HEADER HORMONE 29-APR-20 6YW8 TITLE NMR SOLUTION STRUCTURE OF UNBOUND RECOMBINANT HUMAN NERVE GROWTH TITLE 2 FACTOR (RHNGF) COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-NERVE GROWTH FACTOR; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: BETA-NGF; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: HNGF IS A HOMODIMER. IT HAS 3 DISULFIDE BRIDGES PER COMPND 7 PROTOMER. CHAIN A: CYS 15 TO CYS 80 CYS 58 TO CYS 108 CYS 68 TO CYS COMPND 8 110 CHAIN B: CHAIN A: CYS 15 TO CYS 80 CYS 58 TO CYS 108 CYS 68 TO COMPND 9 CYS 110 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: NGF, NGFB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HUMAN NGF, UNBOUND STRUCTURE, HOMODIMER, CYSTIN-KNOT, HORMONE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.GOLIC GRDADOLNIK,F.PAOLETTI REVDAT 5 13-NOV-24 6YW8 1 REMARK REVDAT 4 03-JUL-24 6YW8 1 REMARK REVDAT 3 30-JUN-21 6YW8 1 JRNL REVDAT 2 19-MAY-21 6YW8 1 JRNL REVDAT 1 12-MAY-21 6YW8 0 JRNL AUTH F.PAOLETTI,F.MERZEL,A.CASSETTA,I.OGRIS,S.COVACEUSZACH, JRNL AUTH 2 J.GRDADOLNIK,D.LAMBA,S.GOLIC GRDADOLNIK JRNL TITL ENDOGENOUS MODULATORS OF NEUROTROPHIN SIGNALING: LANDSCAPE JRNL TITL 2 OF THE TRANSIENT ATP-NGF INTERACTIONS. JRNL REF COMPUT STRUCT BIOTECHNOL J V. 19 2938 2021 JRNL REFN ESSN 2001-0370 JRNL PMID 34136093 JRNL DOI 10.1016/J.CSBJ.2021.05.009 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 2.3.2 REMARK 3 AUTHORS : RIEPING W., HABECK M., BARDIAUX B., BERNARD A., REMARK 3 MALLIAVIN T.E., NILGES M. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6YW8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 29-APR-20. REMARK 100 THE DEPOSITION ID IS D_1292108297. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.1 MM [U-99% 15N] NERVE GROWTH REMARK 210 FACTOR, 50 MM HEPES, 90% H2O/10% REMARK 210 D2O; 0.1 MM [U-99% 13C; U-99% REMARK 210 15N] NERVE GROWTH FACTOR, 50 MM REMARK 210 HEPES, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N NOESY; REMARK 210 3D HNCA; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 ALIPHATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : VNMRS REMARK 210 SPECTROMETER MANUFACTURER : AGILENT REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ARIA 2.3.2, CARA, NMRPIPE 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 LOWEST REMARK 210 ENERGY 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 25 OE2 GLU A 55 1.58 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 PHE A 7 -56.58 -167.68 REMARK 500 1 VAL A 14 -42.42 -153.91 REMARK 500 1 LEU A 39 -56.24 72.63 REMARK 500 1 ASN A 45 -92.82 62.07 REMARK 500 1 PRO A 61 106.12 -45.74 REMARK 500 1 ASP A 65 -75.42 69.46 REMARK 500 1 LYS A 95 -91.44 64.04 REMARK 500 1 GLN A 96 -70.12 -135.70 REMARK 500 1 ALA A 116 -46.93 -158.23 REMARK 500 1 PHE B 7 -56.54 -167.37 REMARK 500 1 VAL B 14 -42.34 -153.71 REMARK 500 1 LEU B 39 -56.56 72.63 REMARK 500 1 ASN B 45 -92.83 61.90 REMARK 500 1 PRO B 61 106.26 -45.78 REMARK 500 1 ASP B 65 -75.08 69.16 REMARK 500 1 LYS B 95 -91.19 63.47 REMARK 500 1 GLN B 96 -70.24 -135.67 REMARK 500 1 ALA B 116 -47.01 -158.61 REMARK 500 2 PRO A 5 46.15 -95.98 REMARK 500 2 PHE A 7 56.92 -147.23 REMARK 500 2 GLU A 11 139.82 -175.09 REMARK 500 2 VAL A 14 -34.99 -158.84 REMARK 500 2 LEU A 39 -59.14 71.77 REMARK 500 2 TYR A 52 88.18 41.87 REMARK 500 2 PRO A 63 44.12 -81.89 REMARK 500 2 ASP A 65 -41.05 -165.53 REMARK 500 2 ILE A 71 135.96 74.15 REMARK 500 2 SER A 73 -38.43 75.75 REMARK 500 2 GLN A 96 -75.15 67.73 REMARK 500 2 PRO B 5 45.93 -95.82 REMARK 500 2 PHE B 7 56.69 -147.56 REMARK 500 2 GLU B 11 140.05 -174.82 REMARK 500 2 VAL B 14 -35.17 -159.86 REMARK 500 2 LEU B 39 -59.22 71.81 REMARK 500 2 TYR B 52 88.12 41.92 REMARK 500 2 PRO B 63 44.29 -81.72 REMARK 500 2 ASP B 65 -41.42 -165.33 REMARK 500 2 ILE B 71 136.22 74.61 REMARK 500 2 SER B 73 -38.35 75.90 REMARK 500 2 GLN B 96 -74.82 67.73 REMARK 500 3 PHE A 7 -81.64 65.00 REMARK 500 3 SER A 13 151.57 69.83 REMARK 500 3 CYS A 15 85.81 -164.29 REMARK 500 3 LEU A 39 -52.03 74.17 REMARK 500 3 ASP A 60 68.38 -118.16 REMARK 500 3 ASN A 62 76.37 -119.73 REMARK 500 3 ASP A 65 -88.91 -175.99 REMARK 500 3 SER A 73 -14.47 78.27 REMARK 500 3 THR A 82 -78.89 76.94 REMARK 500 3 THR A 83 -75.58 68.08 REMARK 500 REMARK 500 THIS ENTRY HAS 502 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34515 RELATED DB: BMRB REMARK 900 NMR SOLUTION STRUCTURE OF UNBOUND RECOMBINANT HUMAN NERVE GROWTH REMARK 900 FACTOR (RHNGF) DBREF 6YW8 A 1 118 UNP P01138 NGF_HUMAN 122 239 DBREF 6YW8 B 1 118 UNP P01138 NGF_HUMAN 122 239 SEQRES 1 A 118 SER SER SER HIS PRO ILE PHE HIS ARG GLY GLU PHE SER SEQRES 2 A 118 VAL CYS ASP SER VAL SER VAL TRP VAL GLY ASP LYS THR SEQRES 3 A 118 THR ALA THR ASP ILE LYS GLY LYS GLU VAL MET VAL LEU SEQRES 4 A 118 GLY GLU VAL ASN ILE ASN ASN SER VAL PHE LYS GLN TYR SEQRES 5 A 118 PHE PHE GLU THR LYS CYS ARG ASP PRO ASN PRO VAL ASP SEQRES 6 A 118 SER GLY CYS ARG GLY ILE ASP SER LYS HIS TRP ASN SER SEQRES 7 A 118 TYR CYS THR THR THR HIS THR PHE VAL LYS ALA LEU THR SEQRES 8 A 118 MET ASP GLY LYS GLN ALA ALA TRP ARG PHE ILE ARG ILE SEQRES 9 A 118 ASP THR ALA CYS VAL CYS VAL LEU SER ARG LYS ALA VAL SEQRES 10 A 118 ARG SEQRES 1 B 118 SER SER SER HIS PRO ILE PHE HIS ARG GLY GLU PHE SER SEQRES 2 B 118 VAL CYS ASP SER VAL SER VAL TRP VAL GLY ASP LYS THR SEQRES 3 B 118 THR ALA THR ASP ILE LYS GLY LYS GLU VAL MET VAL LEU SEQRES 4 B 118 GLY GLU VAL ASN ILE ASN ASN SER VAL PHE LYS GLN TYR SEQRES 5 B 118 PHE PHE GLU THR LYS CYS ARG ASP PRO ASN PRO VAL ASP SEQRES 6 B 118 SER GLY CYS ARG GLY ILE ASP SER LYS HIS TRP ASN SER SEQRES 7 B 118 TYR CYS THR THR THR HIS THR PHE VAL LYS ALA LEU THR SEQRES 8 B 118 MET ASP GLY LYS GLN ALA ALA TRP ARG PHE ILE ARG ILE SEQRES 9 B 118 ASP THR ALA CYS VAL CYS VAL LEU SER ARG LYS ALA VAL SEQRES 10 B 118 ARG SHEET 1 AA1 2 SER A 17 VAL A 22 0 SHEET 2 AA1 2 PHE A 53 CYS A 58 -1 O PHE A 53 N VAL A 22 SHEET 1 AA2 2 THR A 27 THR A 29 0 SHEET 2 AA2 2 GLU A 35 MET A 37 -1 O VAL A 36 N ALA A 28 SHEET 1 AA3 2 GLU A 41 ILE A 44 0 SHEET 2 AA3 2 SER A 47 LYS A 50 -1 O SER A 47 N ILE A 44 SHEET 1 AA4 2 TRP A 76 THR A 91 0 SHEET 2 AA4 2 ALA A 98 ARG A 114 -1 O SER A 113 N ASN A 77 SHEET 1 AA5 2 SER B 17 VAL B 22 0 SHEET 2 AA5 2 PHE B 53 CYS B 58 -1 O PHE B 53 N VAL B 22 SHEET 1 AA6 2 THR B 27 THR B 29 0 SHEET 2 AA6 2 GLU B 35 MET B 37 -1 O VAL B 36 N ALA B 28 SHEET 1 AA7 2 GLU B 41 ILE B 44 0 SHEET 2 AA7 2 SER B 47 LYS B 50 -1 O SER B 47 N ILE B 44 SHEET 1 AA8 2 TRP B 76 THR B 91 0 SHEET 2 AA8 2 ALA B 98 ARG B 114 -1 O SER B 113 N ASN B 77 SSBOND 1 CYS A 15 CYS A 80 1555 1555 2.03 SSBOND 2 CYS A 58 CYS A 108 1555 1555 2.03 SSBOND 3 CYS A 68 CYS A 110 1555 1555 2.03 SSBOND 4 CYS B 15 CYS B 80 1555 1555 2.03 SSBOND 5 CYS B 58 CYS B 108 1555 1555 2.03 SSBOND 6 CYS B 68 CYS B 110 1555 1555 2.03 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