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