PDB Short entry for 2KVD HEADER HORMONE 12-MAR-10 2KVD TITLE MESENCEPHALIC ASTROCYTE-DERIVED NEUROTROPHIC FACTOR (MANF) COMPND MOL_ID: 1; COMPND 2 MOLECULE: MESENCEPHALIC ASTROCYTE-DERIVED NEUROTROPHIC FACTOR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MANF, PROTEIN ARMET, ARGININE-RICH PROTEIN; COMPND 5 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: MESENCEPHALIC ASTROCYTE-DERIVED NEUROTROPHIC FACTOR; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ORIGAMIB (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PFOLD KEYWDS DISULFIDE BOND, GLYCOPROTEIN, GROWTH FACTOR, SECRETED, SIALIC ACID, KEYWDS 2 UNFOLDED PROTEIN RESPONSE, HORMONE EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR M.H.HELLMAN,J.PERANEN,M.SAARMA,P.PERMI REVDAT 3 02-FEB-11 2KVD 1 JRNL REVDAT 2 17-NOV-10 2KVD 1 JRNL REVDAT 1 03-NOV-10 2KVD 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 2KVD 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 RCSB101619. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM [U-98% 13C; U-98% 15N] MANF; REMARK 210 93% H2O/7% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C REMARK 210 NOESY; 3D HNCACB; 3D CBCA(CO)NH; REMARK 210 3D HN(CO)CA; 3D HCAN; 3D HCA(CO) REMARK 210 N; 3D HCCH-TOCSY; 3D HCCH-COSY; REMARK 210 3D H(CCO)NH; 3D C(CO)NH; 2D 1H- REMARK 210 15N HSQC; 2D 1H-13C HSQC; 2D (HB) REMARK 210 CB(CGCD)HD; 2D (HB)CB(CGCDCE)HE 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 O GLU A 7 HG SER A 11 1.69 REMARK 500 O GLU A 125 HG1 THR A 126 1.74 REMARK 500 OE1 GLU A 33 HG SER A 69 1.74 REMARK 500 OE2 GLU A 132 HG SER A 134 1.75 REMARK 500 HH21 ARG A 112 OE2 GLU A 115 1.78 REMARK 500 OD1 ASP A 135 HH21 ARG A 138 1.79 REMARK 500 O PHE A 27 HG SER A 28 1.79 REMARK 500 OE1 GLU A 83 HZ3 LYS A 86 1.81 REMARK 500 OE1 GLU A 94 HZ2 LYS A 96 1.81 REMARK 500 O TYR A 53 HG1 THR A 62 1.81 REMARK 500 OD2 ASP A 19 HH21 ARG A 23 1.82 REMARK 500 OE1 GLU A 67 HZ2 LYS A 70 1.83 REMARK 500 OD1 ASP A 5 HZ2 LYS A 86 1.83 REMARK 500 O ILE A 137 H ASN A 141 1.85 REMARK 500 O LEU A 111 HZ3 LYS A 133 1.85 REMARK 500 O ASP A 107 H LYS A 110 1.87 REMARK 500 O THR A 105 HZ3 LYS A 110 1.87 REMARK 500 O LEU A 36 H CYS A 40 1.88 REMARK 500 H CYS A 130 OD2 ASP A 135 1.88 REMARK 500 O LEU A 103 H ASP A 107 1.88 REMARK 500 O PRO A 71 H HIS A 74 1.88 REMARK 500 O CYS A 9 H LEU A 13 1.89 REMARK 500 O PRO A 77 H ILE A 81 1.89 REMARK 500 O ALA A 152 HH12 ARG A 155 1.90 REMARK 500 O ARG A 44 HD21 ASN A 48 1.91 REMARK 500 O TYR A 12 H PHE A 16 1.91 REMARK 500 O ILE A 137 HD21 ASN A 141 1.91 REMARK 500 O GLU A 142 HZ1 LYS A 146 1.91 REMARK 500 O LYS A 46 H ARG A 49 1.92 REMARK 500 OD2 ASP A 135 HZ1 LYS A 139 1.93 REMARK 500 O ASP A 5 H GLU A 7 1.94 REMARK 500 O PHE A 39 H ALA A 43 1.94 REMARK 500 O ASP A 135 HZ2 LYS A 139 1.96 REMARK 500 HZ3 LYS A 96 OE1 GLN A 100 1.96 REMARK 500 O LEU A 95 H TYR A 97 1.96 REMARK 500 O VAL A 113 H LYS A 117 1.97 REMARK 500 O LYS A 133 H ILE A 137 1.98 REMARK 500 O LYS A 63 HD21 ASN A 66 1.98 REMARK 500 O TYR A 136 H ILE A 140 1.98 REMARK 500 O CYS A 82 H LYS A 86 1.99 REMARK 500 OG SER A 11 HH TYR A 97 1.99 REMARK 500 O GLU A 7 H SER A 11 1.99 REMARK 500 O LEU A 120 H GLU A 125 2.00 REMARK 500 O LYS A 133 H TYR A 136 2.01 REMARK 500 O ILE A 65 H VAL A 68 2.01 REMARK 500 O LEU A 85 H ASP A 89 2.02 REMARK 500 O ILE A 64 H GLU A 67 2.03 REMARK 500 O PRO A 71 H HIS A 75 2.03 REMARK 500 O LYS A 118 H ASP A 122 2.03 REMARK 500 O SER A 90 H GLU A 94 2.04 REMARK 500 REMARK 500 THIS ENTRY HAS 1068 CLOSE CONTACTS 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 23 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 2 TYR A 17 CB - CG - CD1 ANGL. DEV. = -3.7 DEGREES REMARK 500 2 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 ARG A 138 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 4 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 5 ARG A 112 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 6 ARG A 2 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 6 ARG A 15 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 6 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 7 ARG A 15 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 7 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 8 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 8 ARG A 138 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 8 ARG A 155 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 9 ARG A 15 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 9 ARG A 41 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 9 ARG A 112 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 10 ARG A 15 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 10 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 10 ARG A 41 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 10 ARG A 138 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 11 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 13 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 13 ARG A 41 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 13 ARG A 138 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 14 ARG A 138 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 15 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.1 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 CYS A 6 34.98 -71.00 REMARK 500 1 TYR A 12 -57.17 -126.95 REMARK 500 1 SER A 28 -47.43 -164.76 REMARK 500 1 PRO A 29 -156.68 -80.32 REMARK 500 1 ALA A 30 -3.92 -54.42 REMARK 500 1 ALA A 43 -77.51 -39.19 REMARK 500 1 VAL A 78 -26.61 -38.65 REMARK 500 1 LYS A 96 0.79 46.78 REMARK 500 1 ASP A 98 -26.77 -154.06 REMARK 500 1 LYS A 99 -157.04 58.52 REMARK 500 1 SER A 104 -8.45 -51.26 REMARK 500 1 LEU A 111 -175.74 -68.34 REMARK 500 1 THR A 126 -176.95 58.63 REMARK 500 2 TYR A 12 -51.06 -126.01 REMARK 500 2 LEU A 20 -70.13 -54.41 REMARK 500 2 SER A 28 -49.70 -163.38 REMARK 500 2 PRO A 29 -153.35 -81.57 REMARK 500 2 ALA A 30 -3.06 -54.46 REMARK 500 2 ALA A 43 -73.27 -45.87 REMARK 500 2 VAL A 78 -26.35 -37.78 REMARK 500 2 LYS A 96 176.74 -59.51 REMARK 500 2 LYS A 99 -152.50 45.40 REMARK 500 2 SER A 104 -10.66 -47.58 REMARK 500 2 THR A 126 -165.45 42.80 REMARK 500 2 LYS A 128 89.52 -62.20 REMARK 500 2 ALA A 131 -41.59 -164.48 REMARK 500 2 SER A 153 13.49 -141.49 REMARK 500 2 ASP A 157 -10.94 -141.13 REMARK 500 3 CYS A 6 38.91 -141.04 REMARK 500 3 TYR A 12 -55.55 -129.89 REMARK 500 3 SER A 28 -47.34 -167.02 REMARK 500 3 PRO A 29 -154.99 -80.30 REMARK 500 3 ALA A 30 -5.12 -53.71 REMARK 500 3 ALA A 43 -78.36 -41.32 REMARK 500 3 ASP A 58 4.17 59.39 REMARK 500 3 VAL A 78 -27.77 -35.31 REMARK 500 3 LYS A 96 -44.10 -154.44 REMARK 500 3 GLN A 100 -172.94 -68.33 REMARK 500 3 SER A 104 -8.45 -55.34 REMARK 500 3 ASP A 107 96.14 -56.23 REMARK 500 3 LEU A 111 171.26 -54.88 REMARK 500 3 THR A 126 -172.17 54.67 REMARK 500 3 LYS A 150 55.86 32.44 REMARK 500 4 GLU A 7 12.17 -141.13 REMARK 500 4 TYR A 12 -55.04 -142.37 REMARK 500 4 SER A 28 -46.87 -165.97 REMARK 500 4 PRO A 29 -155.17 -80.32 REMARK 500 4 ALA A 30 -3.18 -55.00 REMARK 500 4 ALA A 43 -77.16 -42.92 REMARK 500 4 ALA A 61 10.06 54.74 REMARK 500 REMARK 500 THIS ENTRY HAS 200 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 13 TYR A 97 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KVE RELATED DB: PDB REMARK 900 STRUCTURE OF C-TERMINAL DOMAIN OF MANF REMARK 900 RELATED ID: 16775 RELATED DB: BMRB DBREF 2KVD A 1 158 UNP P55145 MANF_HUMAN 22 179 SEQADV 2KVD GLY A -1 UNP P55145 EXPRESSION TAG SEQADV 2KVD SER A 0 UNP P55145 EXPRESSION TAG SEQRES 1 A 160 GLY SER LEU ARG PRO GLY ASP CYS GLU VAL CYS ILE SER SEQRES 2 A 160 TYR LEU GLY ARG PHE TYR GLN ASP LEU LYS ASP ARG ASP SEQRES 3 A 160 VAL THR PHE SER PRO ALA THR ILE GLU ASN GLU LEU ILE SEQRES 4 A 160 LYS PHE CYS ARG GLU ALA ARG GLY LYS GLU ASN ARG LEU SEQRES 5 A 160 CYS TYR TYR ILE GLY ALA THR ASP ASP ALA ALA THR LYS SEQRES 6 A 160 ILE ILE ASN GLU VAL SER LYS PRO LEU ALA HIS HIS ILE SEQRES 7 A 160 PRO VAL GLU LYS ILE CYS GLU LYS LEU LYS LYS LYS ASP SEQRES 8 A 160 SER GLN ILE CYS GLU LEU LYS TYR ASP LYS GLN ILE ASP SEQRES 9 A 160 LEU SER THR VAL ASP LEU LYS LYS LEU ARG VAL LYS GLU SEQRES 10 A 160 LEU LYS LYS ILE LEU ASP ASP TRP GLY GLU THR CYS LYS SEQRES 11 A 160 GLY CYS ALA GLU LYS SER ASP TYR ILE ARG LYS ILE ASN SEQRES 12 A 160 GLU LEU MET PRO LYS TYR ALA PRO LYS ALA ALA SER ALA SEQRES 13 A 160 ARG THR ASP LEU HELIX 1 1 CYS A 6 SER A 11 1 6 HELIX 2 2 TYR A 12 ARG A 23 1 12 HELIX 3 3 ALA A 30 ARG A 41 1 12 HELIX 4 4 ILE A 65 ALA A 73 1 9 HELIX 5 5 LYS A 80 ASP A 89 1 10 HELIX 6 6 SER A 90 CYS A 93 5 4 HELIX 7 7 ASP A 102 VAL A 106 5 5 HELIX 8 8 ARG A 112 GLY A 124 1 13 HELIX 9 9 GLU A 132 GLU A 142 1 11 SSBOND 1 CYS A 6 CYS A 93 1555 1555 2.04 SSBOND 2 CYS A 9 CYS A 82 1555 1555 2.03 SSBOND 3 CYS A 40 CYS A 51 1555 1555 2.03 SSBOND 4 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