HEADER METAL BINDING PROTEIN 17-MAR-21 7M2M TITLE NMR STRUCTURE OF GCAP5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GUANYLATE CYCLASE ACTIVATOR 1A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GUANYLYL CYCLASE-ACTIVATING PROTEIN 1; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: THE INITIAL MET AT RESIDUE 1 GETS REMOVED DURING THE COMPND 7 MYRISTOYLATION OF THE PROTEIN. THE MYRISTOYL GROUP IS COVALENTLY COMPND 8 ATTACHED (N-ACYL LINKAGE) TO THE AMINO GROUP OF THE GLY AT RESIDUE 2. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: ZEBRAFISH, BRACHYDANIO RERIO; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 GENE: GUCA1E, GUCA1E; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GUANYLATE CYCLASE, GCAP5, EF-HAND, MG2+, CA2+, VISION, KEYWDS 2 PHOTOTRANSDUCTION, METAL BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 9 AUTHOR J.B.AMES,D.L.CUDIA REVDAT 2 03-NOV-21 7M2M 1 JRNL REVDAT 1 20-OCT-21 7M2M 0 JRNL AUTH D.CUDIA,G.P.ROSEMAN,T.E.ASSAFA,M.K.SHAHU,A.SCHOLTEN, JRNL AUTH 2 S.K.MENKE-SELL,H.YAMADA,K.W.KOCH,G.MILHAUSER,J.B.AMES JRNL TITL NMR AND EPR-DEER STRUCTURE OF A DIMERIC GUANYLATE CYCLASE JRNL TITL 2 ACTIVATOR PROTEIN-5 FROM ZEBRAFISH PHOTORECEPTORS. JRNL REF BIOCHEMISTRY V. 60 3058 2021 JRNL REFN ISSN 0006-2960 JRNL PMID 34609135 JRNL DOI 10.1021/ACS.BIOCHEM.1C00612 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER A. T. ET.AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES ARE BASED ON 660 NOE-DERIVED REMARK 3 DISTANCES, 128 DIHEDRAL ANGLE RESTRAINTS REMARK 4 REMARK 4 7M2M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1000255538. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310; 310 REMARK 210 PH : 6.0; 6.0 REMARK 210 IONIC STRENGTH : 10; 10 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-100% 15N] GCAP5, 2.0 REMARK 210 MM MAGNESIUM ION, 10 MM [U-100% REMARK 210 2H] MES, 90% H2O/10% D2O; 0.5 MM REMARK 210 [U-100% 13C; U-100% 15N] GCAP5, REMARK 210 2.0 MM MAGNESIUM ION, 10 MM [U- REMARK 210 100% 2H] MES, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 3D HNCACB; 3D CBCA(CO) REMARK 210 NH; 3D HCCH-TOCSY; 3D 1H-13C REMARK 210 NOESY ALIPHATIC REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CNS, NMRFAM-SPARKY, NMRDRAW REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 9 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 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 1-9 REMARK 465 RES C SSSEQI REMARK 465 ASP A 184 REMARK 465 SER A 185 REMARK 465 TYR A 186 REMARK 465 ILE A 187 REMARK 465 GLU A 188 REMARK 465 GLN A 189 REMARK 465 GLU A 190 REMARK 465 ALA A 191 REMARK 465 GLU A 192 REMARK 465 ILE A 193 REMARK 465 ILE A 194 REMARK 465 GLU A 195 REMARK 465 ASP A 196 REMARK 465 GLN A 197 REMARK 465 ALA A 198 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 TYR A 54 H MET A 58 1.53 REMARK 500 O HIS A 18 H ARG A 22 1.58 REMARK 500 O LYS A 39 O PHE A 42 2.19 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 5 35.84 28.64 REMARK 500 1 SER A 6 -100.51 50.48 REMARK 500 1 MET A 7 139.90 56.84 REMARK 500 1 LYS A 16 128.70 -35.46 REMARK 500 1 CYS A 17 -112.50 -130.75 REMARK 500 1 CYS A 28 124.44 172.34 REMARK 500 1 LEU A 44 88.77 72.78 REMARK 500 1 ILE A 64 73.82 -4.98 REMARK 500 1 ASP A 65 -58.07 -177.86 REMARK 500 1 ASP A 66 -83.33 -168.75 REMARK 500 1 MET A 73 -26.07 93.78 REMARK 500 1 LYS A 84 -83.97 -26.94 REMARK 500 1 SER A 103 -131.07 72.56 REMARK 500 1 ASP A 109 -76.60 142.16 REMARK 500 1 ALA A 124 -105.50 83.66 REMARK 500 2 CYS A 15 -76.74 -105.39 REMARK 500 2 LYS A 16 -50.11 69.46 REMARK 500 2 CYS A 17 -164.56 62.79 REMARK 500 2 PRO A 29 91.38 -65.95 REMARK 500 2 LEU A 44 146.31 72.48 REMARK 500 2 LEU A 47 -94.58 67.90 REMARK 500 2 SER A 48 -144.39 -165.49 REMARK 500 2 ILE A 64 -4.91 67.27 REMARK 500 2 GLU A 74 -34.15 76.18 REMARK 500 2 LYS A 84 156.67 66.69 REMARK 500 2 ASP A 99 -128.85 79.24 REMARK 500 2 ASP A 101 -123.26 43.68 REMARK 500 2 SER A 103 -85.15 62.37 REMARK 500 2 ASP A 109 -98.85 115.04 REMARK 500 2 ALA A 124 -120.50 51.37 REMARK 500 2 LYS A 140 -75.44 173.53 REMARK 500 2 ASP A 146 -45.31 73.77 REMARK 500 3 MET A 7 67.03 73.15 REMARK 500 3 CYS A 15 -69.84 -109.77 REMARK 500 3 LYS A 16 95.93 4.48 REMARK 500 3 HIS A 18 0.40 83.48 REMARK 500 3 LEU A 44 -94.26 32.58 REMARK 500 3 LYS A 45 -104.76 144.87 REMARK 500 3 SER A 48 -168.64 -79.68 REMARK 500 3 ILE A 64 -21.54 70.64 REMARK 500 3 ASP A 66 113.66 29.14 REMARK 500 3 ASP A 67 -140.09 20.62 REMARK 500 3 PHE A 72 -117.27 53.35 REMARK 500 3 GLU A 74 -53.78 179.72 REMARK 500 3 LYS A 84 -127.02 35.69 REMARK 500 3 LEU A 97 -157.38 -107.28 REMARK 500 3 PHE A 98 -5.11 72.68 REMARK 500 3 ASP A 109 -97.22 -82.85 REMARK 500 3 ASN A 122 -146.94 25.97 REMARK 500 3 ASP A 142 51.30 82.40 REMARK 500 REMARK 500 THIS ENTRY HAS 166 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 MG A 700 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 63 OD1 REMARK 620 2 ASP A 65 OD1 154.9 REMARK 620 3 ASP A 67 O 88.7 94.2 REMARK 620 4 ASP A 67 OD1 125.2 77.8 64.5 REMARK 620 5 CYS A 69 O 91.3 109.8 114.8 63.3 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 30888 RELATED DB: BMRB REMARK 900 NMR STRUCTURE OF GCAP5 DBREF 7M2M A 2 198 UNP Q5MAC8 Q5MAC8_DANRE 2 198 SEQADV 7M2M MYR A 1 UNP Q5MAC8 INSERTION SEQRES 1 A 198 MYR GLY ASP SER SER SER MET SER ALA THR GLU LEU SER SEQRES 2 A 198 ALA CYS LYS CYS HIS GLN TRP TYR ARG LYS PHE MET THR SEQRES 3 A 198 GLU CYS PRO SER GLY GLN LEU THR PHE TYR GLU PHE LYS SEQRES 4 A 198 LYS PHE PHE GLY LEU LYS ASN LEU SER GLU LYS SER ASN SEQRES 5 A 198 ALA TYR VAL ASN THR MET PHE LYS THR PHE ASP ILE ASP SEQRES 6 A 198 ASP ASP GLY CYS ILE ASP PHE MET GLU TYR VAL ALA ALA SEQRES 7 A 198 LEU SER LEU VAL LEU LYS GLY GLY VAL GLN GLN LYS LEU SEQRES 8 A 198 ARG TRP TYR PHE LYS LEU PHE ASP MET ASP GLY SER GLY SEQRES 9 A 198 CYS ILE ASP LYS ASP GLU LEU LEU LEU ILE PHE LYS ALA SEQRES 10 A 198 VAL GLN ALA ILE ASN GLY ALA GLU PRO GLU ILE SER ALA SEQRES 11 A 198 GLU ASP LEU ALA ASP ILE VAL PHE ASN LYS ILE ASP VAL SEQRES 12 A 198 ASN GLY ASP GLY GLU LEU SER LEU GLU GLU PHE MET GLU SEQRES 13 A 198 GLY ILE SER ALA ASP GLU LYS ILE SER GLU MET LEU THR SEQRES 14 A 198 GLN SER LEU ASP LEU THR ARG ILE VAL SER ASN ILE TYR SEQRES 15 A 198 ASN ASP SER TYR ILE GLU GLN GLU ALA GLU ILE ILE GLU SEQRES 16 A 198 ASP GLN ALA HET MYR A 1 42 HET MG A 700 1 HETNAM MYR MYRISTIC ACID HETNAM MG MAGNESIUM ION FORMUL 1 MYR C14 H28 O2 FORMUL 2 MG MG 2+ HELIX 1 AA1 SER A 8 LYS A 16 1 9 HELIX 2 AA2 HIS A 18 CYS A 28 1 11 HELIX 3 AA3 THR A 34 PHE A 42 1 9 HELIX 4 AA4 SER A 48 ILE A 64 1 17 HELIX 5 AA5 MET A 73 LEU A 83 1 11 HELIX 6 AA6 GLY A 86 LEU A 97 1 12 HELIX 7 AA7 ASP A 109 ILE A 121 1 13 HELIX 8 AA8 SER A 129 ASN A 139 1 11 HELIX 9 AA9 SER A 150 ASP A 161 1 12 HELIX 10 AB1 GLU A 162 LEU A 172 1 11 HELIX 11 AB2 LEU A 174 ASN A 183 1 10 SHEET 1 AA1 2 GLN A 32 LEU A 33 0 SHEET 2 AA1 2 ILE A 70 ASP A 71 -1 O ILE A 70 N LEU A 33 LINK C1 MYR A 1 N GLY A 2 1555 1555 1.33 LINK OD1 ASP A 63 MG MG A 700 1555 1555 2.82 LINK OD1 ASP A 65 MG MG A 700 1555 1555 2.82 LINK O ASP A 67 MG MG A 700 1555 1555 2.18 LINK OD1 ASP A 67 MG MG A 700 1555 1555 2.76 LINK O CYS A 69 MG MG A 700 1555 1555 2.56 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 HETATM 1 C1 MYR A 1 -3.253 43.665 40.784 1.00 0.00 C HETATM 2 O1 MYR A 1 -4.144 43.476 41.612 1.00 0.00 O HETATM 3 C2 MYR A 1 -3.158 44.983 40.024 1.00 0.00 C HETATM 4 C3 MYR A 1 -1.691 45.319 39.747 1.00 0.00 C HETATM 5 C4 MYR A 1 -1.344 46.663 40.390 1.00 0.00 C HETATM 6 C5 MYR A 1 0.167 46.888 40.312 1.00 0.00 C HETATM 7 C6 MYR A 1 0.772 46.765 41.711 1.00 0.00 C HETATM 8 C7 MYR A 1 0.106 47.779 42.640 1.00 0.00 C HETATM 9 C8 MYR A 1 -0.264 47.104 43.960 1.00 0.00 C HETATM 10 C9 MYR A 1 1.007 46.602 44.645 1.00 0.00 C HETATM 11 C10 MYR A 1 1.596 47.718 45.509 1.00 0.00 C HETATM 12 C11 MYR A 1 2.814 47.185 46.265 1.00 0.00 C HETATM 13 C12 MYR A 1 4.066 47.944 45.820 1.00 0.00 C HETATM 14 C13 MYR A 1 5.307 47.218 46.342 1.00 0.00 C HETATM 15 C14 MYR A 1 6.221 48.215 47.059 1.00 0.00 C HETATM 16 H21 MYR A 1 -3.601 45.770 40.617 1.00 0.00 H HETATM 17 H22 MYR A 1 -3.689 44.896 39.088 1.00 0.00 H HETATM 18 H31 MYR A 1 -1.533 45.381 38.679 1.00 0.00 H HETATM 19 H32 MYR A 1 -1.060 44.549 40.162 1.00 0.00 H HETATM 20 H41 MYR A 1 -1.655 46.657 41.425 1.00 0.00 H HETATM 21 H42 MYR A 1 -1.856 47.455 39.866 1.00 0.00 H HETATM 22 H51 MYR A 1 0.363 47.875 39.921 1.00 0.00 H HETATM 23 H52 MYR A 1 0.608 46.148 39.661 1.00 0.00 H HETATM 24 H61 MYR A 1 1.833 46.961 41.664 1.00 0.00 H HETATM 25 H62 MYR A 1 0.607 45.767 42.090 1.00 0.00 H HETATM 26 H71 MYR A 1 -0.784 48.160 42.170 1.00 0.00 H HETATM 27 H72 MYR A 1 0.789 48.596 42.831 1.00 0.00 H HETATM 28 H81 MYR A 1 -0.922 46.269 43.765 1.00 0.00 H HETATM 29 H82 MYR A 1 -0.762 47.815 44.601 1.00 0.00 H HETATM 30 H91 MYR A 1 1.728 46.310 43.895 1.00 0.00 H HETATM 31 H92 MYR A 1 0.770 45.752 45.267 1.00 0.00 H HETATM 32 H101 MYR A 1 0.852 48.056 46.216 1.00 0.00 H HETATM 33 H102 MYR A 1 1.895 48.543 44.878 1.00 0.00 H HETATM 34 H111 MYR A 1 2.936 46.134 46.050 1.00 0.00 H HETATM 35 H112 MYR A 1 2.667 47.321 47.326 1.00 0.00 H HETATM 36 H121 MYR A 1 4.042 48.948 46.217 1.00 0.00 H HETATM 37 H122 MYR A 1 4.099 47.984 44.741 1.00 0.00 H HETATM 38 H131 MYR A 1 5.839 46.773 45.514 1.00 0.00 H HETATM 39 H132 MYR A 1 5.007 46.445 47.034 1.00 0.00 H HETATM 40 H141 MYR A 1 6.406 47.872 48.067 1.00 0.00 H HETATM 41 H142 MYR A 1 7.156 48.292 46.527 1.00 0.00 H HETATM 42 H143 MYR A 1 5.744 49.183 47.091 1.00 0.00 H