HEADER METAL BINDING PROTEIN 06-APR-16 5J7J TITLE NMR DERIVED STRUCTURE OF CA2+ CALMODULIN BOUND TO PHOSPHORYLATED PSD- TITLE 2 95 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CALMODULIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CAM; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: XENOPUS LAEVIS CALMODULIN; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DISKS LARGE HOMOLOG 4; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: UNP RESIDUES 1-19; COMPND 11 SYNONYM: POSTSYNAPTIC DENSITY PROTEIN 95,PSD-95,SYNAPSE-ASSOCIATED COMPND 12 PROTEIN 90,SAP90; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XENOPUS LAEVIS; SOURCE 3 ORGANISM_COMMON: AFRICAN CLAWED FROG; SOURCE 4 ORGANISM_TAXID: 8355; SOURCE 5 GENE: CALM1, CALM2; 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: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS PHOSPHORYLATED, CALMODULIN, PSD-95, VOLTAGE-GATED CHANNEL, METAL KEYWDS 2 BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 4 AUTHOR M.L.TURNER,J.B.AMES,D.E.ANDERSON REVDAT 3 27-NOV-19 5J7J 1 REMARK REVDAT 2 08-MAY-19 5J7J 1 JRNL REMARK REVDAT 1 25-OCT-17 5J7J 0 JRNL AUTH D.CHOWDHURY,M.TURNER,T.PATRIARCHI,A.C.HERGARDEN,D.ANDERSON, JRNL AUTH 2 Y.ZHANG,J.SUN,C.Y.CHEN,J.B.AMES,J.W.HELL JRNL TITL CA2+/CALMODULIN BINDING TO PSD-95 MEDIATES HOMEOSTATIC JRNL TITL 2 SYNAPTIC SCALING DOWN. JRNL REF EMBO J. V. 37 122 2018 JRNL REFN ESSN 1460-2075 JRNL PMID 29118000 JRNL DOI 10.15252/EMBJ.201695829 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : HADDOCK, HADDOCK REMARK 3 AUTHORS : BONVIN (HADDOCK), BONVIN (HADDOCK) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5J7J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-APR-16. REMARK 100 THE DEPOSITION ID IS D_1000220056. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 318 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 500 UM [U-100% 13C; U-100% 15N] REMARK 210 CALMODULIN, 750 UM PSD-95 REMARK 210 PHOSPHORYLATED, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; IPAP HSQC; 3D 1H REMARK 210 -15N NOESY; 3D HCCH-TOCSY; 3D REMARK 210 CBCA(CO)NH; 3D HNCO; 3D HBHA(CO) REMARK 210 NH; 3D 1H-13C NOESY ALIPHATIC; REMARK 210 2D 1H-13C HSQC 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 : SPARKY, NMRPIPE REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -52.0 KCAL/MOL 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 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 1-4 REMARK 465 RES C SSSEQI REMARK 465 ALA A 1 REMARK 465 ASP A 2 REMARK 465 GLN A 3 REMARK 465 LYS A 148 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 HZ2 LYS A 75 OE1 GLU A 84 1.54 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 ALA A 10 23.80 -143.21 REMARK 500 1 LYS A 21 -43.98 -150.08 REMARK 500 1 ASP A 22 10.42 -66.71 REMARK 500 1 ASP A 64 -137.14 -119.39 REMARK 500 1 SER A 81 -76.35 -120.17 REMARK 500 1 GLU A 82 -90.13 -174.80 REMARK 500 1 LYS A 94 -38.49 -137.03 REMARK 500 1 SER A 101 -134.10 -143.04 REMARK 500 1 ALA A 102 35.60 -80.76 REMARK 500 1 ALA A 103 -117.57 -99.83 REMARK 500 1 ASP A 129 49.28 -107.33 REMARK 500 1 THR A 146 -35.11 -137.97 REMARK 500 1 GLN B 15 -65.86 -120.49 REMARK 500 1 ASP B 16 -53.54 -162.06 REMARK 500 1 GLU B 17 -80.34 -68.39 REMARK 500 2 LYS A 21 -37.73 -155.61 REMARK 500 2 ASP A 64 -141.42 -115.84 REMARK 500 2 ALA A 73 -63.99 -101.13 REMARK 500 2 SER A 81 -59.52 -129.26 REMARK 500 2 GLU A 82 -85.23 -168.49 REMARK 500 2 LYS A 94 -34.21 -132.65 REMARK 500 2 SER A 101 -140.67 -132.17 REMARK 500 2 ALA A 102 48.69 -77.51 REMARK 500 2 ALA A 103 -107.92 -116.47 REMARK 500 2 ASP A 129 51.52 -110.74 REMARK 500 2 GLN B 15 -76.82 -88.83 REMARK 500 2 ASP B 16 -57.13 -145.75 REMARK 500 3 LYS A 21 -40.63 -149.48 REMARK 500 3 ASP A 64 -134.88 -118.83 REMARK 500 3 ARG A 74 -67.09 -28.91 REMARK 500 3 ASP A 78 67.30 -105.26 REMARK 500 3 SER A 81 -62.72 -138.52 REMARK 500 3 GLU A 82 -63.11 -157.17 REMARK 500 3 LYS A 94 -34.42 -136.50 REMARK 500 3 SER A 101 -135.09 -155.19 REMARK 500 3 ALA A 102 33.67 -79.66 REMARK 500 3 ALA A 103 -110.97 -99.56 REMARK 500 3 GLN B 15 -73.83 -113.51 REMARK 500 3 ASP B 16 -55.64 -143.87 REMARK 500 4 LYS A 21 -42.58 -158.50 REMARK 500 4 ASP A 22 13.85 -67.57 REMARK 500 4 ASN A 42 80.99 -164.65 REMARK 500 4 ASP A 64 -148.11 -113.25 REMARK 500 4 ASP A 78 44.59 -103.85 REMARK 500 4 SER A 81 -56.03 -151.39 REMARK 500 4 GLU A 82 -60.07 -168.09 REMARK 500 4 LYS A 94 -31.08 -140.62 REMARK 500 4 SER A 101 -122.31 -163.46 REMARK 500 4 ALA A 102 36.32 -81.28 REMARK 500 4 ALA A 103 -112.25 -102.66 REMARK 500 REMARK 500 THIS ENTRY HAS 53 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 201 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 20 OD1 REMARK 620 2 ASP A 22 OD1 78.7 REMARK 620 3 ASP A 22 OD2 131.7 54.6 REMARK 620 4 ASP A 24 OD1 87.4 77.4 93.5 REMARK 620 5 THR A 26 O 76.9 150.4 151.4 84.9 REMARK 620 6 GLU A 31 OE1 114.1 138.3 96.1 139.3 68.4 REMARK 620 7 GLU A 31 OE2 89.1 89.2 79.3 166.6 106.8 53.4 REMARK 620 N 1 2 3 4 5 6 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 OD1 REMARK 620 2 ASP A 58 OD1 121.5 REMARK 620 3 ASP A 58 OD2 73.2 53.3 REMARK 620 4 ASN A 60 OD1 73.1 109.4 75.4 REMARK 620 5 THR A 62 O 76.3 160.6 136.3 66.2 REMARK 620 6 ASP A 64 OD2 151.1 80.5 115.3 82.2 80.1 REMARK 620 7 GLU A 67 OE1 83.9 72.3 86.6 154.0 120.5 122.9 REMARK 620 8 GLU A 67 OE2 102.2 104.8 140.5 142.2 76.2 87.9 54.0 REMARK 620 N 1 2 3 4 5 6 7 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 OD1 104.2 REMARK 620 3 ASP A 95 OD2 151.5 52.1 REMARK 620 4 ASN A 97 OD1 93.7 69.6 91.7 REMARK 620 5 TYR A 99 O 84.5 138.3 123.4 69.2 REMARK 620 6 GLU A 104 OE1 108.5 116.1 75.6 153.7 98.4 REMARK 620 7 GLU A 104 OE2 82.9 78.1 77.0 145.6 143.5 54.4 REMARK 620 N 1 2 3 4 5 6 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 101.8 REMARK 620 3 ASP A 133 OD2 82.3 76.2 REMARK 620 4 GLN A 135 O 77.0 177.0 100.8 REMARK 620 5 GLU A 140 OE1 89.9 77.8 150.7 104.8 REMARK 620 6 GLU A 140 OE2 129.4 104.2 145.9 78.6 55.2 REMARK 620 N 1 2 3 4 5 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: 2MES RELATED DB: PDB REMARK 900 CONTAINS CAM BOUND TO PSD-95 IN THE NON-PHOSPHORYLATED FORM. REMARK 900 RELATED ID: 30062 RELATED DB: BMRB DBREF 5J7J A 1 148 UNP P62155 CALM_XENLA 2 149 DBREF 5J7J B 1 19 UNP P78352 DLG4_HUMAN 1 19 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 ASN 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 SEQRES 1 B 19 MET ASP CYS LEU CYS ILE VAL THR THR LYS LYS TYR ARG SEQRES 2 B 19 TYR GLN ASP GLU ASP TPO MODRES 5J7J TPO B 19 THR MODIFIED RESIDUE HET TPO B 19 17 HET CA A 201 1 HET CA A 202 1 HET CA A 203 1 HET CA A 204 1 HETNAM TPO PHOSPHOTHREONINE HETNAM CA CALCIUM ION HETSYN TPO PHOSPHONOTHREONINE FORMUL 2 TPO C4 H10 N O6 P FORMUL 3 CA 4(CA 2+) HELIX 1 AA1 THR A 5 ILE A 9 5 5 HELIX 2 AA2 ALA A 10 ASP A 20 1 11 HELIX 3 AA3 THR A 28 SER A 38 1 11 HELIX 4 AA4 THR A 44 ASP A 56 1 13 HELIX 5 AA5 PRO A 66 ASP A 78 1 13 HELIX 6 AA6 GLU A 82 PHE A 92 1 11 HELIX 7 AA7 ALA A 103 GLY A 113 1 11 HELIX 8 AA8 THR A 117 ALA A 128 1 12 HELIX 9 AA9 TYR A 138 MET A 145 1 8 HELIX 10 AB1 ASP B 2 TYR B 14 1 13 SHEET 1 AA1 2 TYR A 99 ILE A 100 0 SHEET 2 AA1 2 VAL A 136 ASN A 137 -1 O VAL A 136 N ILE A 100 LINK OD1 ASP A 20 CA CA A 201 1555 1555 2.23 LINK OD1 ASP A 22 CA CA A 201 1555 1555 2.33 LINK OD2 ASP A 22 CA CA A 201 1555 1555 2.40 LINK OD1 ASP A 24 CA CA A 201 1555 1555 2.24 LINK O THR A 26 CA CA A 201 1555 1555 2.39 LINK OE1 GLU A 31 CA CA A 201 1555 1555 2.48 LINK OE2 GLU A 31 CA CA A 201 1555 1555 2.36 LINK OD1 ASP A 56 CA CA A 202 1555 1555 2.26 LINK OD1 ASP A 58 CA CA A 202 1555 1555 2.31 LINK OD2 ASP A 58 CA CA A 202 1555 1555 2.52 LINK OD1 ASN A 60 CA CA A 202 1555 1555 2.52 LINK O THR A 62 CA CA A 202 1555 1555 2.39 LINK OD2 ASP A 64 CA CA A 202 1555 1555 2.25 LINK OE1 GLU A 67 CA CA A 202 1555 1555 2.42 LINK OE2 GLU A 67 CA CA A 202 1555 1555 2.38 LINK OD1 ASP A 93 CA CA A 203 1555 1555 2.23 LINK OD1 ASP A 95 CA CA A 203 1555 1555 2.26 LINK OD2 ASP A 95 CA CA A 203 1555 1555 2.62 LINK OD1 ASN A 97 CA CA A 203 1555 1555 2.46 LINK O TYR A 99 CA CA A 203 1555 1555 2.45 LINK OE1 GLU A 104 CA CA A 203 1555 1555 2.42 LINK OE2 GLU A 104 CA CA A 203 1555 1555 2.34 LINK OD1 ASP A 129 CA CA A 204 1555 1555 2.25 LINK OD1 ASP A 131 CA CA A 204 1555 1555 2.25 LINK OD2 ASP A 133 CA CA A 204 1555 1555 2.22 LINK O GLN A 135 CA CA A 204 1555 1555 2.43 LINK OE1 GLU A 140 CA CA A 204 1555 1555 2.35 LINK OE2 GLU A 140 CA CA A 204 1555 1555 2.35 LINK C ASP B 18 N TPO B 19 1555 1555 1.33 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 6 ASP A 56 ASP A 58 ASN A 60 THR A 62 SITE 2 AC2 6 ASP A 64 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 5 ASP A 129 ASP A 131 ASP A 133 GLN A 135 SITE 2 AC4 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