HEADER RNA BINDING PROTEIN 16-MAR-22 7X9U TITLE TYPE-II KH MOTIF OF HUMAN MITOCHONDRIAL RBFA COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE RIBOSOME-BINDING FACTOR A, MITOCHONDRIAL; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: RBFA, C18ORF22; SOURCE 6 EXPRESSION_SYSTEM: CELL-FREE GATEWAY CLONING VECTOR N-TERM 8XHIS SOURCE 7 PCELLFREE_G01; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 1508209; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: P050905-10 KEYWDS RIBOSOME, MITOCHONDRIA, MATURATION, STRUCTURAL GENOMICS, PSI-2, KEYWDS 2 PROTEIN STRUCTURE INITIATIVE, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 3 INITIATIVE, RSGI, RNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.KUWASAKO,S.SUZUKI,M.FURUE,M.TAKIZAWA,M.TAKAHASHI,K.TSUDA,T.NAGATA, AUTHOR 2 S.WATANABE,A.TANAKA,N.KOBAYASHI,T.KIGAWA,P.GUNTERT,M.SHIROUZU, AUTHOR 3 S.YOKOYAMA,Y.MUTO,RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE AUTHOR 4 (RSGI) REVDAT 2 15-MAY-24 7X9U 1 REMARK REVDAT 1 25-JAN-23 7X9U 0 JRNL AUTH K.KUWASAKO,S.SUZUKI,N.NAMEKI,M.TAKIZAWA,M.TAKAHASHI,K.TSUDA, JRNL AUTH 2 T.NAGATA,S.WATANABE,A.TANAKA,N.KOBAYASHI,T.KIGAWA,P.GUNTERT, JRNL AUTH 3 M.SHIROUZU,S.YOKOYAMA,Y.MUTO JRNL TITL 1 H, 13 C, AND 15 N RESONANCE ASSIGNMENTS AND SOLUTION JRNL TITL 2 STRUCTURES OF THE KH DOMAIN OF HUMAN RIBOSOME BINDING FACTOR JRNL TITL 3 A, MTRBFA, INVOLVED IN MITOCHONDRIAL RIBOSOME BIOGENESIS. JRNL REF BIOMOL.NMR ASSIGN. V. 16 297 2022 JRNL REFN ESSN 1874-270X JRNL PMID 35666428 JRNL DOI 10.1007/S12104-022-10094-3 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 12 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE REFINED BASED ON REMARK 3 1463 DISTANT CONSTRAINTS DERIVED FROM NOE AND ESTIMATED HYDROGEN REMARK 3 BONDS, AND 212 DIHEDRAL CONSTRAINTS ESTIMATED FROM NOE DATA AND REMARK 3 TALOS PROGRAM. REMARK 4 REMARK 4 7X9U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1300028390. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.79 MM [U-99% 13C; U-99% 15N] REMARK 210 HUMAN MITOCHONDRIAL RBFA, 100 MM REMARK 210 NON NACL, 1 MM [U-99% 2H] D-DTT, REMARK 210 20 MM [U-99% 2H] D-TRIS HCL, REMARK 210 0.02 % W/V NON NAN3, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C,15N-SEPARATED_NOESY REMARK 210 SPECTRA; 3D CBCA(CO)NH; 3D REMARK 210 HNCACB; 3D HCCH-COSY; 3D HCCH- REMARK 210 TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 2-1, KUJIRA 0.863, NMRVIEW REMARK 210 5.0.4, NMRPIPE 2007, TALOS 2007 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS 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: 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 2 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 2 ARG A 14 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 ARG A 80 NE - CZ - NH2 ANGL. DEV. = 4.1 DEGREES REMARK 500 5 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 6 ARG A 14 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 8 ARG A 14 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 9 ARG A 14 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 10 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 11 ARG A 14 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 12 ARG A 80 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 13 ARG A 14 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 15 ARG A 14 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 17 ARG A 14 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 17 ARG A 80 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 19 ARG A 80 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 20 ARG A 8 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 20 ARG A 14 NE - CZ - NH1 ANGL. DEV. = 3.8 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 SER A 5 -173.78 58.43 REMARK 500 2 SER A 5 42.70 -142.83 REMARK 500 2 LEU A 95 56.29 -140.75 REMARK 500 2 GLU A 114 16.61 -140.06 REMARK 500 3 VAL A 121 43.83 -80.25 REMARK 500 4 ASP A 116 35.30 -73.15 REMARK 500 5 ALA A 111 10.21 -140.80 REMARK 500 6 ARG A 96 -41.43 -140.45 REMARK 500 6 GLU A 114 30.64 -81.97 REMARK 500 7 ARG A 8 44.27 -75.91 REMARK 500 7 LYS A 9 30.50 -69.23 REMARK 500 7 ALA A 113 10.07 -140.14 REMARK 500 9 SER A 6 15.62 57.88 REMARK 500 10 SER A 3 -60.80 -154.28 REMARK 500 10 SER A 5 -35.64 64.77 REMARK 500 11 SER A 6 -28.57 64.11 REMARK 500 11 ALA A 122 21.58 -146.99 REMARK 500 12 SER A 5 98.55 -68.15 REMARK 500 12 SER A 6 169.90 59.97 REMARK 500 12 ASN A 97 38.63 -145.21 REMARK 500 12 GLU A 114 32.60 -71.94 REMARK 500 12 SER A 124 18.54 54.57 REMARK 500 13 GLU A 114 44.97 -77.22 REMARK 500 13 ASP A 116 46.52 -72.49 REMARK 500 13 SER A 128 -179.47 61.30 REMARK 500 15 SER A 2 176.19 59.71 REMARK 500 15 ASN A 97 109.50 -59.74 REMARK 500 15 SER A 128 -42.59 -157.69 REMARK 500 16 SER A 6 -40.21 64.81 REMARK 500 16 ARG A 96 -55.33 -21.99 REMARK 500 16 ALA A 111 44.37 -77.08 REMARK 500 16 GLU A 114 -143.10 -86.62 REMARK 500 16 SER A 124 -161.32 58.33 REMARK 500 17 SER A 6 -30.14 63.28 REMARK 500 17 LEU A 112 4.48 -65.66 REMARK 500 18 LEU A 95 37.92 -83.24 REMARK 500 19 ALA A 122 -37.52 -153.44 REMARK 500 19 SER A 127 38.49 -76.99 REMARK 500 20 SER A 5 -99.47 49.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36478 RELATED DB: BMRB REMARK 900 TYPE-II KH MOTIF OF HUMAN MITOCHONDRIAL RBFA DBREF 7X9U A 8 123 UNP Q8N0V3 RBFA_HUMAN 86 201 SEQADV 7X9U GLY A 1 UNP Q8N0V3 EXPRESSION TAG SEQADV 7X9U SER A 2 UNP Q8N0V3 EXPRESSION TAG SEQADV 7X9U SER A 3 UNP Q8N0V3 EXPRESSION TAG SEQADV 7X9U GLY A 4 UNP Q8N0V3 EXPRESSION TAG SEQADV 7X9U SER A 5 UNP Q8N0V3 EXPRESSION TAG SEQADV 7X9U SER A 6 UNP Q8N0V3 EXPRESSION TAG SEQADV 7X9U GLY A 7 UNP Q8N0V3 EXPRESSION TAG SEQADV 7X9U SER A 124 UNP Q8N0V3 EXPRESSION TAG SEQADV 7X9U GLY A 125 UNP Q8N0V3 EXPRESSION TAG SEQADV 7X9U PRO A 126 UNP Q8N0V3 EXPRESSION TAG SEQADV 7X9U SER A 127 UNP Q8N0V3 EXPRESSION TAG SEQADV 7X9U SER A 128 UNP Q8N0V3 EXPRESSION TAG SEQADV 7X9U GLY A 129 UNP Q8N0V3 EXPRESSION TAG SEQRES 1 A 129 GLY SER SER GLY SER SER GLY ARG LYS GLU ASP HIS ALA SEQRES 2 A 129 ARG LEU ARG ALA LEU ASN GLY LEU LEU TYR LYS ALA LEU SEQRES 3 A 129 THR ASP LEU LEU CYS THR PRO GLU VAL SER GLN GLU LEU SEQRES 4 A 129 TYR ASP LEU ASN VAL GLU LEU SER LYS VAL SER LEU THR SEQRES 5 A 129 PRO ASP PHE SER ALA CYS ARG ALA TYR TRP LYS THR THR SEQRES 6 A 129 LEU SER ALA GLU GLN ASN ALA HIS MET GLU ALA VAL LEU SEQRES 7 A 129 GLN ARG SER ALA ALA HIS MET ARG HIS LEU LEU MET SER SEQRES 8 A 129 GLN GLN THR LEU ARG ASN VAL PRO PRO ILE VAL PHE VAL SEQRES 9 A 129 GLN ASP LYS GLY ASN ALA ALA LEU ALA GLU LEU ASP GLN SEQRES 10 A 129 LEU LEU ALA VAL ALA ASP SER GLY PRO SER SER GLY HELIX 1 AA1 ARG A 8 CYS A 31 1 24 HELIX 2 AA2 SER A 36 LEU A 42 1 7 HELIX 3 AA3 SER A 67 MET A 90 1 24 SHEET 1 AA1 3 LEU A 46 LEU A 51 0 SHEET 2 AA1 3 CYS A 58 TRP A 62 -1 O ARG A 59 N SER A 50 SHEET 3 AA1 3 ILE A 101 GLN A 105 1 O VAL A 104 N ALA A 60 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