HEADER SIGNALING PROTEIN 14-SEP-15 2N7K TITLE UNVEILING THE STRUCTURAL DETERMINANTS OF KIAA0323 BINDING PREFERENCE TITLE 2 FOR NEDD8 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEDD8; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NEDDYLIN, NEURAL PRECURSOR CELL EXPRESSED DEVELOPMENTALLY COMPND 5 DOWN-REGULATED PROTEIN 8, NEDD-8, UBIQUITIN-LIKE PROTEIN NEDD8; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: PROTEIN KHNYN; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: RESIDUES 627-678; COMPND 11 SYNONYM: KH AND NYN DOMAIN-CONTAINING PROTEIN; COMPND 12 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: NEDD8; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PGEX6P1; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: KHNYN, KIAA0323; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 EXPRESSION_SYSTEM_VECTOR: PGEX6P1 KEYWDS SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 11 AUTHOR E.SANTONICO,R.NEPRAVISHTA,A.MATTIONI,E.VALENTINI,W.MANDALITI, AUTHOR 2 R.PROCOPIO,M.IANNUCCELLI,L.CASTAGNOLI,S.POLO,M.PACI,G.CESARENI REVDAT 1 14-SEP-16 2N7K 0 JRNL AUTH E.SANTONICO,R.NEPRAVISHTA,A.MATTIONI,E.VALENTINI, JRNL AUTH 2 W.MANDALITI,R.PROCOPIO,M.IANNUCCELLI,L.CASTAGNOLI,S.POLO, JRNL AUTH 3 M.PACI,G.CESARENI JRNL TITL UNVEILING THE STRUCTURAL DETERMINANTS OF KIAA0323 BINDING JRNL TITL 2 PREFERENCE FOR NEDD8 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.3 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2N7K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-SEP-15. REMARK 100 THE RCSB ID CODE IS RCSB104521. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.8 REMARK 210 IONIC STRENGTH : 0.02 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.15-1.5 MM [U-100% 15N] REMARK 210 PROTEIN, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N NOESY; REMARK 210 3D 1H-15N TOCSY; 2D 1H-1H TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CNS 1.3 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 11 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST 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 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-11 REMARK 465 RES C SSSEQI REMARK 465 GLY A 77 REMARK 465 GLY A 78 REMARK 465 LEU A 79 REMARK 465 ARG A 80 REMARK 465 GLN A 81 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 TRP B 97 HA VAL B 103 1.01 REMARK 500 HG LEU B 88 H ARG B 89 1.23 REMARK 500 H ARG A 42 HB2 LEU A 71 1.25 REMARK 500 HZ2 LYS B 81 HE ARG B 114 1.26 REMARK 500 O GLN A 40 HB3 LEU A 71 1.42 REMARK 500 O ILE B 116 H SER B 120 1.54 REMARK 500 O ASN B 117 HB2 GLU B 121 1.56 REMARK 500 O TRP B 97 CA VAL B 103 1.96 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 SER A 46 -45.53 71.03 REMARK 500 1 ALA A 72 136.70 61.41 REMARK 500 1 GLN B 91 -36.84 -147.96 REMARK 500 1 LEU B 92 -174.87 -65.48 REMARK 500 1 GLU B 94 80.69 -50.57 REMARK 500 1 VAL B 95 -82.43 -80.06 REMARK 500 1 GLN B 99 64.41 15.22 REMARK 500 1 ASP B 100 -99.86 47.18 REMARK 500 1 ARG B 109 -94.48 -148.43 REMARK 500 1 GLU B 110 -46.09 -164.49 REMARK 500 2 SER A 46 -51.27 75.58 REMARK 500 2 GLN A 49 -138.05 -178.70 REMARK 500 2 MET A 50 143.34 -32.14 REMARK 500 2 GLN B 91 -47.81 -143.77 REMARK 500 2 LEU B 92 -154.05 -70.12 REMARK 500 2 LEU B 93 -124.53 -81.80 REMARK 500 2 VAL B 95 -82.71 -78.47 REMARK 500 2 GLN B 99 75.77 -7.54 REMARK 500 2 ASP B 100 -103.63 43.52 REMARK 500 2 GLN B 108 -88.47 48.13 REMARK 500 2 ARG B 109 -39.71 -150.22 REMARK 500 3 SER A 46 -47.56 71.07 REMARK 500 3 GLN B 91 -61.99 -96.07 REMARK 500 3 GLU B 94 -93.20 -148.92 REMARK 500 3 VAL B 95 -84.34 -79.19 REMARK 500 3 GLN B 99 70.23 4.68 REMARK 500 3 ASP B 100 -103.57 43.21 REMARK 500 3 ARG B 109 -103.34 -144.79 REMARK 500 3 GLU B 110 -44.40 -153.80 REMARK 500 4 ALA A 72 129.29 63.26 REMARK 500 4 VAL B 95 -82.01 -79.21 REMARK 500 4 GLN B 99 83.93 -59.86 REMARK 500 4 ASP B 100 -91.41 64.90 REMARK 500 4 GLN B 108 103.53 -56.72 REMARK 500 4 PRO B 111 170.02 -41.84 REMARK 500 5 GLN B 91 -37.77 -145.81 REMARK 500 5 LEU B 92 -167.25 -67.40 REMARK 500 5 GLU B 94 76.56 -56.80 REMARK 500 5 VAL B 95 -80.01 -79.89 REMARK 500 5 GLN B 99 85.50 -54.27 REMARK 500 5 ASP B 100 -107.07 35.65 REMARK 500 5 GLN B 108 108.07 -57.60 REMARK 500 5 PRO B 111 178.24 -52.72 REMARK 500 6 SER A 46 -48.49 70.73 REMARK 500 6 ALA A 72 103.33 61.15 REMARK 500 6 LEU A 73 -48.64 -142.17 REMARK 500 6 GLU B 94 82.96 -60.76 REMARK 500 6 VAL B 95 -82.98 -80.15 REMARK 500 6 GLN B 99 55.31 27.68 REMARK 500 6 ASP B 100 -90.74 56.28 REMARK 500 REMARK 500 THIS ENTRY HAS 98 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25808 RELATED DB: BMRB DBREF 2N7K A 1 81 UNP Q15843 NEDD8_HUMAN 1 81 DBREF 2N7K B 77 128 UNP O15037 KHNYN_HUMAN 627 678 SEQRES 1 A 81 MET LEU ILE LYS VAL LYS THR LEU THR GLY LYS GLU ILE SEQRES 2 A 81 GLU ILE ASP ILE GLU PRO THR ASP LYS VAL GLU ARG ILE SEQRES 3 A 81 LYS GLU ARG VAL GLU GLU LYS GLU GLY ILE PRO PRO GLN SEQRES 4 A 81 GLN GLN ARG LEU ILE TYR SER GLY LYS GLN MET ASN ASP SEQRES 5 A 81 GLU LYS THR ALA ALA ASP TYR LYS ILE LEU GLY GLY SER SEQRES 6 A 81 VAL LEU HIS LEU VAL LEU ALA LEU ARG GLY GLY GLY GLY SEQRES 7 A 81 LEU ARG GLN SEQRES 1 B 52 GLY GLY ILE ARG LYS THR ARG GLU THR GLU ARG LEU ARG SEQRES 2 B 52 ARG GLN LEU LEU GLU VAL PHE TRP GLY GLN ASP HIS LYS SEQRES 3 B 52 VAL ASP PHE ILE LEU GLN ARG GLU PRO TYR CYS ARG ASP SEQRES 4 B 52 ILE ASN GLN LEU SER GLU ALA LEU LEU SER LEU ASN PHE HELIX 1 1 LYS A 22 GLY A 35 1 14 HELIX 2 2 PRO A 37 GLN A 41 5 5 HELIX 3 3 THR A 55 LYS A 60 5 6 HELIX 4 4 LYS B 81 GLN B 91 1 11 HELIX 5 5 HIS B 101 ILE B 106 1 6 HELIX 6 6 PRO B 111 PHE B 128 1 18 SHEET 1 A 5 GLU A 12 ASP A 16 0 SHEET 2 A 5 LEU A 2 LYS A 6 -1 N VAL A 5 O ILE A 13 SHEET 3 A 5 VAL A 66 LEU A 69 1 O LEU A 67 N LYS A 4 SHEET 4 A 5 LEU A 43 TYR A 45 -1 N ILE A 44 O HIS A 68 SHEET 5 A 5 LYS A 48 GLN A 49 -1 N LYS A 48 O TYR A 45 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