HEADER RECEPTOR/OXIDOREDUCTASE COMPLEX 23-APR-99 1OM2 TITLE SOLUTION NMR STRUCTURE OF THE MITOCHONDRIAL PROTEIN IMPORT RECEPTOR TITLE 2 TOM20 FROM RAT IN A COMPLEX WITH A PRESEQUENCE PEPTIDE DERIVED FROM TITLE 3 RAT ALDEHYDE DEHYDROGENASE (ALDH) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (MITOCHONDRIAL IMPORT RECEPTOR SUBUNIT TOM20); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 51-145; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: CYTOSOLIC DOMAIN, LIMITED PROTEOLYZED FRAGMENT; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: PROTEIN (MITOCHONDRIAL ALDEHYDE DEHYDROGENASE); COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: RESIDUES 12-22; COMPND 11 SYNONYM: ALDH; COMPND 12 EC: 1.2.1.3; COMPND 13 ENGINEERED: YES; COMPND 14 MUTATION: YES; COMPND 15 OTHER_DETAILS: C-TERMINAL HALF OF THE PRESEQUENCE OF MITOCHONDRIAL COMPND 16 PRECURSOR SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 ORGANELLE: MITOCHONDRIA; SOURCE 6 CELLULAR_LOCATION: MITOCHONDRIAL OUTER MEMBRANE; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET-21A; SOURCE 12 MOL_ID: 2; SOURCE 13 SYNTHETIC: YES; SOURCE 14 OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE SOURCE 15 OF THIS PEPTIDE IS NATUALLY FOUND IN RATTUS NORVEGICUS (RAT). THE SOURCE 16 EXPRESSION SYSTEM WAS ESCHERICHIA COLI, STRAIN BL21(DE3), PLASMID SOURCE 17 PET-17XB. KEYWDS MITOCHONDRIAL PROTEIN IMPORT ACROSS OUTER MEMBRANE, RECEPTOR FOR KEYWDS 2 PRESEQUENCES, MITOCHONDRIAL TARGETING SIGNAL, PRESEQUENCE PEPTIDE, KEYWDS 3 RECEPTOR-OXIDOREDUCTASE COMPLEX COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Y.ABE,T.SHODAI,T.MUTO,K.MIHARA,H.TORII,S.NISHIKAWA,T.ENDO,D.KOHDA REVDAT 5 27-DEC-23 1OM2 1 REMARK REVDAT 4 23-FEB-22 1OM2 1 REMARK SEQADV REVDAT 3 24-FEB-09 1OM2 1 VERSN REVDAT 2 15-MAR-00 1OM2 1 JRNL REVDAT 1 02-FEB-00 1OM2 0 JRNL AUTH Y.ABE,T.SHODAI,T.MUTO,K.MIHARA,H.TORII,S.NISHIKAWA,T.ENDO, JRNL AUTH 2 D.KOHDA JRNL TITL STRUCTURAL BASIS OF PRESEQUENCE RECOGNITION BY THE JRNL TITL 2 MITOCHONDRIAL PROTEIN IMPORT RECEPTOR TOM20. JRNL REF CELL(CAMBRIDGE,MASS.) V. 100 551 2000 JRNL REFN ISSN 0092-8674 JRNL PMID 10721992 JRNL DOI 10.1016/S0092-8674(00)80691-1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 1.5, EMBOSS 5.0 REMARK 3 AUTHORS : GUNTERT & WUTHRICH, NAKAI & NAKAMURA REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DEPOSITED COORDINATES WERE CALCULATED REMARK 3 BASED ON 1012 NOE-DERIVED DISTANCE, 80 SLOWLY EXCHANGING AMIDE REMARK 3 PROTON-DERIVED DISTANCE, AND 39 DIHEDRAL ANGLE RESTRAINTS. NO REMARK 3 VIOLATIONS OF DISTANCE RESTRAINTS EXCEED 0.33 ANGSTROMS, AND NO REMARK 3 VIOLATIONS OF ANGLE CONSTRAINTS EXCEED 2.8 DEGREES. REMARK 4 REMARK 4 1OM2 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-APR-99. REMARK 100 THE DEPOSITION ID IS D_1000000933. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 0.02M REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 90% WATER/10% D2O, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : HNCA; HN(CO)CA; CBCA(CO)NH; REMARK 210 HNCACB; HBHA(CO)NH; C(CO)NH- REMARK 210 TOCSY HC(CO)NH-TOCSY; HCCH-COSY; REMARK 210 HCCH-TOCSY; 15N-RESOLVED NOESY; REMARK 210 15N-RESOLVED TOCSY; HNHA; {1H}- REMARK 210 15N NOE; 3D F1 13C-FILTERED-F3 REMARK 210 13C-RESOLVED NOESY; 2D F1/F2 13C- REMARK 210 FILTERED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ REMARK 210 SPECTROMETER MODEL : DMX600; DMX750 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DYANA, EMBOSS REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS FOLLOWED REMARK 210 BY RESTRAINED ENERGY REMARK 210 MINIMIZATION WITH AMBER FORCE REMARK 210 FIELD REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE INTRA-TOM20 PROTEIN NOES WERE OBTAINED AT PH5.4 AND REMARK 210 0.02M CHAPSO ( DETERGENT) IN THE ABSENCE OF THE PEPTIDE USING 3D REMARK 210 15N-RESOLVED AND 3D 13C- RESOLVED NOESY SPECTRA. THE INTRA- REMARK 210 PEPTIDE NOES AND INTERMOLECULAR NOES WERE COLLECTED AT PH6.8 IN REMARK 210 THE ABSENCE OF CHAPSO USING 2D AND 3D NOESY SPECTRA WITH ISOTOPE REMARK 210 FILTERS. THE NOE ASSIGNMENT WAS COMPLETED BY USING SEQUENCE- REMARK 210 SPECIFICALLY DEUTERATED DERIVATIVES OF THE PEPTIDE. THESE THREE REMARK 210 NOE SETS WERE COMBINED TO CALCULATE THE COMPLEX STRUCTURE OF REMARK 210 TOM20 AND THE PRESEQUENCE PEPTIDE. 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 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 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 3 VAL A 59 CA - CB - CG1 ANGL. DEV. = 9.2 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 ASP A 9 -20.13 -149.03 REMARK 500 1 LEU A 10 -17.96 77.76 REMARK 500 1 SER A 85 41.96 -76.51 REMARK 500 1 ALA A 86 -61.32 -166.79 REMARK 500 1 ARG B 3 85.52 -150.53 REMARK 500 1 ARG B 6 -69.32 -93.11 REMARK 500 2 SER A 5 74.96 -115.13 REMARK 500 2 LEU A 7 63.17 36.53 REMARK 500 2 SER A 85 43.13 -76.15 REMARK 500 2 ALA A 86 -49.28 -169.08 REMARK 500 2 LEU A 89 45.25 36.31 REMARK 500 2 ARG B 3 83.33 58.44 REMARK 500 2 LEU B 4 -112.27 -74.68 REMARK 500 2 SER B 5 -7.63 60.34 REMARK 500 3 LYS A 6 74.27 -104.15 REMARK 500 3 PRO A 8 -86.15 -61.80 REMARK 500 3 LEU A 10 -23.45 70.76 REMARK 500 3 LEU A 64 107.78 -176.06 REMARK 500 3 PRO A 65 105.56 -55.72 REMARK 500 3 THR A 78 -44.33 -144.66 REMARK 500 3 SER A 85 37.25 -79.63 REMARK 500 3 ALA A 86 38.82 -170.12 REMARK 500 3 SER A 88 -41.01 169.60 REMARK 500 3 ARG B 3 115.29 -162.28 REMARK 500 3 LEU B 4 72.29 -67.31 REMARK 500 3 SER B 5 -8.81 -159.42 REMARK 500 4 SER A 5 -170.00 -172.80 REMARK 500 4 LEU A 7 70.34 50.11 REMARK 500 4 PRO A 8 -100.28 -76.34 REMARK 500 4 LEU A 10 -24.88 69.99 REMARK 500 4 ASP A 35 47.64 -80.23 REMARK 500 4 THR A 78 -51.10 -151.64 REMARK 500 4 SER A 85 45.04 -77.47 REMARK 500 4 ALA A 86 -45.64 -171.87 REMARK 500 4 SER A 88 -42.90 -176.84 REMARK 500 4 LEU A 89 35.53 -93.68 REMARK 500 4 ASP A 92 62.87 -156.26 REMARK 500 4 PRO B 2 85.26 -68.64 REMARK 500 4 ARG B 3 59.84 -163.65 REMARK 500 5 SER A 5 -159.29 -174.78 REMARK 500 5 LYS A 6 99.00 11.46 REMARK 500 5 LEU A 7 70.49 57.53 REMARK 500 5 PRO A 8 -104.07 -72.00 REMARK 500 5 LEU A 10 -13.09 71.41 REMARK 500 5 LEU A 64 129.00 -175.99 REMARK 500 5 THR A 78 -53.52 -140.04 REMARK 500 5 SER A 85 45.05 -77.35 REMARK 500 5 ALA A 86 -47.38 -171.71 REMARK 500 5 SER A 88 -44.04 -175.86 REMARK 500 5 LEU A 89 35.14 -96.93 REMARK 500 REMARK 500 THIS ENTRY HAS 218 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1OM2 A 1 95 UNP Q62760 TOM20_RAT 51 145 DBREF 1OM2 B 1 11 UNP P11884 ALDH2_RAT 12 22 SEQADV 1OM2 GLY A 90 UNP Q62760 ALA 140 VARIANT SEQADV 1OM2 TYR B 10 UNP P11884 ALA 21 ENGINEERED MUTATION SEQRES 1 A 95 ARG ALA GLY LEU SER LYS LEU PRO ASP LEU LYS ASP ALA SEQRES 2 A 95 GLU ALA VAL GLN LYS PHE PHE LEU GLU GLU ILE GLN LEU SEQRES 3 A 95 GLY GLU GLU LEU LEU ALA GLN GLY ASP TYR GLU LYS GLY SEQRES 4 A 95 VAL ASP HIS LEU THR ASN ALA ILE ALA VAL CYS GLY GLN SEQRES 5 A 95 PRO GLN GLN LEU LEU GLN VAL LEU GLN GLN THR LEU PRO SEQRES 6 A 95 PRO PRO VAL PHE GLN MET LEU LEU THR LYS LEU PRO THR SEQRES 7 A 95 ILE SER GLN ARG ILE VAL SER ALA GLN SER LEU GLY GLU SEQRES 8 A 95 ASP ASP VAL GLU SEQRES 1 B 11 GLY PRO ARG LEU SER ARG LEU LEU SER TYR ALA HELIX 1 A1 VAL A 16 GLN A 33 1HELIX A OF THE TPR MOTIF 18 HELIX 2 A2 TYR A 36 VAL A 49 1HELIX B OF THE TPR MOTIF 14 HELIX 3 A3 GLN A 54 GLN A 62 1 9 HELIX 4 A4 VAL A 68 THR A 74 1 7 HELIX 5 A5 THR A 78 ILE A 83 1MOBILE RELATIVE TO THE CORE 6 HELIX 6 H1 SER B 5 ALA B 11 1NOT WELL DEFINED 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