HEADER TRANSFERASE 12-JUN-17 5W4S TITLE SOLUTION STRUCTURE OF C2 DOMAIN FROM PROTEIN KINASE C ALPHA IN TERNARY TITLE 2 COMPLEX WITH CALCIUM AND V5-PHM PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN KINASE C ALPHA TYPE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C2 DOMAIN RESIDUES 155-293; COMPND 5 SYNONYM: PKC-ALPHA; COMPND 6 EC: 2.7.11.13; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: V5-PHM PEPTIDE; COMPND 10 CHAIN: B; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: PRKCA, PKCA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 11 ORGANISM_TAXID: 10116 KEYWDS TRANSFERASE, PHOSPHORYLATION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Y.YANG,T.I.IGUMENOVA REVDAT 3 14-JUN-23 5W4S 1 LINK REVDAT 2 27-NOV-19 5W4S 1 REMARK REVDAT 1 25-APR-18 5W4S 0 JRNL AUTH Y.YANG,C.SHU,P.LI,T.I.IGUMENOVA JRNL TITL STRUCTURAL BASIS OF PROTEIN KINASE C ALPHA REGULATION BY THE JRNL TITL 2 C-TERMINAL TAIL. JRNL REF BIOPHYS. J. V. 114 1590 2018 JRNL REFN ESSN 1542-0086 JRNL PMID 29642029 JRNL DOI 10.1016/J.BPJ.2017.12.030 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5W4S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JUN-17. REMARK 100 THE DEPOSITION ID IS D_1000228178. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 296.15; 296.15 REMARK 210 PH : 6.0; 6.0 REMARK 210 IONIC STRENGTH : 0.076; 0.077 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 2.225 MM CALCIUM ION, 0.89 MM [U REMARK 210 -13C; U-15N] C2 DOMAIN OF REMARK 210 PROTEIN KINASE C ALPHA, 6.7 MM REMARK 210 MES, 67 MM POTASSIUM CHLORIDE, REMARK 210 0.2 MG/ML SODIUM AZIDE, 2 MM V5- REMARK 210 PHM PEPTIDE, 92% H2O/8% D2O; REMARK 210 3.75 MM CALCIUM ION, 1.47 MM [U- REMARK 210 13C; U-15N] C2 DOMAIN OF PROTEIN REMARK 210 KINASE C ALPHA, 6.7 MM MES, 67 REMARK 210 MM POTASSIUM CHLORIDE, 0.2 MG/ML REMARK 210 SODIUM AZIDE, 0.6 MM V5-PHM REMARK 210 PEPTIDE, 92% H2O/8% D2O; 2.225 REMARK 210 MM CALCIUM ION, 0.89 MM [U-13C; REMARK 210 U-15N] C2 DOMAIN OF PROTEIN REMARK 210 KINASE C ALPHA, 6.7 MM MES, 67 REMARK 210 MM POTASSIUM CHLORIDE, 0.2 MG/ML REMARK 210 SODIUM AZIDE, 2 MM V5-PHM REMARK 210 PEPTIDE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D C(CO)NH; 3D H(CCO) REMARK 210 NH; 3D HCCH-TOCSY; 3D HCCH-COSY; REMARK 210 3D AROMATIC HCCH-TOCSY; 3D 1H- REMARK 210 13C NOESY ALIPHATIC; 3D 1H-15N REMARK 210 NOESY; 2D [F2-15N,13C FILTERED] REMARK 210 NOESY; 2D [F1,F2-15N,13C REMARK 210 FILTERED] NOESY; 2D [F1,F2-15N, REMARK 210 13C FILTERED] TOCSY; 3D [F1-15N, REMARK 210 13C FILTERED] 1H-15N NOESY; 3D REMARK 210 [F1-15N,13C FILTERED] 1H-13C REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, NMRPIPE, SPARKY, ARIA, REMARK 210 HADDOCK REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 400 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 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 230 OD2 ASP A 235 1.57 REMARK 500 HZ1 LYS A 197 OE1 GLU A 243 1.59 REMARK 500 HZ2 LYS A 213 O1P SEP B 657 1.59 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 THR A 156 37.55 -140.36 REMARK 500 1 ARG A 178 -83.83 -79.87 REMARK 500 1 ILE A 215 -84.51 -85.65 REMARK 500 1 ARG A 216 -172.61 -170.99 REMARK 500 1 SER A 217 97.08 -65.36 REMARK 500 1 THR A 218 147.71 -170.45 REMARK 500 1 ARG A 249 -63.09 69.11 REMARK 500 1 ASN A 253 14.23 -164.60 REMARK 500 1 ASN A 287 72.81 -157.51 REMARK 500 1 GLN B 650 -165.40 -111.82 REMARK 500 1 PHE B 656 -71.86 -142.79 REMARK 500 2 LYS A 158 51.50 -142.80 REMARK 500 2 ARG A 178 -84.81 -78.82 REMARK 500 2 ARG A 216 -169.71 -72.80 REMARK 500 2 LEU A 231 -163.44 -100.33 REMARK 500 2 SER A 234 38.32 -80.64 REMARK 500 2 ARG A 249 -67.16 70.19 REMARK 500 2 ASN A 253 11.53 -152.62 REMARK 500 2 PHE B 656 -55.68 -137.12 REMARK 500 3 THR A 156 80.52 -150.61 REMARK 500 3 LYS A 158 46.65 -152.07 REMARK 500 3 ARG A 178 -83.61 -85.76 REMARK 500 3 PRO A 185 94.11 -66.24 REMARK 500 3 ASP A 193 84.37 -153.21 REMARK 500 3 ASN A 206 68.44 66.55 REMARK 500 3 GLU A 207 -24.77 -144.49 REMARK 500 3 PRO A 233 39.31 -69.21 REMARK 500 3 ASP A 248 51.15 -119.29 REMARK 500 3 ARG A 249 -65.74 66.96 REMARK 500 3 ASN A 253 -30.11 -158.75 REMARK 500 3 GLN B 650 -159.07 -111.00 REMARK 500 3 ASP B 652 -46.81 -131.08 REMARK 500 3 PHE B 656 -81.27 -127.76 REMARK 500 4 LYS A 158 56.68 -155.43 REMARK 500 4 ARG A 178 -87.64 -91.07 REMARK 500 4 ASN A 206 34.18 71.39 REMARK 500 4 PRO A 233 -8.33 -52.22 REMARK 500 4 ARG A 249 -73.42 64.75 REMARK 500 4 ASN A 253 -19.45 -162.96 REMARK 500 4 PRO A 291 -71.27 -56.34 REMARK 500 4 GLN B 650 -164.12 -118.55 REMARK 500 4 PHE B 656 -76.26 -122.20 REMARK 500 5 LYS A 158 81.79 -166.34 REMARK 500 5 ARG A 178 -83.30 -90.11 REMARK 500 5 SER A 217 106.02 -59.67 REMARK 500 5 LEU A 231 -167.57 -106.49 REMARK 500 5 ARG A 249 -75.02 66.21 REMARK 500 5 ASN A 253 -29.47 -164.01 REMARK 500 5 ASN A 287 48.53 -143.62 REMARK 500 5 PRO A 291 -73.42 -49.73 REMARK 500 REMARK 500 THIS ENTRY HAS 174 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 302 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET A 186 O REMARK 620 2 ASP A 187 OD1 73.9 REMARK 620 3 ASP A 246 OD2 94.0 80.4 REMARK 620 4 ASP A 248 OD1 143.1 70.5 71.3 REMARK 620 5 ASP A 248 OD2 152.3 109.5 113.7 54.2 REMARK 620 6 ASP A 254 OD2 86.7 155.8 86.8 124.5 94.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 187 OD1 REMARK 620 2 ASP A 187 OD2 53.7 REMARK 620 3 ASP A 193 OD2 135.1 81.9 REMARK 620 4 ASP A 246 OD1 99.4 99.0 79.1 REMARK 620 5 ASP A 246 OD2 67.9 107.5 129.3 50.4 REMARK 620 6 TRP A 247 O 146.2 149.8 76.8 97.7 102.5 REMARK 620 7 ASP A 248 OD1 69.0 117.8 152.8 113.0 65.5 77.5 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2NCE RELATED DB: PDB REMARK 900 RELATED ID: 30305 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF C2 DOMAIN FROM PROTEIN KINASE C ALPHA IN REMARK 900 TERNARY COMPLEX WITH CALCIUM AND V5-PHM PEPTIDE DBREF 5W4S A 155 293 UNP P05696 KPCA_RAT 155 293 DBREF 5W4S B 648 659 PDB 5W4S 5W4S 648 659 SEQRES 1 A 139 HIS THR GLU LYS ARG GLY ARG ILE TYR LEU LYS ALA GLU SEQRES 2 A 139 VAL THR ASP GLU LYS LEU HIS VAL THR VAL ARG ASP ALA SEQRES 3 A 139 LYS ASN LEU ILE PRO MET ASP PRO ASN GLY LEU SER ASP SEQRES 4 A 139 PRO TYR VAL LYS LEU LYS LEU ILE PRO ASP PRO LYS ASN SEQRES 5 A 139 GLU SER LYS GLN LYS THR LYS THR ILE ARG SER THR LEU SEQRES 6 A 139 ASN PRO GLN TRP ASN GLU SER PHE THR PHE LYS LEU LYS SEQRES 7 A 139 PRO SER ASP LYS ASP ARG ARG LEU SER VAL GLU ILE TRP SEQRES 8 A 139 ASP TRP ASP ARG THR THR ARG ASN ASP PHE MET GLY SER SEQRES 9 A 139 LEU SER PHE GLY VAL SER GLU LEU MET LYS MET PRO ALA SEQRES 10 A 139 SER GLY TRP TYR LYS LEU LEU ASN GLN GLU GLU GLY GLU SEQRES 11 A 139 TYR TYR ASN VAL PRO ILE PRO GLU GLY SEQRES 1 B 12 ACE ASP GLN SER ASP PHE GLU GLY PHE SEP TYR NH2 HET ACE B 648 6 HET SEP B 657 14 HET NH2 B 659 3 HET CA A 301 1 HET CA A 302 1 HETNAM ACE ACETYL GROUP HETNAM SEP PHOSPHOSERINE HETNAM NH2 AMINO GROUP HETNAM CA CALCIUM ION HETSYN SEP PHOSPHONOSERINE FORMUL 2 ACE C2 H4 O FORMUL 2 SEP C3 H8 N O6 P FORMUL 2 NH2 H2 N FORMUL 3 CA 2(CA 2+) HELIX 1 AA1 LYS A 232 LYS A 236 5 5 HELIX 2 AA2 VAL A 263 MET A 269 1 7 HELIX 3 AA3 ASN A 279 TYR A 286 1 8 SHEET 1 AA1 4 GLN A 222 PHE A 229 0 SHEET 2 AA1 4 LYS A 172 LYS A 181 -1 N VAL A 175 O PHE A 227 SHEET 3 AA1 4 ARG A 161 THR A 169 -1 N GLU A 167 O HIS A 174 SHEET 4 AA1 4 ALA A 271 LYS A 276 -1 O ALA A 271 N ALA A 166 SHEET 1 AA2 4 PRO A 194 TYR A 195 0 SHEET 2 AA2 4 ARG A 239 ASP A 248 -1 O TRP A 245 N TYR A 195 SHEET 3 AA2 4 LYS A 197 LEU A 200 -1 N LYS A 199 O SER A 241 SHEET 4 AA2 4 GLN A 210 LYS A 211 -1 O GLN A 210 N LEU A 198 SHEET 1 AA3 3 PRO A 194 TYR A 195 0 SHEET 2 AA3 3 ARG A 239 ASP A 248 -1 O TRP A 245 N TYR A 195 SHEET 3 AA3 3 THR A 251 GLY A 262 -1 O LEU A 259 N VAL A 242 LINK C ACE B 648 N ASP B 649 1555 1555 1.33 LINK C PHE B 656 N SEP B 657 1555 1555 1.32 LINK C SEP B 657 N TYR B 658 1555 1555 1.32 LINK C TYR B 658 N NH2 B 659 1555 1555 1.33 LINK O MET A 186 CA CA A 302 1555 1555 2.45 LINK OD1 ASP A 187 CA CA A 301 1555 1555 2.50 LINK OD2 ASP A 187 CA CA A 301 1555 1555 2.30 LINK OD1 ASP A 187 CA CA A 302 1555 1555 2.28 LINK OD2 ASP A 193 CA CA A 301 1555 1555 2.20 LINK OD1 ASP A 246 CA CA A 301 1555 1555 2.27 LINK OD2 ASP A 246 CA CA A 301 1555 1555 2.75 LINK OD2 ASP A 246 CA CA A 302 1555 1555 2.28 LINK O TRP A 247 CA CA A 301 1555 1555 2.34 LINK OD1 ASP A 248 CA CA A 301 1555 1555 2.29 LINK OD1 ASP A 248 CA CA A 302 1555 1555 2.43 LINK OD2 ASP A 248 CA CA A 302 1555 1555 2.35 LINK OD2 ASP A 254 CA CA A 302 1555 1555 2.19 CISPEP 1 ILE A 201 PRO A 202 1 -0.09 CISPEP 2 ILE A 201 PRO A 202 2 0.07 CISPEP 3 ILE A 201 PRO A 202 3 0.02 CISPEP 4 ILE A 201 PRO A 202 4 -0.39 CISPEP 5 ILE A 201 PRO A 202 5 -0.66 CISPEP 6 ILE A 201 PRO A 202 6 0.18 CISPEP 7 ILE A 201 PRO A 202 7 -0.28 CISPEP 8 ILE A 201 PRO A 202 8 -0.32 CISPEP 9 ILE A 201 PRO A 202 9 0.85 CISPEP 10 ILE A 201 PRO A 202 10 -0.15 CISPEP 11 ILE A 201 PRO A 202 11 -0.08 CISPEP 12 ILE A 201 PRO A 202 12 0.13 CISPEP 13 ILE A 201 PRO A 202 13 0.33 CISPEP 14 ILE A 201 PRO A 202 14 0.29 CISPEP 15 ILE A 201 PRO A 202 15 0.21 CISPEP 16 ILE A 201 PRO A 202 16 0.06 CISPEP 17 ILE A 201 PRO A 202 17 0.31 CISPEP 18 ILE A 201 PRO A 202 18 -0.43 CISPEP 19 ILE A 201 PRO A 202 19 -0.09 CISPEP 20 ILE A 201 PRO A 202 20 0.17 SITE 1 AC1 6 ASP A 187 ASP A 193 ASP A 246 TRP A 247 SITE 2 AC1 6 ASP A 248 CA A 302 SITE 1 AC2 6 MET A 186 ASP A 187 ASP A 246 ASP A 248 SITE 2 AC2 6 ASP A 254 CA A 301 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