HEADER SIGNALING PROTEIN 22-AUG-23 8QAJ TITLE NMR SOLUTION STRUCTURE OF C-TERMINAL DOMAIN OF CDNF COMPND MOL_ID: 1; COMPND 2 MOLECULE: CEREBRAL DOPAMINE NEUROTROPHIC FACTOR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ARMET-LIKE PROTEIN 1,CONSERVED DOPAMINE NEUROTROPHIC FACTOR; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: GSHM EXPRESSION ARTEFACT SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CDNF, ARMETL1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NEUROTROPHIC FACTOR, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR H.TOSSAVAINEN,P.PERMI REVDAT 3 24-SEP-25 8QAJ 1 JRNL REVDAT 2 13-NOV-24 8QAJ 1 REMARK REVDAT 1 11-SEP-24 8QAJ 0 JRNL AUTH L.Y.YU,T.VILJAKAINEN,L.BECKETT,J.NAM,A.HYYSALO, JRNL AUTH 2 P.LUNINGSCHROR,K.ALBERT,T.KOPPINEN,T.HYVARINEN, JRNL AUTH 3 H.TOSSAVAINEN,M.HELLMAN,M.AIRAVAARA,M.SENDTNER,P.PERMI, JRNL AUTH 4 P.LINDHOLM,M.SAARMA,M.H.VOUTILAINEN JRNL TITL NON-INVASIVE PERIPHERAL DELIVERY OF CDNF FRAGMENT PROTECTS JRNL TITL 2 NEURONS IN MODELS OF PARKINSON'S AND ALS JRNL REF BIORXIV 2025 JRNL REFN ISSN 2692-8205 JRNL DOI 10.1101/2025.02.09.637291 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA, AMBER REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH (CYANA), CASE, REMARK 3 DARDEN, CHEATHAM III, SIMMERLING, WANG, DUKE, LUO, REMARK 3 ... AND KOLLMAN (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8QAJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1292132920. 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 : 0.15 REMARK 210 PRESSURE : AMBIENT ATM REMARK 210 SAMPLE CONTENTS : 1 MM [U-13C; U-15N] C-CDNF, 20 REMARK 210 MM SODIUM PHOSPHATE, 50 MM REMARK 210 SODIUM CHLORIDE, 93% H2O/7% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D HN(COCA)CB; 3D REMARK 210 HNCACB; 3D HN(CO)CA; 3D HNCO; 3D REMARK 210 HCACO; 3D C(CO)NH; 3D H(CCO)NH; REMARK 210 2D (HB)CB(CGCD)HD; 2D (HB) REMARK 210 CB(CGCDCE)HE; 3D HCCH-COSY; 3D REMARK 210 HCCMHM-TOCSY; 3D 1H-13C NOESY; REMARK 210 3D 1H-15N NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, CCPNMR ANALYSIS REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 300 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 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 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 117 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 ARG A 114 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 ARG A 117 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 2 ARG A 133 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 3 ARG A 114 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 3 ARG A 117 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 4 ARG A 114 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 ARG A 133 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 5 ARG A 114 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 5 ARG A 117 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 6 ARG A 114 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 6 ARG A 133 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 8 ARG A 114 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 8 ARG A 117 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 8 ARG A 133 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 9 ARG A 114 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 10 ARG A 114 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 10 ARG A 117 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 11 ARG A 114 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 12 ARG A 114 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 12 ARG A 117 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 13 ARG A 114 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 13 ARG A 117 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 13 ARG A 133 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 14 ARG A 114 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 14 ARG A 117 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 14 ARG A 133 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 15 ARG A 117 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 15 ARG A 133 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 16 ARG A 133 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 17 ARG A 114 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 17 ARG A 133 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 18 ARG A 114 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 18 ARG A 117 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 18 ARG A 133 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 19 ARG A 117 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 20 ARG A 114 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 20 ARG A 117 NE - CZ - NH1 ANGL. DEV. = 3.2 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 2 ASP A 107 71.95 -115.01 REMARK 500 4 LYS A 101 -33.19 -142.50 REMARK 500 5 GLU A 103 39.76 -77.51 REMARK 500 5 LEU A 106 -3.10 -141.78 REMARK 500 6 ARG A 133 -61.51 -121.77 REMARK 500 6 THR A 159 73.13 48.18 REMARK 500 7 LEU A 106 70.69 55.22 REMARK 500 7 ASP A 107 36.48 -88.97 REMARK 500 7 ARG A 133 -63.69 -95.49 REMARK 500 7 CYS A 135 18.15 56.32 REMARK 500 8 CYS A 135 5.01 59.79 REMARK 500 9 MET A 100 9.00 -150.43 REMARK 500 9 ARG A 133 -78.57 -108.72 REMARK 500 9 ALA A 154 43.23 -76.79 REMARK 500 10 ASP A 107 73.82 -103.69 REMARK 500 10 LYS A 158 -87.24 -133.89 REMARK 500 10 THR A 159 -26.81 -152.66 REMARK 500 11 ASP A 107 71.03 -109.02 REMARK 500 11 PRO A 157 20.20 -68.28 REMARK 500 13 LYS A 104 47.86 -77.41 REMARK 500 13 LYS A 158 -14.87 56.19 REMARK 500 13 GLU A 160 51.85 -151.52 REMARK 500 14 TYR A 102 74.11 56.43 REMARK 500 14 THR A 105 96.99 -69.21 REMARK 500 14 LEU A 106 12.95 -142.45 REMARK 500 15 GLU A 103 58.27 -92.67 REMARK 500 15 ALA A 136 -37.06 -142.01 REMARK 500 15 LYS A 158 -12.74 61.65 REMARK 500 16 LYS A 101 -65.23 -134.58 REMARK 500 16 LYS A 104 -37.31 -136.63 REMARK 500 16 THR A 159 -17.36 -140.67 REMARK 500 17 SER A 98 2.22 -154.92 REMARK 500 17 HIS A 99 40.50 -68.99 REMARK 500 17 LEU A 106 1.88 -68.82 REMARK 500 17 ALA A 154 38.65 -79.98 REMARK 500 18 ALA A 136 -50.05 -148.80 REMARK 500 18 ALA A 154 47.53 -79.02 REMARK 500 18 PRO A 157 101.26 -49.77 REMARK 500 19 LYS A 101 -38.05 -137.42 REMARK 500 19 ALA A 136 -19.03 -146.17 REMARK 500 20 THR A 105 80.98 52.58 REMARK 500 20 ALA A 136 -34.16 -146.07 REMARK 500 20 LYS A 158 30.87 -76.20 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 7 ARG A 133 0.08 SIDE CHAIN REMARK 500 10 ARG A 117 0.09 SIDE CHAIN REMARK 500 14 TYR A 102 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34847 RELATED DB: BMRB REMARK 900 NMR SOLUTION STRUCTURE OF C-TERMINAL DOMAIN OF CDNF DBREF 8QAJ A 101 161 UNP Q49AH0 CDNF_HUMAN 127 187 SEQADV 8QAJ GLY A 97 UNP Q49AH0 EXPRESSION TAG SEQADV 8QAJ SER A 98 UNP Q49AH0 EXPRESSION TAG SEQADV 8QAJ HIS A 99 UNP Q49AH0 EXPRESSION TAG SEQADV 8QAJ MET A 100 UNP Q49AH0 EXPRESSION TAG SEQRES 1 A 65 GLY SER HIS MET LYS TYR GLU LYS THR LEU ASP LEU ALA SEQRES 2 A 65 SER VAL ASP LEU ARG LYS MET ARG VAL ALA GLU LEU LYS SEQRES 3 A 65 GLN ILE LEU HIS SER TRP GLY GLU GLU CYS ARG ALA CYS SEQRES 4 A 65 ALA GLU LYS THR ASP TYR VAL ASN LEU ILE GLN GLU LEU SEQRES 5 A 65 ALA PRO LYS TYR ALA ALA THR HIS PRO LYS THR GLU LEU HELIX 1 AA1 ASP A 107 VAL A 111 5 5 HELIX 2 AA2 ARG A 117 TRP A 128 1 12 HELIX 3 AA3 GLU A 137 ALA A 153 1 17 SSBOND 1 CYS A 132 CYS A 135 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 ENDMDL MODEL 2 ENDMDL MODEL 3 ENDMDL MODEL 4 ENDMDL MODEL 5 ENDMDL MODEL 6 ENDMDL MODEL 7 ENDMDL MODEL 8 ENDMDL MODEL 9 ENDMDL MODEL 10 ENDMDL MODEL 11 ENDMDL MODEL 12 ENDMDL MODEL 13 ENDMDL MODEL 14 ENDMDL MODEL 15 ENDMDL MODEL 16 ENDMDL MODEL 17 ENDMDL MODEL 18 ENDMDL MODEL 19 ENDMDL MODEL 20 ENDMDL CONECT 585 629 CONECT 629 585 MASTER 225 0 0 3 0 0 0 6 522 1 2 5 END