HEADER APOPTOSIS 12-JUN-03 1PN5 TITLE NMR STRUCTURE OF THE NALP1 PYRIN DOMAIN (PYD) COMPND MOL_ID: 1; COMPND 2 MOLECULE: NACHT-, LRR- AND PYD-CONTAINING PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PYRIN DOMAIN (PYD); COMPND 5 SYNONYM: DEATH EFFECTOR FILAMENT-FORMING CED-4-LIKE APOPTOSIS COMPND 6 PROTEIN, NUCLEOTIDE-BINDING DOMAIN AND CASPASE RECRUITMENT DOMAIN, COMPND 7 CASPASE RECRUITMENT DOMAIN PROTEIN 7; COMPND 8 ENGINEERED: YES; COMPND 9 OTHER_DETAILS: RESIDUES 1-56 CORRESPOND TO THE FUSED IMMUNOGLOBULIN G COMPND 10 BINDING PROTEIN G (SWS P06654, RESIDUES 228-282) SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: NALP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET20B+ KEYWDS 5 ALPHA-HELIX BUNDLE, APOPTOSIS EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.HILLER,A.KOHL,F.FIORITO,T.HERRMANN,G.WIDER,J.TSCHOPP,M.G.GRUTTER, AUTHOR 2 K.WUTHRICH REVDAT 4 22-MAY-24 1PN5 1 REMARK REVDAT 3 27-OCT-21 1PN5 1 REMARK SEQADV REVDAT 2 24-FEB-09 1PN5 1 VERSN REVDAT 1 07-OCT-03 1PN5 0 JRNL AUTH S.HILLER,A.KOHL,F.FIORITO,T.HERRMANN,G.WIDER,J.TSCHOPP, JRNL AUTH 2 M.G.GRUTTER,K.WUTHRICH JRNL TITL NMR STRUCTURE OF THE APOPTOSIS- AND INFLAMMATION-RELATED JRNL TITL 2 NALP1 PYRIN DOMAIN JRNL REF STRUCTURE V. 11 1199 2003 JRNL REFN ISSN 0969-2126 JRNL PMID 14527388 JRNL DOI 10.1016/J.STR.2003.08.009 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR, ATNOS REMARK 3 AUTHORS : BRUKER (XWINNMR), HERRMANN (ATNOS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1PN5 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JUN-03. REMARK 100 THE DEPOSITION ID IS D_1000019442. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1MM NALP1 PYD U-15N,13C; 50MM NA REMARK 210 / PO4 - BUFFER; 50MM NACL; 1MM REMARK 210 CHAPS; 20MM DTT (D10); 0.02% REMARK 210 NAN3; 0.1MM EDTA; PROTEASE REMARK 210 INHIBITOR COCKTAIL (COMPLETE, REMARK 210 ROCHE); 95% H2O, 5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DYANA, CANDID, ATNOS, CARA REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 17 REMARK 210 REMARK 210 REMARK: PROTEIN WAS EXPRESSED AS A FUSION PROTEIN WITH G B1 TO REMARK 210 ENHANCE SOLUBILITY (ZHOU ET AL., J. BIOMOL. NMR 20, 11-14) 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 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: 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: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 3 LEU A 85 CB - CG - CD1 ANGL. DEV. = 11.6 DEGREES REMARK 500 9 ARG A 93 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 14 ARG A 66 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES 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 63 65.04 -172.54 REMARK 500 1 TRP A 64 -66.31 -150.53 REMARK 500 1 LYS A 75 -168.75 -126.83 REMARK 500 1 GLU A 78 -9.07 -143.37 REMARK 500 1 ALA A 90 91.29 24.15 REMARK 500 1 HIS A 91 -8.37 -52.92 REMARK 500 1 ARG A 93 104.14 59.40 REMARK 500 1 SER A 95 49.96 -72.75 REMARK 500 1 SER A 96 -45.56 -150.21 REMARK 500 1 ALA A 101 115.26 54.88 REMARK 500 1 GLU A 104 14.07 -142.75 REMARK 500 1 TYR A 119 -77.48 -121.75 REMARK 500 1 GLN A 122 -79.60 -63.61 REMARK 500 1 ALA A 124 -72.75 -65.04 REMARK 500 1 LEU A 137 70.64 -104.12 REMARK 500 1 GLU A 146 0.91 -66.90 REMARK 500 1 HIS A 150 -171.45 67.59 REMARK 500 2 ALA A 60 105.72 97.44 REMARK 500 2 TRP A 64 -78.46 -159.37 REMARK 500 2 SER A 92 -164.37 60.61 REMARK 500 2 SER A 94 87.49 50.23 REMARK 500 2 THR A 99 142.06 66.76 REMARK 500 2 GLN A 122 -81.62 -68.41 REMARK 500 2 ALA A 148 7.16 94.92 REMARK 500 3 GLU A 81 -61.95 -28.83 REMARK 500 3 ALA A 90 -71.97 -63.93 REMARK 500 3 HIS A 91 106.29 -175.56 REMARK 500 3 SER A 92 -76.94 -148.06 REMARK 500 3 GLU A 98 94.68 58.06 REMARK 500 3 PRO A 103 -168.01 -78.03 REMARK 500 3 THR A 106 -11.51 60.61 REMARK 500 3 GLN A 122 -90.96 -73.74 REMARK 500 3 LEU A 137 63.41 -118.50 REMARK 500 3 ALA A 142 -70.28 -63.19 REMARK 500 3 ALA A 148 -84.58 65.50 REMARK 500 3 HIS A 150 -89.94 -127.89 REMARK 500 4 TRP A 64 -67.87 -102.70 REMARK 500 4 GLU A 78 -18.33 -144.31 REMARK 500 4 HIS A 91 -52.43 -133.69 REMARK 500 4 ARG A 93 -103.63 -126.85 REMARK 500 4 SER A 95 -175.44 54.33 REMARK 500 4 SER A 96 95.09 -69.81 REMARK 500 4 ALA A 101 152.41 66.80 REMARK 500 4 GLN A 122 -71.06 -64.14 REMARK 500 4 TRP A 125 -50.46 -121.08 REMARK 500 4 GLN A 145 49.99 -148.67 REMARK 500 4 GLU A 146 20.87 -141.54 REMARK 500 4 HIS A 150 -178.87 54.75 REMARK 500 5 LYS A 89 -76.53 -62.59 REMARK 500 5 ALA A 90 -168.73 39.21 REMARK 500 REMARK 500 THIS ENTRY HAS 223 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER A 95 SER A 96 11 149.95 REMARK 500 LYS A 89 ALA A 90 12 -149.61 REMARK 500 ARG A 93 SER A 94 12 -136.87 REMARK 500 SER A 96 GLY A 97 12 144.61 REMARK 500 ALA A 101 GLN A 102 12 -148.13 REMARK 500 ALA A 90 HIS A 91 16 -139.53 REMARK 500 GLN A 118 TYR A 119 16 -149.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 2 ARG A 66 0.11 SIDE CHAIN REMARK 500 2 ARG A 123 0.09 SIDE CHAIN REMARK 500 5 PHE A 82 0.08 SIDE CHAIN REMARK 500 6 TYR A 119 0.10 SIDE CHAIN REMARK 500 7 ARG A 138 0.09 SIDE CHAIN REMARK 500 13 ARG A 66 0.10 SIDE CHAIN REMARK 500 13 PHE A 82 0.08 SIDE CHAIN REMARK 500 17 TYR A 114 0.07 SIDE CHAIN REMARK 500 18 TYR A 119 0.07 SIDE CHAIN REMARK 500 19 PHE A 73 0.08 SIDE CHAIN REMARK 500 19 ARG A 123 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 650 REMARK 650 HELIX REMARK 650 DETERMINATION METHOD: AUTHOR REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES 1-58 ARE MISSING FROM THE COORDINATES REMARK 999 BECAUSE THEY WERE NOT INCLUDED IN THE MODEL. REMARK 999 RESIDUES 57 AND 58 ARE INDEPENDENT LINKING RESIDUES, REMARK 999 WHICH HAVE BEEN INSERTED TO PROVIDE DISTANCE AND REMARK 999 FLEXIBILTIY IN THIS TWO-DOMAIN FUSION PROTEIN. DBREF 1PN5 A 2 56 UNP P06654 SPG1_STRSG 228 282 DBREF 1PN5 A 59 151 UNP Q9C000 NAL1_HUMAN 1 93 SEQADV 1PN5 MET A 1 UNP P06654 INITIATING METHIONINE SEQADV 1PN5 GLN A 2 UNP P06654 THR 228 ENGINEERED MUTATION SEQADV 1PN5 GLY A 57 UNP P06654 SEE REMARK 999 SEQADV 1PN5 SER A 58 UNP P06654 SEE REMARK 999 SEQADV 1PN5 LEU A 152 UNP Q9C000 EXPRESSION TAG SEQADV 1PN5 GLU A 153 UNP Q9C000 EXPRESSION TAG SEQADV 1PN5 HIS A 154 UNP Q9C000 EXPRESSION TAG SEQADV 1PN5 HIS A 155 UNP Q9C000 EXPRESSION TAG SEQADV 1PN5 HIS A 156 UNP Q9C000 EXPRESSION TAG SEQADV 1PN5 HIS A 157 UNP Q9C000 EXPRESSION TAG SEQADV 1PN5 HIS A 158 UNP Q9C000 EXPRESSION TAG SEQADV 1PN5 HIS A 159 UNP Q9C000 EXPRESSION TAG SEQRES 1 A 159 MET GLN TYR LYS LEU ILE LEU ASN GLY LYS THR LEU LYS SEQRES 2 A 159 GLY GLU THR THR THR GLU ALA VAL ASP ALA ALA THR ALA SEQRES 3 A 159 GLU LYS VAL PHE LYS GLN TYR ALA ASN ASP ASN GLY VAL SEQRES 4 A 159 ASP GLY GLU TRP THR TYR ASP ASP ALA THR LYS THR PHE SEQRES 5 A 159 THR VAL THR GLU GLY SER MET ALA GLY GLY ALA TRP GLY SEQRES 6 A 159 ARG LEU ALA CYS TYR LEU GLU PHE LEU LYS LYS GLU GLU SEQRES 7 A 159 LEU LYS GLU PHE GLN LEU LEU LEU ALA ASN LYS ALA HIS SEQRES 8 A 159 SER ARG SER SER SER GLY GLU THR PRO ALA GLN PRO GLU SEQRES 9 A 159 LYS THR SER GLY MET GLU VAL ALA SER TYR LEU VAL ALA SEQRES 10 A 159 GLN TYR GLY GLU GLN ARG ALA TRP ASP LEU ALA LEU HIS SEQRES 11 A 159 THR TRP GLU GLN MET GLY LEU ARG SER LEU CYS ALA GLN SEQRES 12 A 159 ALA GLN GLU GLY ALA GLY HIS SER LEU GLU HIS HIS HIS SEQRES 13 A 159 HIS HIS HIS HELIX 1 1 ARG A 66 LEU A 71 1 6 HELIX 2 2 LYS A 76 ASN A 88 1 13 HELIX 3 3 MET A 109 ALA A 117 1 9 HELIX 4 4 GLU A 121 GLN A 134 1 14 HELIX 5 5 ARG A 138 GLN A 143 1 6 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