HEADER HORMONE 12-MAR-10 2KVE TITLE C-TERMINAL DOMAIN OF MESENCEPHALIC ASTROCYTE-DERIVED NEUROTROPHIC TITLE 2 FACTOR (MANF) COMPND MOL_ID: 1; COMPND 2 MOLECULE: MESENCEPHALIC ASTROCYTE-DERIVED NEUROTROPHIC FACTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN, UNP RESIDUES 117-179; COMPND 5 SYNONYM: MANF, PROTEIN ARMET, ARGININE-RICH PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ORIGAMIB(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET15B KEYWDS DISULFIDE BOND, GLYCOPROTEIN, GROWTH FACTOR, SECRETED, SIALIC ACID, KEYWDS 2 UNFOLDED PROTEIN RESPONSE, HORMONE EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR M.H.HELLMAN,M.SAARMA,P.PERMI REVDAT 3 02-FEB-11 2KVE 1 JRNL REVDAT 2 17-NOV-10 2KVE 1 JRNL REVDAT 1 03-NOV-10 2KVE 0 JRNL AUTH M.H.HELLMAN,U.ARUMAE,L.-Y.YU,P.LINDHOLM,J.PERANEN,M.SAARMA, JRNL AUTH 2 P.PERMI JRNL TITL MESENCEPHALIC ASTROCYTE-DERIVED NEUROTROPHIC FACTOR (MANF) JRNL TITL 2 HAS A UNIQUE MECHANISM TO RESCUE APOPTOTIC NEURONS JRNL REF J.BIOL.CHEM. V. 286 2675 2011 JRNL REFN ISSN 0021-9258 JRNL PMID 21047780 JRNL DOI 10.1074/JBC.M110.146738 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 8.0 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, AND KOLLM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KVE COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-MAR-10. REMARK 100 THE RCSB ID CODE IS RCSB101620. 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 : 50 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM [U-99% 13C; U-99% 15N] C- REMARK 210 MANF; 93% H2O/7% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 2D 1H-13C-CT-HSQC; 3D CBCA(CO)NH; REMARK 210 3D HNCACB; 3D C(CO)NH; 3D H(CCO) REMARK 210 NH; 2D (HB)CB(CGCD)HD; 2D (HB) REMARK 210 CB(CGCDCE)HE; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : UNITY INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 2.0.26, AMBER 8.0 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING, TORSION REMARK 210 ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 400 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 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: 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 HG1 THR A 156 O LEU A 158 1.74 REMARK 500 HG SER A 104 O LYS A 150 1.75 REMARK 500 OD1 ASP A 135 HH21 ARG A 138 1.77 REMARK 500 HZ3 LYS A 139 OE2 GLU A 142 1.81 REMARK 500 HZ3 LYS A 99 OD1 ASP A 102 1.83 REMARK 500 O VAL A 113 H LYS A 117 1.87 REMARK 500 O LYS A 117 H ASP A 121 1.89 REMARK 500 O ASP A 102 H THR A 105 1.89 REMARK 500 O ILE A 140 H MET A 144 1.90 REMARK 500 O MET A 144 H ALA A 148 1.91 REMARK 500 O ILE A 137 H ASN A 141 1.95 REMARK 500 O ASP A 135 H LYS A 139 1.96 REMARK 500 O LYS A 118 H ASP A 122 1.96 REMARK 500 O ALA A 148 H ALA A 151 1.96 REMARK 500 O TYR A 136 H ILE A 140 1.97 REMARK 500 O GLY A 95 H TYR A 97 2.01 REMARK 500 O ALA A 148 H ALA A 152 2.01 REMARK 500 O LEU A 111 HZ2 LYS A 133 2.02 REMARK 500 O ARG A 138 H GLU A 142 2.02 REMARK 500 O LEU A 120 H GLU A 125 2.04 REMARK 500 O ILE A 140 H LEU A 143 2.05 REMARK 500 O ASP A 107 H LYS A 110 2.06 REMARK 500 O ARG A 112 H LEU A 116 2.09 REMARK 500 O ASP A 102 H VAL A 106 2.09 REMARK 500 O SER A 134 H ARG A 138 2.10 REMARK 500 O GLU A 132 H ASP A 135 2.12 REMARK 500 O LEU A 143 H TYR A 147 2.16 REMARK 500 O ARG A 112 H GLU A 115 2.16 REMARK 500 O LEU A 143 H LYS A 146 2.18 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 2 ARG A 155 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 ARG A 138 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 7 ARG A 138 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 8 ARG A 138 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 13 ARG A 155 NE - CZ - NH1 ANGL. DEV. = 3.4 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 LYS A 96 -19.87 62.63 REMARK 500 1 ASP A 98 -14.26 -149.04 REMARK 500 1 ASP A 102 -18.66 -141.41 REMARK 500 1 ALA A 151 -24.32 -143.67 REMARK 500 2 LEU A 103 -24.29 63.61 REMARK 500 2 THR A 105 18.43 -144.79 REMARK 500 2 ALA A 131 -6.20 -148.05 REMARK 500 2 ALA A 148 -158.75 -102.24 REMARK 500 2 ALA A 151 31.85 -144.34 REMARK 500 2 ALA A 152 9.82 58.88 REMARK 500 2 ASP A 157 -31.49 -130.57 REMARK 500 3 TYR A 97 -46.07 -144.03 REMARK 500 3 ASP A 102 -44.04 -153.44 REMARK 500 3 ALA A 151 -21.97 -147.93 REMARK 500 4 GLN A 100 18.91 -145.04 REMARK 500 4 LEU A 103 0.19 -64.64 REMARK 500 4 ALA A 148 52.56 -142.12 REMARK 500 5 LYS A 96 39.78 -80.71 REMARK 500 5 LYS A 99 -36.46 -132.28 REMARK 500 5 ALA A 131 -38.04 -153.70 REMARK 500 5 ALA A 148 -100.65 -127.53 REMARK 500 5 SER A 153 -30.38 -150.00 REMARK 500 6 CYS A 127 69.70 -67.12 REMARK 500 6 ALA A 131 -17.14 -144.68 REMARK 500 6 ALA A 148 54.82 -148.34 REMARK 500 7 ASP A 98 21.18 -141.85 REMARK 500 7 LYS A 99 -167.79 -120.40 REMARK 500 7 LEU A 103 -29.60 -144.30 REMARK 500 7 ASP A 107 78.50 62.60 REMARK 500 7 ALA A 131 -15.70 -141.06 REMARK 500 7 LYS A 150 16.38 52.46 REMARK 500 7 ALA A 151 12.97 -153.67 REMARK 500 8 CYS A 127 64.37 39.01 REMARK 500 8 ALA A 151 12.49 53.87 REMARK 500 8 ALA A 154 11.92 -147.49 REMARK 500 8 ASP A 157 -34.30 63.62 REMARK 500 9 ASP A 102 -47.06 -141.28 REMARK 500 9 ALA A 131 16.04 -144.12 REMARK 500 9 ALA A 148 53.91 -141.17 REMARK 500 9 ALA A 151 -5.83 -151.74 REMARK 500 10 LEU A 103 -37.91 62.73 REMARK 500 10 ALA A 131 -15.17 -146.27 REMARK 500 10 LYS A 150 -49.35 -147.89 REMARK 500 10 SER A 153 33.54 -156.71 REMARK 500 11 TYR A 97 15.82 -143.07 REMARK 500 11 ASP A 102 -50.63 -136.60 REMARK 500 11 LYS A 128 -14.69 59.16 REMARK 500 11 ALA A 148 60.34 -151.11 REMARK 500 11 ALA A 151 26.92 -143.32 REMARK 500 12 LEU A 103 -46.33 64.25 REMARK 500 REMARK 500 THIS ENTRY HAS 62 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KVD RELATED DB: PDB REMARK 900 COORDINATES FOR THE FULL-LENGTH MANF REMARK 900 RELATED ID: 16776 RELATED DB: BMRB DBREF 2KVE A 96 158 UNP P55145 MANF_HUMAN 117 179 SEQADV 2KVE MET A 94 UNP P55145 EXPRESSION TAG SEQADV 2KVE GLY A 95 UNP P55145 EXPRESSION TAG SEQRES 1 A 65 MET GLY LYS TYR ASP LYS GLN ILE ASP LEU SER THR VAL SEQRES 2 A 65 ASP LEU LYS LYS LEU ARG VAL LYS GLU LEU LYS LYS ILE SEQRES 3 A 65 LEU ASP ASP TRP GLY GLU THR CYS LYS GLY CYS ALA GLU SEQRES 4 A 65 LYS SER ASP TYR ILE ARG LYS ILE ASN GLU LEU MET PRO SEQRES 5 A 65 LYS TYR ALA PRO LYS ALA ALA SER ALA ARG THR ASP LEU HELIX 1 1 ARG A 112 GLY A 124 1 13 HELIX 2 2 GLU A 132 ALA A 148 1 17 HELIX 3 3 ALA A 148 SER A 153 1 6 SSBOND 1 CYS A 127 CYS A 130 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