HEADER SIGNALING PROTEIN 13-APR-13 4BIT TITLE SOLUTION STRUCTURE OF CEREBRAL DOPAMINE NEUROTROPHIC FACTOR (CDNF) COMPND MOL_ID: 1; COMPND 2 MOLECULE: CEREBRAL DOPAMINE NEUROTROPHIC FACTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 27-187; COMPND 5 SYNONYM: ARMET-LIKE PROTEIN 1, CONSERVED DOPAMINE NEUROTROPHIC COMPND 6 FACTOR; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 ORGAN: BRAIN; SOURCE 6 CELL: NEURON; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VARIANT: ROSETTA B 4; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_VECTOR: PET25B KEYWDS SIGNALING PROTEIN, PARKINSON EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.LATGE,K.M.S.CABRAL,D.P.RAYMUNDO,D.FOGUEL,T.HERRMANN,M.S.ALMEIDA REVDAT 6 14-JUN-23 4BIT 1 REMARK REVDAT 5 24-JAN-18 4BIT 1 AUTHOR JRNL REMARK REVDAT 4 04-MAY-16 4BIT 1 ATOM MASTER REVDAT 3 26-AUG-15 4BIT 1 JRNL REVDAT 2 22-JUL-15 4BIT 1 JRNL REVDAT 1 23-APR-14 4BIT 0 JRNL AUTH C.LATGE,K.M.S.CABRAL,G.A.P.DE OLIVEIRA,D.P.RAYMUNDO, JRNL AUTH 2 J.A.FREITAS,L.JOHANSON,L.F.ROMAO,F.L.PALHANO,T.HERRMANN, JRNL AUTH 3 M.S.ALMEIDA,D.FOGUEL JRNL TITL THE SOLUTION STRUCTURE AND DYNAMICS OF FULL-LENGTH HUMAN JRNL TITL 2 CEREBRAL DOPAMINE NEUROTROPHIC FACTOR AND ITS JRNL TITL 3 NEUROPROTECTIVE ROLE AGAINST ALPHA-SYNUCLEIN OLIGOMERS. JRNL REF J.BIOL.CHEM. V. 290 20527 2015 JRNL REFN ISSN 0021-9258 JRNL PMID 26149686 JRNL DOI 10.1074/JBC.M115.662254 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.3 REMARK 3 AUTHORS : A.T.BRUNGER,P.D.ADAMS,G.M.CLORE,W.L. REMARK 3 DELANO,P.GROS,R.W.GROSSE-KUNSTLEVE,J.-S. JIANG, REMARK 3 J.KUSZEWSKI,M.NILGES,N.S.PANNU,R.J. READ,L.M.RICE, REMARK 3 T.SIMONSON,G.L.WARREN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: USING RECOORD SCRIPTS. REMARK 4 REMARK 4 4BIT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-APR-13. REMARK 100 THE DEPOSITION ID IS D_1290056497. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.0; 298.0; 298.0 REMARK 210 PH : 6.0; 6.0; 6.0 REMARK 210 IONIC STRENGTH : 150; 150; 150 REMARK 210 PRESSURE : 1.0 ATM; 1.0 ATM; 1.0 ATM REMARK 210 SAMPLE CONTENTS : 20 MM MES, PH 6.0, 150 MM NACL, REMARK 210 5MM NAN3, 10% D20 REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NOESY; TOCSY; HSQC; COSY; REMARK 210 HNCACB; CBCACONH; HBHACONH; HNCO REMARK 210 SPECTROMETER FIELD STRENGTH : 1000 MHZ; 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : UNIO 10, CNS 1.3 REMARK 210 METHOD USED : CNS USING RECOORD SCRIPTS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY ON 13C, 15N-LABELED CDNF. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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: 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 HZ1 LYS A 85 OE2 GLU A 88 1.53 REMARK 500 HZ2 LYS A 91 OE1 GLU A 99 1.53 REMARK 500 OE1 GLU A 137 HZ3 LYS A 138 1.54 REMARK 500 HZ2 LYS A 158 O LEU A 161 1.56 REMARK 500 OE2 GLU A 147 HZ3 LYS A 151 1.56 REMARK 500 OE1 GLU A 88 HZ3 LYS A 92 1.57 REMARK 500 OE1 GLU A 12 HZ3 LYS A 51 1.57 REMARK 500 HZ1 LYS A 51 OE2 GLU A 160 1.59 REMARK 500 OE1 GLU A 2 HH21 ARG A 6 1.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 3 MET A 81 N MET A 81 CA -0.131 REMARK 500 4 VAL A 30 C ASN A 31 N -0.144 REMARK 500 5 TYR A 58 CB TYR A 58 CG 0.096 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 5 GLN A 96 CB - CA - C ANGL. DEV. = -13.0 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 10 -66.00 71.61 REMARK 500 1 LYS A 15 -82.61 -172.76 REMARK 500 1 THR A 67 -149.14 47.72 REMARK 500 1 LYS A 68 61.87 76.56 REMARK 500 1 LEU A 70 -84.17 -108.23 REMARK 500 1 VAL A 73 -51.13 74.50 REMARK 500 1 MET A 81 72.79 -115.12 REMARK 500 1 PRO A 82 140.13 -39.62 REMARK 500 1 LEU A 93 -52.38 -121.06 REMARK 500 1 GLU A 99 32.30 -84.43 REMARK 500 1 GLU A 103 175.86 -48.10 REMARK 500 1 ASP A 107 37.47 -74.80 REMARK 500 1 ALA A 136 -84.58 -128.37 REMARK 500 1 ALA A 153 79.03 17.16 REMARK 500 1 PRO A 157 81.22 -65.82 REMARK 500 2 ASP A 10 -165.12 164.54 REMARK 500 2 ARG A 28 20.65 80.91 REMARK 500 2 LYS A 68 -77.47 -126.10 REMARK 500 2 ILE A 69 72.71 72.91 REMARK 500 2 LEU A 70 -70.06 -110.78 REMARK 500 2 VAL A 73 -65.82 75.37 REMARK 500 2 MET A 81 72.01 -118.30 REMARK 500 2 ALA A 83 0.64 -58.75 REMARK 500 2 LYS A 85 65.03 -164.26 REMARK 500 2 ILE A 86 -63.21 -121.09 REMARK 500 2 LEU A 90 -118.86 -84.33 REMARK 500 2 LYS A 91 -104.00 -140.04 REMARK 500 2 TYR A 102 -101.09 -113.90 REMARK 500 2 ALA A 136 -74.86 -103.88 REMARK 500 2 PRO A 157 78.56 -58.65 REMARK 500 3 ARG A 6 127.21 77.52 REMARK 500 3 PRO A 7 -154.00 -82.28 REMARK 500 3 ALA A 9 -86.59 53.64 REMARK 500 3 GLU A 16 -76.13 -111.64 REMARK 500 3 LEU A 25 -70.37 -86.76 REMARK 500 3 GLU A 72 -103.75 61.80 REMARK 500 3 VAL A 73 -39.28 -161.30 REMARK 500 3 MET A 77 0.18 -37.24 REMARK 500 3 VAL A 79 -133.59 -79.06 REMARK 500 3 HIS A 80 30.09 -75.40 REMARK 500 3 MET A 81 -109.20 -122.34 REMARK 500 3 PRO A 82 -176.12 -66.34 REMARK 500 3 LYS A 85 -9.70 -143.29 REMARK 500 3 ASP A 94 98.93 -170.11 REMARK 500 3 GLU A 99 31.31 -85.85 REMARK 500 3 ALA A 134 -69.15 -109.57 REMARK 500 3 ALA A 136 -81.44 -95.12 REMARK 500 3 TYR A 152 -48.70 -131.18 REMARK 500 3 PRO A 157 86.37 -66.15 REMARK 500 4 GLU A 2 -50.39 -130.94 REMARK 500 REMARK 500 THIS ENTRY HAS 347 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 4 ARG A 28 0.15 SIDE CHAIN REMARK 500 6 ARG A 114 0.11 SIDE CHAIN REMARK 500 7 ARG A 133 0.08 SIDE CHAIN REMARK 500 8 ARG A 28 0.10 SIDE CHAIN REMARK 500 9 ARG A 114 0.08 SIDE CHAIN REMARK 500 9 ARG A 133 0.08 SIDE CHAIN REMARK 500 11 ARG A 75 0.08 SIDE CHAIN REMARK 500 12 ARG A 6 0.08 SIDE CHAIN REMARK 500 12 ARG A 20 0.13 SIDE CHAIN REMARK 500 12 ARG A 114 0.07 SIDE CHAIN REMARK 500 14 ARG A 20 0.11 SIDE CHAIN REMARK 500 16 ARG A 28 0.08 SIDE CHAIN REMARK 500 17 ARG A 114 0.09 SIDE CHAIN REMARK 500 18 ARG A 20 0.08 SIDE CHAIN REMARK 500 19 ARG A 6 0.09 SIDE CHAIN REMARK 500 19 ARG A 114 0.11 SIDE CHAIN REMARK 500 20 ARG A 28 0.11 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19164 RELATED DB: BMRB DBREF 4BIT A 1 161 UNP Q49AH0 CDNF_HUMAN 27 187 SEQRES 1 A 161 GLN GLU ALA GLY GLY ARG PRO GLY ALA ASP CYS GLU VAL SEQRES 2 A 161 CYS LYS GLU PHE LEU ASN ARG PHE TYR LYS SER LEU ILE SEQRES 3 A 161 ASP ARG GLY VAL ASN PHE SER LEU ASP THR ILE GLU LYS SEQRES 4 A 161 GLU LEU ILE SER PHE CYS LEU ASP THR LYS GLY LYS GLU SEQRES 5 A 161 ASN ARG LEU CYS TYR TYR LEU GLY ALA THR LYS ASP ALA SEQRES 6 A 161 ALA THR LYS ILE LEU SER GLU VAL THR ARG PRO MET SER SEQRES 7 A 161 VAL HIS MET PRO ALA MET LYS ILE CYS GLU LYS LEU LYS SEQRES 8 A 161 LYS LEU ASP SER GLN ILE CYS GLU LEU LYS TYR GLU LYS SEQRES 9 A 161 THR LEU ASP LEU ALA SER VAL ASP LEU ARG LYS MET ARG SEQRES 10 A 161 VAL ALA GLU LEU LYS GLN ILE LEU HIS SER TRP GLY GLU SEQRES 11 A 161 GLU CYS ARG ALA CYS ALA GLU LYS THR ASP TYR VAL ASN SEQRES 12 A 161 LEU ILE GLN GLU LEU ALA PRO LYS TYR ALA ALA THR HIS SEQRES 13 A 161 PRO LYS THR GLU LEU HELIX 1 1 GLU A 12 ASP A 27 1 16 HELIX 2 2 SER A 33 CYS A 45 1 13 HELIX 3 3 GLY A 50 LEU A 59 1 10 HELIX 4 4 VAL A 73 SER A 78 1 6 HELIX 5 5 PRO A 82 LYS A 85 5 4 HELIX 6 6 ILE A 86 LYS A 91 1 6 HELIX 7 7 LEU A 106 SER A 110 5 5 HELIX 8 8 ARG A 117 TRP A 128 1 12 HELIX 9 9 GLU A 137 ALA A 153 1 17 SSBOND 1 CYS A 11 CYS A 98 1555 1555 2.03 SSBOND 2 CYS A 14 CYS A 87 1555 1555 2.03 SSBOND 3 CYS A 45 CYS A 56 1555 1555 2.02 SSBOND 4 CYS A 132 CYS A 135 1555 1555 2.06 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 MODEL 2 MODEL 3 MODEL 4 MODEL 5 MODEL 6 MODEL 7 MODEL 8 MODEL 9 MODEL 10 MODEL 11 MODEL 12 MODEL 13 MODEL 14 MODEL 15 MODEL 16 MODEL 17 MODEL 18 MODEL 19 MODEL 20