HEADER SIGNALING PROTEIN 17-NOV-10 2L6A TITLE THREE-DIMENSIONAL STRUCTURE OF THE N-TERMINAL EFFECTOR PYRIN DOMAIN OF TITLE 2 NLRP12 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NACHT, LRR AND PYD DOMAINS-CONTAINING PROTEIN 12; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-98; COMPND 5 SYNONYM: MONARCH-1, PYRIN-CONTAINING APAF1-LIKE PROTEIN 7, REGULATED COMPND 6 BY NITRIC OXIDE; COMPND 7 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: NLRP12, NALP12, PYPAF7, RNO; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3)-RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PHIS PARALLEL STOP KEYWDS NLRP12, PYRIN, DEATH DOMAIN, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.S.PINHEIRO,W.PETI REVDAT 5 15-MAY-24 2L6A 1 REMARK REVDAT 4 14-JUN-23 2L6A 1 REMARK REVDAT 3 05-FEB-20 2L6A 1 REMARK SEQADV REVDAT 2 28-DEC-11 2L6A 1 JRNL REVDAT 1 02-NOV-11 2L6A 0 JRNL AUTH A.S.PINHEIRO,C.EIBL,Z.EKMAN-VURAL,R.SCHWARZENBACHER,W.PETI JRNL TITL THE NLRP12 PYRIN DOMAIN: STRUCTURE, DYNAMICS, AND FUNCTIONAL JRNL TITL 2 INSIGHTS. JRNL REF J.MOL.BIOL. V. 413 790 2011 JRNL REFN ISSN 0022-2836 JRNL PMID 21978668 JRNL DOI 10.1016/J.JMB.2011.09.024 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 2.1, CNS REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), BRUNGER, ADAMS, CLORE, REMARK 3 GROS, NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT WAS DONE IN EXPLICIT SOLVENT REMARK 3 USING CNS AND THE RECOORD SCRIPT PACKAGE. REMARK 4 REMARK 4 2L6A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-NOV-10. REMARK 100 THE DEPOSITION ID IS D_1000102010. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.5 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 600 UM [U-99% 15N] NLRP12 PYD-1, REMARK 210 20 MM SODIUM PHOSPHATE-2, 500 MM REMARK 210 SODIUM CHLORIDE-3, 0.5 MM TCEP-4, REMARK 210 90% H2O/10% D2O; 600 UM [U-99% REMARK 210 13C; U-99% 15N] NLRP12 PYD-5, 20 REMARK 210 MM SODIUM PHOSPHATE-6, 500 MM REMARK 210 SODIUM CHLORIDE-7, 0.5 MM TCEP-8, REMARK 210 90% H2O/10% D2O; 600 UM NLRP12 REMARK 210 PYD-9, 20 MM SODIUM PHOSPHATE-10, REMARK 210 500 MM SODIUM CHLORIDE-11, 0.5 REMARK 210 MM TCEP-12, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCA; 3D HNCACB; 3D CBCA(CO) REMARK 210 NH; 3D HNCO; 3D HN(CA)CO; 3D REMARK 210 HBHA(CO)NH; 3D C(CO)NH; 3D HCCH- REMARK 210 TOCSY; 3D 1H-15N NOESY; 3D 1H- REMARK 210 13C NOESY; 2D 1H-1H NOESY; 2D 1H- REMARK 210 1H TOCSY; 2D 1H-1H COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 2.1, CARA, CYANA 2.1 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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 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 HZ3 LYS A 31 OE1 GLU A 51 1.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 4 GLY A 43 N GLY A 43 CA -0.107 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 ASP A 10 -109.17 -93.00 REMARK 500 1 PRO A 46 173.63 -55.86 REMARK 500 1 GLU A 94 -88.71 58.13 REMARK 500 1 LEU A 96 143.19 67.62 REMARK 500 1 ARG A 98 -74.44 -147.48 REMARK 500 1 THR A 100 -53.47 71.51 REMARK 500 2 HIS A 2 -86.87 64.81 REMARK 500 2 LEU A 4 -164.28 -110.27 REMARK 500 2 ARG A 9 -62.43 -143.77 REMARK 500 2 ASP A 10 -89.99 57.95 REMARK 500 2 GLU A 42 -53.95 -122.05 REMARK 500 2 TRP A 47 -74.04 25.61 REMARK 500 2 ARG A 84 50.15 -144.31 REMARK 500 2 LEU A 96 -82.72 -147.71 REMARK 500 2 ARG A 98 109.19 66.87 REMARK 500 2 ASP A 99 -69.69 -164.11 REMARK 500 3 LEU A 4 84.92 62.81 REMARK 500 3 THR A 6 121.53 77.98 REMARK 500 3 TRP A 47 -78.88 31.78 REMARK 500 3 PHE A 66 -77.22 -83.66 REMARK 500 3 ARG A 84 70.32 -101.23 REMARK 500 3 GLN A 92 -179.76 59.15 REMARK 500 3 ASP A 95 -151.39 -110.51 REMARK 500 3 VAL A 97 79.30 73.11 REMARK 500 4 MET A 3 -160.32 67.66 REMARK 500 4 LEU A 4 116.04 77.59 REMARK 500 4 ALA A 7 -59.31 -147.25 REMARK 500 4 THR A 17 -60.98 -107.59 REMARK 500 4 ALA A 37 109.27 -57.60 REMARK 500 4 LYS A 44 -43.19 -149.81 REMARK 500 4 TRP A 47 -77.08 21.23 REMARK 500 4 ARG A 84 59.32 -112.26 REMARK 500 4 ARG A 93 -18.18 -141.90 REMARK 500 4 ASP A 99 -75.72 -164.34 REMARK 500 4 THR A 100 -85.80 66.82 REMARK 500 4 VAL A 101 175.77 170.87 REMARK 500 5 ARG A 5 -148.43 -163.49 REMARK 500 5 ALA A 7 90.55 -66.32 REMARK 500 5 ARG A 9 -69.17 64.48 REMARK 500 5 TRP A 47 -80.40 20.11 REMARK 500 5 PHE A 66 -60.52 -91.62 REMARK 500 5 ARG A 84 71.73 -103.86 REMARK 500 5 VAL A 97 -80.79 -97.62 REMARK 500 5 ARG A 98 -57.90 -154.63 REMARK 500 6 ASN A 83 74.62 59.92 REMARK 500 6 ARG A 84 56.01 -145.94 REMARK 500 6 GLN A 92 -84.55 50.59 REMARK 500 6 ARG A 93 24.05 -174.11 REMARK 500 6 ASP A 95 -165.88 -123.70 REMARK 500 6 THR A 100 24.16 -149.64 REMARK 500 REMARK 500 THIS ENTRY HAS 158 RAMACHANDRAN OUTLIERS. 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 8 ARG A 73 0.09 SIDE CHAIN REMARK 500 18 ARG A 73 0.07 SIDE CHAIN REMARK 500 20 ARG A 81 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17305 RELATED DB: BMRB DBREF 2L6A A 3 100 UNP P59046 NAL12_HUMAN 1 98 SEQADV 2L6A GLY A 1 UNP P59046 EXPRESSION TAG SEQADV 2L6A HIS A 2 UNP P59046 EXPRESSION TAG SEQADV 2L6A VAL A 101 UNP P59046 EXPRESSION TAG SEQADV 2L6A GLU A 102 UNP P59046 EXPRESSION TAG SEQRES 1 A 102 GLY HIS MET LEU ARG THR ALA GLY ARG ASP GLY LEU CYS SEQRES 2 A 102 ARG LEU SER THR TYR LEU GLU GLU LEU GLU ALA VAL GLU SEQRES 3 A 102 LEU LYS LYS PHE LYS LEU TYR LEU GLY THR ALA THR GLU SEQRES 4 A 102 LEU GLY GLU GLY LYS ILE PRO TRP GLY SER MET GLU LYS SEQRES 5 A 102 ALA GLY PRO LEU GLU MET ALA GLN LEU LEU ILE THR HIS SEQRES 6 A 102 PHE GLY PRO GLU GLU ALA TRP ARG LEU ALA LEU SER THR SEQRES 7 A 102 PHE GLU ARG ILE ASN ARG LYS ASP LEU TRP GLU ARG GLY SEQRES 8 A 102 GLN ARG GLU ASP LEU VAL ARG ASP THR VAL GLU HELIX 1 1 GLY A 11 GLU A 20 1 10 HELIX 2 2 GLU A 23 THR A 36 1 14 HELIX 3 3 GLY A 54 PHE A 66 1 13 HELIX 4 4 GLY A 67 GLU A 80 1 14 HELIX 5 5 ARG A 81 ASN A 83 5 3 HELIX 6 6 ARG A 84 ARG A 90 1 7 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