HEADER METAL BINDING PROTEIN 06-MAR-20 6Y94 TITLE CA2+-BOUND CALMODULIN MUTANT N53I COMPND MOL_ID: 1; COMPND 2 MOLECULE: CALMODULIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CALM1, CALM, CAM, CAM1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: ROSETTA 2 KEYWDS MUTANT, METAL-BINDING, SIGNALING PROTEIN, CPVT, METAL BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR C.HOLT,L.H.NIELSEN,K.LAU,M.BROHUS,A.B.SORENSEN,K.T.LARSEN,C.SOMMER, AUTHOR 2 F.V.PETEGEM,M.T.OVERGAARD,R.WIMMER REVDAT 5 19-JUN-24 6Y94 1 REMARK REVDAT 4 14-JUN-23 6Y94 1 REMARK REVDAT 3 10-JUN-20 6Y94 1 JRNL REVDAT 2 06-MAY-20 6Y94 1 JRNL REVDAT 1 29-APR-20 6Y94 0 JRNL AUTH C.HOLT,L.HAMBORG,K.LAU,M.BROHUS,A.B.SORENSEN,K.T.LARSEN, JRNL AUTH 2 C.SOMMER,F.VAN PETEGEM,M.T.OVERGAARD,R.WIMMER JRNL TITL THE ARRHYTHMOGENIC N53I VARIANT SUBTLY CHANGES THE STRUCTURE JRNL TITL 2 AND DYNAMICS IN THE CALMODULIN N-TERMINAL DOMAIN, ALTERING JRNL TITL 3 ITS INTERACTION WITH THE CARDIAC RYANODINE RECEPTOR. JRNL REF J.BIOL.CHEM. V. 295 7620 2020 JRNL REFN ESSN 1083-351X JRNL PMID 32317284 JRNL DOI 10.1074/JBC.RA120.013430 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : YASARA 14.12.2 REMARK 3 AUTHORS : YASARA BIOSCIENCES GMBH DR. ELMAR KRIEGER WAGRAMER REMARK 3 STRASSE 25/3/45 1220 VIENNA AUSTRIA / EUROPE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6Y94 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1292106796. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.1; 298.1; 298.1 REMARK 210 PH : 6.57; 6.57; 6.57 REMARK 210 IONIC STRENGTH : 182; 42; 42 REMARK 210 PRESSURE : 1 ATM; 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 0.56 MM [U-99% 13C; U-99% 15N] REMARK 210 CALMODULIN N53I, 2 MM HEPES, 100 REMARK 210 MM POTASSIUM CHLORIDE, 10 MM REMARK 210 CALCIUM CHLORIDE, 50 MM SODIUM REMARK 210 ACETATE, 2 MM SODIUM AZIDE, 0.05 REMARK 210 MM TSP, 95% H2O/5% D2O; 1.0 MM REMARK 210 [U-99% 15N] CALMODULIN N53I, 2 REMARK 210 MM HEPES, 10 MM POTASSIUM REMARK 210 CHLORIDE, 10 MM CALCIUM CHLORIDE, REMARK 210 2 MM SODIUM AZIDE, 0.05 MM TSP, REMARK 210 95% H2O/5% D2O; 1.0 MM [U-99% REMARK 210 13C; U-99% 15N] CALMODULIN, 2 MM REMARK 210 HEPES, 10 MM POTASSIUM CHLORIDE, REMARK 210 10 MM CALCIUM CHLORIDE, 2 MM REMARK 210 SODIUM AZIDE, 0.05 MM TSP, 95% REMARK 210 H2O/5% 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 1H-15N TOCSY; 3D REMARK 210 CBCA(CO)NH; 3D HNCACB; 3D REMARK 210 HBHA(CO)NH; 3D HCCH-TOCSY; 3D REMARK 210 HNCO; 3D HN(CA)CO; 2D (HB) REMARK 210 CB(CGCD)HD; 2D (HB)CB(CGCDCE)HE; REMARK 210 3D 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 15N-T1; 15N-T2; {1H}- REMARK 210 15N NOE; T2 RELAXATION DISPERSION REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III; AVANCE III HD REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 3.0, TALOS TALOS+, CARA REMARK 210 1.8.4.2, TOPSPIN 3.2 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 25 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 KCAL/MOL 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: 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 ALA A 147 -166.64 -106.27 REMARK 500 2 MET A 76 46.52 -90.86 REMARK 500 4 ASP A 2 96.37 -57.29 REMARK 500 4 ASN A 42 57.18 -117.17 REMARK 500 4 ASP A 78 -166.50 -79.70 REMARK 500 4 ASP A 80 92.45 -13.93 REMARK 500 4 LYS A 115 54.57 -114.69 REMARK 500 5 LYS A 115 67.20 -109.18 REMARK 500 6 LYS A 115 53.68 -92.88 REMARK 500 7 ASN A 42 59.83 -119.44 REMARK 500 7 ASP A 56 44.43 -80.58 REMARK 500 7 ASP A 80 -142.30 -93.75 REMARK 500 8 LEU A 4 -54.44 -159.76 REMARK 500 8 ASP A 78 -154.92 60.16 REMARK 500 8 ALA A 147 57.06 -147.79 REMARK 500 9 ASP A 78 72.56 77.58 REMARK 500 11 ASN A 42 59.55 -116.57 REMARK 500 11 ASP A 78 -163.53 60.56 REMARK 500 12 ASP A 56 49.07 -79.60 REMARK 500 15 ASN A 42 51.72 31.72 REMARK 500 16 ASN A 42 60.54 -115.60 REMARK 500 18 ASP A 93 49.83 -94.98 REMARK 500 19 LYS A 77 -145.23 -108.23 REMARK 500 19 ASP A 80 96.96 -56.46 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 201 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 20 OD2 REMARK 620 2 ASP A 22 OD2 102.9 REMARK 620 3 ASP A 24 OD2 77.4 101.0 REMARK 620 4 THR A 26 O 80.8 170.3 88.5 REMARK 620 5 GLU A 31 OE1 77.7 76.6 153.8 95.7 REMARK 620 6 GLU A 31 OE2 123.2 87.3 155.8 83.3 50.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 202 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 56 OD2 REMARK 620 2 ASP A 58 OD1 75.7 REMARK 620 3 ASP A 58 OD2 81.7 50.3 REMARK 620 4 ASN A 60 OD1 76.9 71.4 121.1 REMARK 620 5 THR A 62 O 84.5 144.9 154.3 76.1 REMARK 620 6 GLU A 67 OE1 102.7 131.8 81.6 156.5 80.4 REMARK 620 7 GLU A 67 OE2 151.9 127.8 101.5 122.1 81.0 51.1 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 203 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 93 OD1 REMARK 620 2 ASP A 95 OD2 78.0 REMARK 620 3 ASN A 97 OD1 92.2 80.1 REMARK 620 4 TYR A 99 O 83.3 150.0 77.3 REMARK 620 5 GLU A 104 OE1 125.8 121.5 137.8 88.4 REMARK 620 6 GLU A 104 OE2 86.0 83.7 163.7 118.4 52.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 204 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 129 OD1 REMARK 620 2 ASP A 131 OD1 85.1 REMARK 620 3 ASP A 133 OD2 87.2 81.8 REMARK 620 4 GLN A 135 O 82.9 153.8 74.4 REMARK 620 5 ASN A 137 OD1 176.2 98.5 94.3 94.2 REMARK 620 6 GLU A 140 OE1 94.8 82.1 163.6 122.0 84.6 REMARK 620 7 GLU A 140 OE2 108.5 131.6 142.8 74.4 68.3 51.3 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 204 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34496 RELATED DB: BMRB REMARK 900 CA2+-BOUND CALMODULIN MUTANT N53I DBREF 6Y94 A 1 148 UNP P0DP23 CALM1_HUMAN 2 149 SEQADV 6Y94 ILE A 53 UNP P0DP23 ASN 54 ENGINEERED MUTATION SEQRES 1 A 148 ALA ASP GLN LEU THR GLU GLU GLN ILE ALA GLU PHE LYS SEQRES 2 A 148 GLU ALA PHE SER LEU PHE ASP LYS ASP GLY ASP GLY THR SEQRES 3 A 148 ILE THR THR LYS GLU LEU GLY THR VAL MET ARG SER LEU SEQRES 4 A 148 GLY GLN ASN PRO THR GLU ALA GLU LEU GLN ASP MET ILE SEQRES 5 A 148 ILE GLU VAL ASP ALA ASP GLY ASN GLY THR ILE ASP PHE SEQRES 6 A 148 PRO GLU PHE LEU THR MET MET ALA ARG LYS MET LYS ASP SEQRES 7 A 148 THR ASP SER GLU GLU GLU ILE ARG GLU ALA PHE ARG VAL SEQRES 8 A 148 PHE ASP LYS ASP GLY ASN GLY TYR ILE SER ALA ALA GLU SEQRES 9 A 148 LEU ARG HIS VAL MET THR ASN LEU GLY GLU LYS LEU THR SEQRES 10 A 148 ASP GLU GLU VAL ASP GLU MET ILE ARG GLU ALA ASP ILE SEQRES 11 A 148 ASP GLY ASP GLY GLN VAL ASN TYR GLU GLU PHE VAL GLN SEQRES 12 A 148 MET MET THR ALA LYS HET CA A 201 1 HET CA A 202 1 HET CA A 203 1 HET CA A 204 1 HETNAM CA CALCIUM ION FORMUL 2 CA 4(CA 2+) HELIX 1 AA1 THR A 5 ASP A 20 1 16 HELIX 2 AA2 THR A 28 LEU A 39 1 12 HELIX 3 AA3 THR A 44 GLU A 54 1 11 HELIX 4 AA4 PHE A 65 ARG A 74 1 10 HELIX 5 AA5 SER A 81 ASP A 93 1 13 HELIX 6 AA6 ALA A 102 GLY A 113 1 12 HELIX 7 AA7 THR A 117 GLU A 127 1 11 HELIX 8 AA8 TYR A 138 ALA A 147 1 10 SHEET 1 AA1 2 THR A 26 ILE A 27 0 SHEET 2 AA1 2 ILE A 63 ASP A 64 -1 O ILE A 63 N ILE A 27 SHEET 1 AA2 2 TYR A 99 SER A 101 0 SHEET 2 AA2 2 GLN A 135 ASN A 137 -1 O VAL A 136 N ILE A 100 LINK OD2 ASP A 20 CA CA A 201 1555 1555 2.41 LINK OD2 ASP A 22 CA CA A 201 1555 1555 2.45 LINK OD2 ASP A 24 CA CA A 201 1555 1555 2.42 LINK O THR A 26 CA CA A 201 1555 1555 2.43 LINK OE1 GLU A 31 CA CA A 201 1555 1555 2.51 LINK OE2 GLU A 31 CA CA A 201 1555 1555 2.62 LINK OD2 ASP A 56 CA CA A 202 1555 1555 2.39 LINK OD1 ASP A 58 CA CA A 202 1555 1555 2.60 LINK OD2 ASP A 58 CA CA A 202 1555 1555 2.49 LINK OD1 ASN A 60 CA CA A 202 1555 1555 2.48 LINK O THR A 62 CA CA A 202 1555 1555 2.50 LINK OE1 GLU A 67 CA CA A 202 1555 1555 2.49 LINK OE2 GLU A 67 CA CA A 202 1555 1555 2.52 LINK OD1 ASP A 93 CA CA A 203 1555 1555 2.38 LINK OD2 ASP A 95 CA CA A 203 1555 1555 2.37 LINK OD1 ASN A 97 CA CA A 203 1555 1555 2.46 LINK O TYR A 99 CA CA A 203 1555 1555 2.44 LINK OE1 GLU A 104 CA CA A 203 1555 1555 2.47 LINK OE2 GLU A 104 CA CA A 203 1555 1555 2.49 LINK OD1 ASP A 129 CA CA A 204 1555 1555 2.38 LINK OD1 ASP A 131 CA CA A 204 1555 1555 2.38 LINK OD2 ASP A 133 CA CA A 204 1555 1555 2.41 LINK O GLN A 135 CA CA A 204 1555 1555 2.53 LINK OD1 ASN A 137 CA CA A 204 1555 1555 2.67 LINK OE1 GLU A 140 CA CA A 204 1555 1555 2.54 LINK OE2 GLU A 140 CA CA A 204 1555 1555 2.45 SITE 1 AC1 5 ASP A 20 ASP A 22 ASP A 24 THR A 26 SITE 2 AC1 5 GLU A 31 SITE 1 AC2 5 ASP A 56 ASP A 58 ASN A 60 THR A 62 SITE 2 AC2 5 GLU A 67 SITE 1 AC3 5 ASP A 93 ASP A 95 ASN A 97 TYR A 99 SITE 2 AC3 5 GLU A 104 SITE 1 AC4 6 ASP A 129 ASP A 131 ASP A 133 GLN A 135 SITE 2 AC4 6 ASN A 137 GLU A 140 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