HEADER CALCIUM BINDING PROTEIN/PROTEIN FIBRIL 13-FEB-13 2M55 TITLE NMR STRUCTURE OF THE COMPLEX OF AN N-TERMINALLY ACETYLATED ALPHA- TITLE 2 SYNUCLEIN PEPTIDE WITH CALMODULIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CALMODULIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CAM; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: ALPHA-SYNUCLEIN; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: UNP RESIDUES 1-19; COMPND 10 SYNONYM: NON-A BETA COMPONENT OF AD AMYLOID, NON-A4 COMPONENT OF COMPND 11 AMYLOID PRECURSOR, NACP; COMPND 12 ENGINEERED: 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, CALM2, CAM2, CAMB, CALM3, CALML2, SOURCE 6 CAM3, CAMC, CAMIII; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET30B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606 KEYWDS PROTEIN/PEPTIDE, CA-BINDING, CALCIUM BINDING PROTEIN-PROTEIN FIBRIL KEYWDS 2 COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.M.GRUSCHUS,T.YAP,S.PISTOLESI,A.S.MALTSEV,J.C.LEE REVDAT 4 14-JUN-23 2M55 1 REMARK SEQADV LINK REVDAT 3 25-DEC-13 2M55 1 SOURCE REVDAT 2 18-DEC-13 2M55 1 JRNL REVDAT 1 08-MAY-13 2M55 0 JRNL AUTH J.M.GRUSCHUS,T.L.YAP,S.PISTOLESI,A.S.MALTSEV,J.C.LEE JRNL TITL NMR STRUCTURE OF CALMODULIN COMPLEXED TO AN N-TERMINALLY JRNL TITL 2 ACETYLATED ALPHA-SYNUCLEIN PEPTIDE. JRNL REF BIOCHEMISTRY V. 52 3436 2013 JRNL REFN ISSN 0006-2960 JRNL PMID 23607618 JRNL DOI 10.1021/BI400199P REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH, X-PLOR NIH REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR REMARK 3 NIH), SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X- REMARK 3 PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2M55 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-FEB-13. REMARK 100 THE DEPOSITION ID IS D_1000103221. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 6.36 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 600 UM [U-99% 13C; U-99% 15N] REMARK 210 CALMODULIN, 600 UM ALPHA- REMARK 210 SYNUCLEIN, 50 MM MES, 100 MM REMARK 210 POTASSIUM CHLORIDE, 3 MM CALCIUM REMARK 210 ION, 95% H2O/5% D2O; 700 UM [U- REMARK 210 13C; U-15N]-MET,VAL,PHE,GLY,LEU, REMARK 210 ALA ALPHA-SYNUCLEIN, 700 UM REMARK 210 CALMODULIN, 50 MM MES, 100 MM REMARK 210 POTASSIUM CHLORIDE, 3 MM CALCIUM REMARK 210 ION, 0.1% SODIUM AZIDE, 95% H2O/ REMARK 210 5% D2O; 150 UM [U-99% 13C; U-99% REMARK 210 15N] CALMODULIN, 150 UM ALPHA- REMARK 210 SYNUCLEIN, 50 MM MES, 100 MM REMARK 210 POTASSIUM CHLORIDE, 3 MM CALCIUM REMARK 210 ION, 10 MG/ML PF1 PHAGE, 95% H2O/ REMARK 210 5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 2D 1H-15N HSQC; 2D 1H- REMARK 210 13C HSQC ALIPHATIC; 3D CBCA(CO)NH REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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: 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 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 H ASP A 95 OE2 GLU A 104 1.56 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 LEU A 39 16.84 -66.56 REMARK 500 1 LYS B 212 -80.33 -92.13 REMARK 500 2 LEU A 39 20.68 -69.54 REMARK 500 2 LYS B 212 -6.71 -166.58 REMARK 500 2 VAL B 216 -9.15 -50.50 REMARK 500 3 LEU A 39 19.42 -68.45 REMARK 500 3 ASP A 129 97.96 -68.57 REMARK 500 3 THR A 146 52.36 -94.04 REMARK 500 3 VAL B 215 -9.68 -55.47 REMARK 500 4 GLN A 3 -163.79 53.61 REMARK 500 4 LEU A 39 15.73 -66.72 REMARK 500 4 ASP A 129 97.37 -68.05 REMARK 500 4 LYS B 212 -106.14 -97.68 REMARK 500 5 LEU A 39 23.25 -69.71 REMARK 500 5 THR A 79 -73.01 -95.26 REMARK 500 5 THR A 146 56.39 -97.27 REMARK 500 5 GLU B 213 -93.46 -173.16 REMARK 500 5 VAL B 215 -5.09 -57.66 REMARK 500 6 LEU A 39 13.48 -69.92 REMARK 500 6 THR A 79 -65.10 -91.97 REMARK 500 6 GLU B 213 -52.32 71.70 REMARK 500 7 LEU A 39 20.28 -69.39 REMARK 500 7 THR A 79 47.20 -141.90 REMARK 500 7 GLU B 213 -104.05 -177.85 REMARK 500 8 LEU A 39 16.24 -65.33 REMARK 500 8 THR A 146 55.71 -96.36 REMARK 500 9 LEU A 39 18.15 -67.55 REMARK 500 9 GLU B 213 -103.77 177.62 REMARK 500 9 ALA B 217 30.00 -73.16 REMARK 500 10 LEU A 39 22.04 -69.03 REMARK 500 10 THR A 79 -77.20 -102.05 REMARK 500 10 THR A 146 42.65 -74.21 REMARK 500 10 VAL B 203 -6.54 -59.19 REMARK 500 10 VAL B 215 -7.83 -57.89 REMARK 500 10 ALA B 217 21.29 -70.29 REMARK 500 11 LEU A 39 22.18 -66.76 REMARK 500 11 THR A 79 -67.97 -97.82 REMARK 500 11 THR A 146 42.15 -73.53 REMARK 500 12 LEU A 39 21.65 -66.95 REMARK 500 12 THR A 79 -69.77 -94.21 REMARK 500 12 ASP A 133 -20.06 62.24 REMARK 500 12 LYS B 212 -32.59 -156.97 REMARK 500 12 ALA B 217 8.32 -63.25 REMARK 500 13 LEU A 39 18.21 -67.53 REMARK 500 13 ASP A 78 -178.95 -170.39 REMARK 500 13 ASP A 129 97.81 -68.80 REMARK 500 13 LYS B 212 -73.97 -97.76 REMARK 500 14 LEU A 39 21.82 -66.45 REMARK 500 14 ASP A 80 -34.27 75.81 REMARK 500 14 LYS B 212 -71.60 -106.97 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 A 300 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 20 OD1 REMARK 620 2 ASP A 22 OD2 114.3 REMARK 620 3 ASP A 24 OD2 118.4 98.4 REMARK 620 4 ASP A 24 OD1 73.2 127.7 46.1 REMARK 620 5 THR A 26 O 56.4 163.3 98.3 65.6 REMARK 620 6 GLU A 31 OE2 55.5 63.4 145.8 121.0 101.8 REMARK 620 7 GLU A 31 OE1 91.2 63.8 150.3 163.2 101.0 49.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 56 OD1 REMARK 620 2 ASP A 58 OD2 110.5 REMARK 620 3 ASP A 58 OD1 61.5 51.1 REMARK 620 4 ASN A 60 OD1 91.8 71.2 61.2 REMARK 620 5 THR A 62 O 125.1 109.6 129.0 67.9 REMARK 620 6 GLU A 67 OE2 102.3 72.5 96.5 143.7 124.5 REMARK 620 7 GLU A 67 OE1 116.9 108.3 144.3 147.8 83.0 47.9 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 302 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 93 OD1 REMARK 620 2 ASP A 95 OD2 134.8 REMARK 620 3 ASN A 97 OD1 68.9 125.8 REMARK 620 4 TYR A 99 O 73.9 150.9 50.9 REMARK 620 5 GLU A 104 OE2 72.9 68.9 133.7 137.5 REMARK 620 6 GLU A 104 OE1 70.8 98.0 134.3 97.5 46.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 303 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 129 OD1 REMARK 620 2 ASP A 131 OD1 85.7 REMARK 620 3 ASP A 133 OD1 102.5 75.8 REMARK 620 4 GLN A 135 O 143.3 114.6 57.9 REMARK 620 5 GLU A 140 OE1 142.3 90.0 112.6 71.3 REMARK 620 6 GLU A 140 OE2 97.2 58.5 128.2 119.4 50.2 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 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 303 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19036 RELATED DB: BMRB DBREF 2M55 A 1 148 UNP P62158 CALM_HUMAN 2 149 DBREF 2M55 B 201 219 UNP P37840 SYUA_HUMAN 1 19 SEQADV 2M55 ACE B 200 UNP P37840 ACETYLATION SEQADV 2M55 NH2 B 220 UNP P37840 AMIDATION 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 21 ACE MET ASP VAL PHE MET LYS GLY LEU SER LYS ALA LYS SEQRES 2 B 21 GLU GLY VAL VAL ALA ALA ALA NH2 HET ACE B 200 6 HET NH2 B 220 3 HET CA A 300 1 HET CA A 301 1 HET CA A 302 1 HET CA A 303 1 HETNAM ACE ACETYL GROUP HETNAM NH2 AMINO GROUP HETNAM CA CALCIUM ION FORMUL 2 ACE C2 H4 O FORMUL 2 NH2 H2 N FORMUL 3 CA 4(CA 2+) HELIX 1 1 THR A 5 ASP A 20 1 16 HELIX 2 2 THR A 28 LEU A 39 1 12 HELIX 3 3 THR A 44 ASP A 56 1 13 HELIX 4 4 PHE A 65 ASP A 78 1 14 HELIX 5 5 ASP A 80 ASP A 93 1 14 HELIX 6 6 SER A 101 LEU A 112 1 12 HELIX 7 7 THR A 117 ASP A 129 1 13 HELIX 8 8 TYR A 138 THR A 146 1 9 HELIX 9 9 MET B 201 ALA B 217 1 17 SHEET 1 A 2 THR A 26 ILE A 27 0 SHEET 2 A 2 ILE A 63 ASP A 64 -1 O ILE A 63 N ILE A 27 SHEET 1 B 2 TYR A 99 ILE A 100 0 SHEET 2 B 2 VAL A 136 ASN A 137 -1 O VAL A 136 N ILE A 100 LINK C ACE B 200 N MET B 201 1555 1555 1.30 LINK C ALA B 219 N NH2 B 220 1555 1555 1.31 LINK OD1 ASP A 20 CA CA A 300 1555 1555 2.69 LINK OD2 ASP A 22 CA CA A 300 1555 1555 2.69 LINK OD2 ASP A 24 CA CA A 300 1555 1555 2.68 LINK OD1 ASP A 24 CA CA A 300 1555 1555 2.82 LINK O THR A 26 CA CA A 300 1555 1555 2.22 LINK OE2 GLU A 31 CA CA A 300 1555 1555 2.76 LINK OE1 GLU A 31 CA CA A 300 1555 1555 2.27 LINK OD1 ASP A 56 CA CA A 301 1555 1555 2.57 LINK OD2 ASP A 58 CA CA A 301 1555 1555 2.66 LINK OD1 ASP A 58 CA CA A 301 1555 1555 2.27 LINK OD1 ASN A 60 CA CA A 301 1555 1555 2.56 LINK O THR A 62 CA CA A 301 1555 1555 2.32 LINK OE2 GLU A 67 CA CA A 301 1555 1555 2.61 LINK OE1 GLU A 67 CA CA A 301 1555 1555 2.70 LINK OD1 ASP A 93 CA CA A 302 1555 1555 2.56 LINK OD2 ASP A 95 CA CA A 302 1555 1555 2.70 LINK OD1 ASN A 97 CA CA A 302 1555 1555 2.67 LINK O TYR A 99 CA CA A 302 1555 1555 2.68 LINK OE2 GLU A 104 CA CA A 302 1555 1555 2.76 LINK OE1 GLU A 104 CA CA A 302 1555 1555 2.71 LINK OD1 ASP A 129 CA CA A 303 1555 1555 2.20 LINK OD1 ASP A 131 CA CA A 303 1555 1555 2.39 LINK OD1 ASP A 133 CA CA A 303 1555 1555 2.32 LINK O GLN A 135 CA CA A 303 1555 1555 2.61 LINK OE1 GLU A 140 CA CA A 303 1555 1555 2.29 LINK OE2 GLU A 140 CA CA A 303 1555 1555 2.71 SITE 1 AC1 6 ASP A 20 ASP A 22 ASP A 24 THR A 26 SITE 2 AC1 6 THR A 28 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 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 MODEL 2 MODEL 3 MODEL 4 MODEL 5 MODEL 6 MODEL 7 MODEL 8 MODEL 9 MODEL 10 MODEL 11 MODEL 12 MODEL 13 MODEL 14 MODEL 15 MODEL 16 MODEL 17 MODEL 18 MODEL 19 MODEL 20