D HN(CA)CO REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 2.1, CYANA 2.1, AMBER REMARK 210 8.0, CARA, PECAN, WHAT IF, REMARK 210 PROCHECKNMR, ATNOSCANDID 1.2 REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 400 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 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 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY A 1 REMARK 465 SER A 2 REMARK 465 PHE A 3 REMARK 465 THR A 4 REMARK 465 MET A 5 REMARK 465 SER A 6 REMARK 465 TYR A 7 REMARK 465 CYS A 8 REMARK 465 ARG A 9 REMARK 465 GLN A 10 REMARK 465 GLU A 11 REMARK 465 GLY A 12 REMARK 465 LYS A 13 REMARK 465 ASP A 14 REMARK 465 ARG A 15 REMARK 465 ILE A 16 REMARK 465 ILE A 17 REMARK 465 PHE A 18 REMARK 465 VAL A 19 REMARK 465 THR A 20 REMARK 465 LYS A 21 REMARK 465 GLU A 22 REMARK 465 ASP A 23 REMARK 465 HIS A 24 REMARK 465 GLU A 25 REMARK 465 THR A 26 REMARK 465 PRO A 27 REMARK 465 SER A 28 REMARK 465 SER A 29 REMARK 465 ALA A 30 REMARK 465 GLU A 31 REMARK 465 LEU A 32 REMARK 465 VAL A 33 REMARK 465 ALA A 34 REMARK 465 ASP A 35 REMARK 465 ASP A 36 REMARK 465 PRO A 37 REMARK 465 ASN A 38 REMARK 465 ASP A 39 REMARK 465 PRO A 40 REMARK 465 TYR A 41 REMARK 465 GLU A 42 REMARK 465 GLU A 43 REMARK 465 HIS A 44 REMARK 465 PRO A 110 REMARK 465 GLN A 111 REMARK 465 GLU A 112 REMARK 465 ASP A 113 REMARK 465 GLU A 114 REMARK 465 ASP A 115 REMARK 465 GLU A 116 REMARK 465 GLU A 117 REMARK 465 GLU A 118 REMARK 465 GLU A 119 REMARK 465 ARG A 120 REMARK 465 GLU A 121 REMARK 465 LYS A 122 REMARK 465 LYS A 123 REMARK 465 PRO A 124 REMARK 465 ALA A 125 REMARK 465 GLU A 126 REMARK 465 GLN A 127 REMARK 465 ALA A 128 REMARK 465 GLU A 129 REMARK 465 GLU A 130 REMARK 465 THR A 131 REMARK 465 ALA A 132 REMARK 465 PRO A 133 REMARK 465 ILE A 134 REMARK 465 GLU A 135 REMARK 465 ALA A 136 REMARK 465 THR A 137 REMARK 465 ALA A 138 REMARK 465 THR A 139 REMARK 465 LYS A 140 REMARK 465 GLU A 141 REMARK 465 GLU A 142 REMARK 465 GLU A 143 REMARK 465 GLY A 144 REMARK 465 SER A 145 REMARK 465 SER A 146 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: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 ARG A 96 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 2 ARG A 96 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 ARG A 96 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 9 ARG A 96 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 12 ARG A 96 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 13 ARG A 96 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 14 ARG A 96 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 16 ARG A 96 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 16 ARG A 96 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES 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 TRP A 55 56.32 -66.11 REMARK 500 1 ASN A 56 -20.16 -154.99 REMARK 500 1 THR A 83 4.21 52.92 REMARK 500 1 GLU A 85 -75.51 147.86 REMARK 500 1 LYS A 87 103.41 -41.95 REMARK 500 1 PRO A 106 -90.81 -76.03 REMARK 500 2 LEU A 46 -22.69 58.46 REMARK 500 2 THR A 83 13.83 52.57 REMARK 500 2 GLU A 85 -57.74 118.17 REMARK 500 2 LYS A 87 96.18 -53.09 REMARK 500 2 ASP A 107 19.44 -150.36 REMARK 500 3 PRO A 67 -72.57 -73.32 REMARK 500 3 GLU A 84 -127.49 -99.34 REMARK 500 3 LYS A 87 93.35 -54.22 REMARK 500 3 TYR A 105 72.64 -118.76 REMARK 500 3 ASP A 107 31.31 -163.96 REMARK 500 4 LEU A 46 -27.49 175.91 REMARK 500 4 TRP A 55 0.02 -67.08 REMARK 500 4 THR A 83 -20.02 60.99 REMARK 500 4 GLU A 84 -60.34 -26.49 REMARK 500 4 GLU A 85 -79.31 162.71 REMARK 500 4 LYS A 87 101.25 -46.96 REMARK 500 4 ASP A 107 7.61 -168.74 REMARK 500 5 LEU A 46 -56.69 70.28 REMARK 500 5 PRO A 49 0.31 -68.15 REMARK 500 5 TRP A 55 22.07 -72.11 REMARK 500 5 THR A 83 72.49 37.50 REMARK 500 5 GLU A 84 -93.28 -97.50 REMARK 500 5 GLU A 85 -55.10 -159.59 REMARK 500 5 LYS A 87 106.01 -45.83 REMARK 500 5 ASP A 107 94.21 -165.80 REMARK 500 5 LEU A 108 -4.12 -163.66 REMARK 500 6 LEU A 46 -11.76 -178.79 REMARK 500 6 PRO A 49 39.44 -73.33 REMARK 500 6 ASN A 50 -0.34 -150.28 REMARK 500 6 TRP A 55 -9.47 -59.52 REMARK 500 6 GLU A 84 -114.71 -107.47 REMARK 500 6 GLU A 85 -59.07 -168.85 REMARK 500 6 LYS A 87 106.27 -52.01 REMARK 500 6 ASP A 107 13.92 -160.25 REMARK 500 7 CYS A 59 -66.00 -176.40 REMARK 500 7 LYS A 87 93.56 -68.07 REMARK 500 7 SER A 89 -75.42 -18.04 REMARK 500 7 CYS A 91 9.41 -61.85 REMARK 500 7 ASP A 107 16.22 -161.60 REMARK 500 8 CYS A 59 -68.77 -127.59 REMARK 500 8 GLU A 84 -115.39 -83.01 REMARK 500 8 GLU A 85 -64.68 -159.72 REMARK 500 8 LYS A 87 80.39 -59.33 REMARK 500 8 ASP A 107 61.36 -159.64 REMARK 500 REMARK 500 THIS ENTRY HAS 142 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 12 ARG A 96 0.14 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 15763 RELATED DB: BMRB DBREF 2K3J A 5 146 UNP Q8N4Q1 MIA40_HUMAN 1 142 SEQADV 2K3J GLY A 1 UNP Q8N4Q1 EXPRESSION TAG SEQADV 2K3J SER A 2 UNP Q8N4Q1 EXPRESSION TAG SEQADV 2K3J PHE A 3 UNP Q8N4Q1 EXPRESSION TAG SEQADV 2K3J THR A 4 UNP Q8N4Q1 EXPRESSION TAG SEQRES 1 A 146 GLY SER PHE THR MET SER TYR CYS ARG GLN GLU GLY LYS SEQRES 2 A 146 ASP ARG ILE ILE PHE VAL THR LYS GLU ASP HIS GLU THR SEQRES 3 A 146 PRO SER SER ALA GLU LEU VAL ALA ASP ASP PRO ASN ASP SEQRES 4 A 146 PRO TYR GLU GLU HIS GLY LEU ILE LEU PRO ASN GLY ASN SEQRES 5 A 146 ILE ASN TRP ASN CYS PRO CYS LEU GLY GLY MET ALA SER SEQRES 6 A 146 GLY PRO CYS GLY GLU GLN PHE LYS SER ALA PHE SER CYS SEQRES 7 A 146 PHE HIS TYR SER THR GLU GLU ILE LYS GLY SER ASP CYS SEQRES 8 A 146 VAL ASP GLN PHE ARG ALA MET GLN GLU CYS MET GLN LYS SEQRES 9 A 146 TYR PRO ASP LEU TYR PRO GLN GLU ASP GLU ASP GLU GLU SEQRES 10 A 146 GLU GLU ARG GLU LYS LYS PRO ALA GLU GLN ALA GLU GLU SEQRES 11 A 146 THR ALA PRO ILE GLU ALA THR ALA THR LYS GLU GLU GLU SEQRES 12 A 146 GLY SER SER HELIX 1 1 CYS A 57 ALA A 64 1 8 HELIX 2 2 CYS A 68 THR A 83 1 16 HELIX 3 3 CYS A 91 TYR A 105 1 15 SSBOND 1 CYS A 68 CYS A 101 1555 1555 2.04 SSBOND 2 CYS A 78 CYS A 91 1555 1555 2.04 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