HEADER CALCIUM-BINDING PROTEIN/METAL TRANSPORT 21-FEB-13 2M5E TITLE STRUCTURE OF THE C-DOMAIN OF CALCIUM-SATURATED CALMODULIN BOUND TO THE TITLE 2 IQ MOTIF OF NAV1.2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CALMODULIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 77-149; COMPND 5 SYNONYM: CAM; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: SODIUM CHANNEL PROTEIN TYPE 2 SUBUNIT ALPHA; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: UNP RESIDUES 1901-1927; COMPND 11 SYNONYM: SODIUM CHANNEL PROTEIN BRAIN II SUBUNIT ALPHA, SODIUM COMPND 12 CHANNEL PROTEIN TYPE II SUBUNIT ALPHA, VOLTAGE-GATED SODIUM CHANNEL COMPND 13 SUBUNIT ALPHA NAV1.2; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PARAMECIUM TETRAURELIA; SOURCE 3 ORGANISM_TAXID: 5888; SOURCE 4 STRAIN: D4-2; SOURCE 5 GENE: CAM, GSPATT00015825001; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PT7-7; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 13 ORGANISM_COMMON: RAT; SOURCE 14 ORGANISM_TAXID: 10116; SOURCE 15 GENE: SCN2A, SCN2A1; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS CALCIUM BINDING PROTEIN, NAV1.2, ION CHANNEL GATING, IQ MOTIF, METAL KEYWDS 2 BINDING, SODIUM CHANNELS, METAL TRANSPORT, VOLTAGE DEPENDENT, KEYWDS 3 VOLTAGE GATED, CALCIUM BINDING PROTEIN-METAL TRANSPORT COMPLEX, KEYWDS 4 NEURONAL PEPTIDES, EF-HAND, CALCIUM-BINDING PROTEIN-METAL TRANSPORT KEYWDS 5 COMPLEX EXPDTA SOLUTION NMR NUMMDL 21 MDLTYP MINIMIZED AVERAGE AUTHOR C.A.FOWLER,M.D.FELDKAMP,L.YU,M.A.SHEA REVDAT 4 14-JUN-23 2M5E 1 REMARK LINK REVDAT 3 19-APR-17 2M5E 1 JRNL REVDAT 2 19-NOV-14 2M5E 1 JRNL REVDAT 1 23-JUL-14 2M5E 0 JRNL AUTH L.HOVEY,C.A.FOWLER,R.MAHLING,Z.LIN,M.S.MILLER,D.C.MARX, JRNL AUTH 2 J.B.YODER,E.H.KIM,K.M.TEFFT,B.C.WAITE,M.D.FELDKAMP,L.YU, JRNL AUTH 3 M.A.SHEA JRNL TITL CALCIUM TRIGGERS REVERSAL OF CALMODULIN ON NESTED JRNL TITL 2 ANTI-PARALLEL SITES IN THE IQ MOTIF OF THE NEURONAL JRNL TITL 3 VOLTAGE-DEPENDENT SODIUM CHANNEL NAV1.2. JRNL REF BIOPHYS. CHEM. V. 224 1 2017 JRNL REFN ISSN 1873-4200 JRNL PMID 28343066 JRNL DOI 10.1016/J.BPC.2017.02.006 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.D.FELDKAMP,L.YU,M.A.SHEA REMARK 1 TITL STRUCTURAL AND ENERGETIC DETERMINANTS OF APO CALMODULIN REMARK 1 TITL 2 BINDING TO THE IQ MOTIF OF THE NAV1.2 VOLTAGE-DEPENDENT REMARK 1 TITL 3 SODIUM CHANNEL REMARK 1 REF STRUCTURE V. 19 733 2011 REMARK 1 REFN ISSN 0969-2126 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 2.1, CNSSOLVE 1.21 REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), BRUNGER, ADAMS, CLORE, REMARK 3 GROS, NILGES AND READ (CNSSOLVE) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESIDUES 1901-1903 AND 1925-1927 IN THE REMARK 3 PEPTIDE ARE COMPLETELY UNRESTRAINED REMARK 4 REMARK 4 2M5E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-FEB-13. REMARK 100 THE DEPOSITION ID IS D_1000103230. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.5 MM [U-100% 13C; U-100% 15N] REMARK 210 C-DOMAIN OF CALMODULIN, 1.5 MM REMARK 210 IQ MOTIF PEPTIDE OF NAV1.2, 3.3 REMARK 210 MM CALCIUM ION, 10 MM [U-2H] REMARK 210 IMIDAZOLE, 100 MM POTASSIUM REMARK 210 CHLORIDE, 0.01 % SODIUM AZIDE, REMARK 210 50 UM [U-2H] EDTA, 95% H2O/5% REMARK 210 D2O; 1.5 MM [U-100% 13C; U-100% REMARK 210 15N] C-DOMAIN OF CALMODULIN, 1.5 REMARK 210 MM IQ MOTIF PEPTIDE OF NAV1.2, REMARK 210 3.3 MM CALCIUM ION, 10 MM [U-2H] REMARK 210 IMIDAZOLE, 100 MM POTASSIUM REMARK 210 CHLORIDE, 0.01 % SODIUM AZIDE, REMARK 210 50 UM [U-2H] EDTA, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HMQC; REMARK 210 3D HNCA; 3D HN(CO)CA; 3D HNCACB; REMARK 210 3D HN(COCA)CB; 3D HNCO; 3D HN(CA) REMARK 210 CO; 3D C(CO)NH; 3D H(CCO)NH; 3D REMARK 210 1H-15N NOESY; 3D 1H-13C NOESY; REMARK 210 3D HCCH-TOCSY; 3D 1H-13C EDITED, REMARK 210 12C FILTERED NOESY; 2D 1H-1H REMARK 210 DOUBLY 12C,14N FILTERED NOESY; REMARK 210 2D 1H-1H 12C,14N FILTERED TOCSY; REMARK 210 2D 1H-1H 12C FILTERED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE II REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY 3.115, NMRPIPE, ANALYSIS REMARK 210 2.1.5, ARIA 2.3, CNSSOLVE 1.21, REMARK 210 X-PLOR NIH 2.23, PROCHECKNMR REMARK 210 3.5.4 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 300 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 21 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 MODELS 1-21 REMARK 470 RES CSSEQI ATOMS REMARK 470 LYS A 148 O REMARK 470 LYS B1927 O 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 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 GLU A 78 -53.95 -124.45 REMARK 500 1 LYS B1903 -52.21 78.93 REMARK 500 1 LYS B1926 -66.60 69.20 REMARK 500 2 VAL A 146 39.94 -96.36 REMARK 500 2 LYS B1903 160.91 60.94 REMARK 500 2 VAL B1925 101.17 59.31 REMARK 500 2 LYS B1926 34.69 -170.18 REMARK 500 3 LYS A 77 -66.32 -144.25 REMARK 500 3 VAL A 146 32.21 -98.41 REMARK 500 3 ARG B1902 168.28 60.02 REMARK 500 4 GLU A 78 -66.71 69.08 REMARK 500 4 VAL A 146 39.80 -97.56 REMARK 500 4 SER A 147 43.87 -94.32 REMARK 500 4 LYS B1903 105.33 60.86 REMARK 500 4 GLN B1904 33.33 -151.45 REMARK 500 5 LYS A 77 145.21 62.97 REMARK 500 5 GLU A 78 -47.56 -170.42 REMARK 500 5 VAL A 146 38.86 -96.97 REMARK 500 5 SER A 147 -176.62 -66.62 REMARK 500 5 LYS B1922 -70.17 -81.66 REMARK 500 5 LYS B1924 178.05 58.09 REMARK 500 6 VAL A 146 39.91 -96.04 REMARK 500 6 LYS B1903 163.29 60.75 REMARK 500 6 VAL B1925 115.47 63.61 REMARK 500 6 LYS B1926 -42.24 -165.15 REMARK 500 7 GLU A 78 -69.12 68.08 REMARK 500 7 ASP A 93 86.86 -65.69 REMARK 500 7 VAL A 146 33.18 -98.42 REMARK 500 7 GLN B1904 87.20 60.25 REMARK 500 7 LYS B1924 110.53 60.19 REMARK 500 8 GLU A 78 -48.51 -166.52 REMARK 500 8 ASP A 93 92.92 -69.95 REMARK 500 8 ASP A 129 91.50 -69.59 REMARK 500 8 VAL A 146 32.47 -98.33 REMARK 500 8 LYS B1926 -46.03 -169.80 REMARK 500 9 SER A 147 -171.35 -60.07 REMARK 500 9 GLN B1904 -45.15 -161.79 REMARK 500 9 LYS B1924 173.75 60.26 REMARK 500 9 LYS B1926 -42.89 -174.04 REMARK 500 10 GLN B1904 33.56 -98.44 REMARK 500 10 LYS B1924 -76.15 64.95 REMARK 500 10 VAL B1925 110.71 67.53 REMARK 500 10 LYS B1926 -46.85 -148.94 REMARK 500 11 LYS A 77 120.82 62.92 REMARK 500 11 GLU A 78 -51.36 -152.58 REMARK 500 11 GLN B1904 79.43 -117.87 REMARK 500 11 LYS B1924 175.01 -59.89 REMARK 500 11 VAL B1925 138.72 64.05 REMARK 500 12 LYS B1903 79.97 -154.12 REMARK 500 12 GLN B1904 -61.02 -165.26 REMARK 500 REMARK 500 THIS ENTRY HAS 77 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 A2001 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 93 OD2 REMARK 620 2 ASP A 93 OD1 27.1 REMARK 620 3 ASP A 95 OD1 144.5 117.4 REMARK 620 4 ASP A 95 OD2 165.0 139.4 23.4 REMARK 620 5 ASN A 97 OD1 55.0 63.2 124.4 134.0 REMARK 620 6 LEU A 99 O 55.1 81.5 157.0 134.3 74.6 REMARK 620 7 GLU A 104 OE2 116.3 132.8 89.1 67.7 133.7 67.9 REMARK 620 8 GLU A 104 OE1 103.9 98.7 72.4 66.7 158.9 92.8 50.3 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A2002 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 129 OD1 REMARK 620 2 ASP A 131 OD1 146.8 REMARK 620 3 ASP A 131 OD2 155.2 14.1 REMARK 620 4 ASP A 133 OD1 65.1 124.8 132.3 REMARK 620 5 ASP A 133 OD2 100.7 82.5 90.8 42.3 REMARK 620 6 HIS A 135 O 55.8 155.7 142.0 66.1 104.6 REMARK 620 7 GLU A 140 OE2 87.7 85.5 78.1 149.5 167.6 87.6 REMARK 620 8 GLU A 140 OE1 93.2 106.0 92.3 116.5 139.0 53.5 48.3 REMARK 620 N 1 2 3 4 5 6 7 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 2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 2002 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KXW RELATED DB: PDB REMARK 900 STRUCTURE OF THE C-DOMAIN FRAGMENT OF APO-CALMODULIN BOUND TO THE REMARK 900 IQ MOTIF OF NAV1.2 REMARK 900 RELATED ID: 1EXR RELATED DB: PDB REMARK 900 THE 1.0 ANGSTROM CRYSTAL STRUCTURE OF CA2+-BOUND CALMODULIN REMARK 900 RELATED ID: 19050 RELATED DB: BMRB DBREF 2M5E A 76 148 UNP P07463 CALM_PARTE 77 149 DBREF 2M5E B 1901 1927 UNP P04775 SCN2A_RAT 1901 1927 SEQRES 1 A 73 MET LYS GLU GLN ASP SER GLU GLU GLU LEU ILE GLU ALA SEQRES 2 A 73 PHE LYS VAL PHE ASP ARG ASP GLY ASN GLY LEU ILE SER SEQRES 3 A 73 ALA ALA GLU LEU ARG HIS VAL MET THR ASN LEU GLY GLU SEQRES 4 A 73 LYS LEU THR ASP ASP GLU VAL ASP GLU MET ILE ARG GLU SEQRES 5 A 73 ALA ASP ILE ASP GLY ASP GLY HIS ILE ASN TYR GLU GLU SEQRES 6 A 73 PHE VAL ARG MET MET VAL SER LYS SEQRES 1 B 27 LYS ARG LYS GLN GLU GLU VAL SER ALA ILE VAL ILE GLN SEQRES 2 B 27 ARG ALA TYR ARG ARG TYR LEU LEU LYS GLN LYS VAL LYS SEQRES 3 B 27 LYS HET CA A2001 1 HET CA A2002 1 HETNAM CA CALCIUM ION FORMUL 3 CA 2(CA 2+) HELIX 1 1 GLU A 78 ASP A 80 5 3 HELIX 2 2 SER A 81 ASP A 93 1 13 HELIX 3 3 SER A 101 GLY A 113 1 13 HELIX 4 4 THR A 117 ASP A 129 1 13 HELIX 5 5 ASN A 137 VAL A 146 1 10 HELIX 6 6 GLN B 1904 LYS B 1924 1 21 LINK OD2 ASP A 93 CA CA A2001 1555 1555 4.11 LINK OD1 ASP A 93 CA CA A2001 1555 1555 2.51 LINK OD1 ASP A 95 CA CA A2001 1555 1555 4.26 LINK OD2 ASP A 95 CA CA A2001 1555 1555 2.51 LINK OD1 ASN A 97 CA CA A2001 1555 1555 2.51 LINK O LEU A 99 CA CA A2001 1555 1555 2.77 LINK OE2 GLU A 104 CA CA A2001 1555 1555 2.81 LINK OE1 GLU A 104 CA CA A2001 1555 1555 2.19 LINK OD1 ASP A 129 CA CA A2002 1555 1555 2.51 LINK OD1 ASP A 131 CA CA A2002 1555 1555 4.58 LINK OD2 ASP A 131 CA CA A2002 1555 1555 2.55 LINK OD1 ASP A 133 CA CA A2002 1555 1555 3.26 LINK OD2 ASP A 133 CA CA A2002 1555 1555 2.48 LINK O HIS A 135 CA CA A2002 1555 1555 2.85 LINK OE2 GLU A 140 CA CA A2002 1555 1555 2.16 LINK OE1 GLU A 140 CA CA A2002 1555 1555 2.93 SITE 1 AC1 5 ASP A 93 ASP A 95 ASN A 97 LEU A 99 SITE 2 AC1 5 GLU A 104 SITE 1 AC2 5 ASP A 129 ASP A 131 ASP A 133 HIS A 135 SITE 2 AC2 5 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