HEADER APOPTOSIS 21-FEB-19 6O1Q TITLE THE N-TERMINAL DOMAIN OF NPHP1 FOLDS INTO AN ANTIPARALLEL THREE- TITLE 2 STRANDED COILED COIL COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEPHROCYSTIN-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL RESIDUES 1-115; COMPND 5 SYNONYM: JUVENILE NEPHRONOPHTHISIS 1 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 GENE: NPHP1, NPH1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NEPHRONOPHTHISIS, APOPTOSIS EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR G.MUSCO,V.MANNELLA REVDAT 2 28-AUG-19 6O1Q 1 JRNL REVDAT 1 14-AUG-19 6O1Q 0 JRNL AUTH V.MANNELLA,G.QUILICI,E.A.NIGRO,M.LAMPIS,C.MINICI,M.DEGANO, JRNL AUTH 2 A.BOLETTA,G.MUSCO JRNL TITL THE N-TERMINAL DOMAIN OF NPHP1 FOLDS INTO A MONOMERIC JRNL TITL 2 LEFT-HANDED ANTIPARALLEL THREE-STRANDED COILED COIL WITH JRNL TITL 3 ANTI-APOPTOTIC FUNCTION. JRNL REF ACS CHEM.BIOL. V. 14 1845 2019 JRNL REFN ESSN 1554-8937 JRNL PMID 31345020 JRNL DOI 10.1021/ACSCHEMBIO.9B00582 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6O1Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-FEB-19. REMARK 100 THE DEPOSITION ID IS D_1000239865. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.3 REMARK 210 IONIC STRENGTH : 0.15 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.8 MM [U-99% 13C; U-99% 15N] REMARK 210 NPHP1 CC, 100% D2O; 0.8 MM [U-99% REMARK 210 13C; U-99% 15N] NPHP1CC, 90% REMARK 210 H2O/10% D2O; 0.9 MM [U-99% 15N] REMARK 210 NPHP1CC, 90% H2O/10% D2O; 0.7 MM REMARK 210 NPHP1CC, 90% H2O/10% D2O; 0.7 MM REMARK 210 NPHP1CC, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY; REMARK 210 2D 1H-15N HSQC; 3D HNHA; 3D 1H- REMARK 210 15N NOESY; 3D HNCA; 3D H(CCO)NH; REMARK 210 3D HNCACB; 3D CBCA(CO)NH; 3D REMARK 210 C(CO)NH; 3D HNCO; 3D HCCH-TOCSY; REMARK 210 2D 1H-13C HSQC; 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ARIA, ANALYSIS REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 40 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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: 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 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 MET A 5 44.73 -155.67 REMARK 500 1 PRO A 78 95.60 -63.10 REMARK 500 1 ALA A 80 -91.27 48.28 REMARK 500 1 ASN A 111 54.05 -104.79 REMARK 500 1 THR A 113 -60.37 -95.13 REMARK 500 2 GLN A 10 63.59 -152.33 REMARK 500 2 ARG A 11 -38.06 -140.00 REMARK 500 2 LEU A 70 43.08 -82.37 REMARK 500 2 LYS A 72 63.45 -117.13 REMARK 500 2 VAL A 115 47.41 -104.39 REMARK 500 3 ARG A 8 71.79 55.33 REMARK 500 3 SER A 71 61.50 69.04 REMARK 500 3 PRO A 78 58.22 -94.33 REMARK 500 3 VAL A 79 -73.56 -67.53 REMARK 500 3 ALA A 80 -84.45 -149.25 REMARK 500 3 ASN A 111 57.32 -116.66 REMARK 500 3 THR A 113 -67.52 -97.60 REMARK 500 4 ASP A 12 76.88 57.57 REMARK 500 4 SER A 76 36.99 -156.37 REMARK 500 4 VAL A 79 51.91 -101.78 REMARK 500 4 GLU A 114 -75.84 68.09 REMARK 500 5 MET A 5 39.57 -97.29 REMARK 500 5 ASP A 12 76.27 59.50 REMARK 500 5 LEU A 70 51.90 -103.71 REMARK 500 5 GLU A 75 175.91 66.55 REMARK 500 5 SER A 76 -173.86 66.45 REMARK 500 5 PRO A 78 80.03 -68.51 REMARK 500 5 VAL A 115 48.13 -96.42 REMARK 500 6 LYS A 72 10.69 -147.07 REMARK 500 6 ARG A 109 54.25 -119.64 REMARK 500 6 ASN A 111 69.94 -153.95 REMARK 500 6 ILE A 112 -80.92 -91.72 REMARK 500 7 ARG A 9 -54.63 70.66 REMARK 500 7 SER A 71 42.81 -94.41 REMARK 500 7 GLU A 75 41.71 -91.18 REMARK 500 7 VAL A 79 -70.81 -80.91 REMARK 500 7 ALA A 80 -63.95 -155.57 REMARK 500 7 ARG A 109 -166.92 65.76 REMARK 500 7 GLU A 110 46.45 -78.23 REMARK 500 8 MET A 3 -159.01 60.94 REMARK 500 8 ALA A 4 -60.01 -90.47 REMARK 500 8 ASP A 12 72.82 59.53 REMARK 500 8 LYS A 72 48.07 -103.38 REMARK 500 8 GLU A 75 108.64 81.25 REMARK 500 8 SER A 76 -61.70 -103.86 REMARK 500 8 ALA A 77 63.00 -162.02 REMARK 500 8 ALA A 80 -58.29 -158.70 REMARK 500 8 ASN A 111 52.98 -100.02 REMARK 500 8 GLU A 114 135.25 70.37 REMARK 500 9 LEU A 70 39.59 -92.85 REMARK 500 REMARK 500 THIS ENTRY HAS 60 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30575 RELATED DB: BMRB REMARK 900 THE PUTATIVE COILED COIL DOMAIN OF NPHP1 FOLDS AS A THREE HELIX REMARK 900 BUNDLE DBREF 6O1Q A 5 119 UNP O15259 NPHP1_HUMAN 1 115 SEQADV 6O1Q GLY A 1 UNP O15259 EXPRESSION TAG SEQADV 6O1Q PRO A 2 UNP O15259 EXPRESSION TAG SEQADV 6O1Q MET A 3 UNP O15259 EXPRESSION TAG SEQADV 6O1Q ALA A 4 UNP O15259 EXPRESSION TAG SEQRES 1 A 119 GLY PRO MET ALA MET LEU ALA ARG ARG GLN ARG ASP PRO SEQRES 2 A 119 LEU GLN ALA LEU ARG ARG ARG ASN GLN GLU LEU LYS GLN SEQRES 3 A 119 GLN VAL ASP SER LEU LEU SER GLU SER GLN LEU LYS GLU SEQRES 4 A 119 ALA LEU GLU PRO ASN LYS ARG GLN HIS ILE TYR GLN ARG SEQRES 5 A 119 CYS ILE GLN LEU LYS GLN ALA ILE ASP GLU ASN LYS ASN SEQRES 6 A 119 ALA LEU GLN LYS LEU SER LYS ALA ASP GLU SER ALA PRO SEQRES 7 A 119 VAL ALA ASN TYR ASN GLN ARG LYS GLU GLU GLU HIS THR SEQRES 8 A 119 LEU LEU ASP LYS LEU THR GLN GLN LEU GLN GLY LEU ALA SEQRES 9 A 119 VAL THR ILE SER ARG GLU ASN ILE THR GLU VAL GLY ALA SEQRES 10 A 119 PRO THR HELIX 1 AA1 ASP A 12 GLN A 36 1 25 HELIX 2 AA2 LYS A 38 LEU A 41 5 4 HELIX 3 AA3 GLU A 42 LEU A 70 1 29 HELIX 4 AA4 ALA A 80 ARG A 109 1 30 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