PDB Short entry for 2M5V HEADER IMMUNE SYSTEM 11-MAR-13 2M5V TITLE THREE-DIMENSIONAL STRUCTURE OF HUMAN NLRP10/PYNOD PYRIN DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: NACHT, LRR AND PYD DOMAINS-CONTAINING PROTEIN 10; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-100; COMPND 5 SYNONYM: NUCLEOTIDE-BINDING OLIGOMERIZATION DOMAIN PROTEIN 8; COMPND 6 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: NLRP10, NALP10, NOD8, PYNOD; 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: PETM11 KEYWDS NLRP10, PYNOD, PYRIN DOMAIN, IMMUNE SYSTEM EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.Y.SU,C.F.CHANG,C.I.CHANG REVDAT 4 14-JUN-23 2M5V 1 REMARK SEQADV REVDAT 3 31-JUL-13 2M5V 1 JRNL REVDAT 2 05-JUN-13 2M5V 1 JRNL REMARK REVDAT 1 03-APR-13 2M5V 0 JRNL AUTH M.Y.SU,C.I.KUO,C.F.CHANG,C.I.CHANG JRNL TITL THREE-DIMENSIONAL STRUCTURE OF HUMAN NLRP10/PYNOD PYRIN JRNL TITL 2 DOMAIN REVEALS A HOMOTYPIC INTERACTION SITE DISTINCT FROM JRNL TITL 3 ITS MOUSE HOMOLOGUE. JRNL REF PLOS ONE V. 8 67843 2013 JRNL REFN ESSN 1932-6203 JRNL PMID 23861819 JRNL DOI 10.1371/JOURNAL.PONE.0067843 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.Y.SU,C.I.CHANG,C.F.CHANG REMARK 1 TITL (1)H, (13)C AND (15)N RESONANCE ASSIGNMENTS OF THE PYRIN REMARK 1 TITL 2 DOMAIN FROM HUMAN PYNOD. REMARK 1 REF BIOMOL.NMR ASSIGN. 2012 REMARK 1 REFN ESSN 1874-270X REMARK 1 PMID 22618865 REMARK 1 DOI 10.1007/S12104-012-9396-8 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2M5V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-MAR-13. REMARK 100 THE DEPOSITION ID IS D_1000103247. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 140 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.2 MM [U-13C; U-15N] PYNOD PYD, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D C(CO)NH; 3D HNCO; REMARK 210 3D HCCH-TOCSY; 3D 1H-15N NOESY; REMARK 210 3D 1H-13C NOESY; 3D H(CCO)NH; 3D REMARK 210 1H-15N TOCSY; 3D HBHA(CO)NH; 3D REMARK 210 HN(CO)CA REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 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 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: 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 2 158.40 64.11 REMARK 500 1 MET A 3 -173.33 64.72 REMARK 500 1 ALA A 4 107.70 64.18 REMARK 500 1 MET A 5 78.12 -111.75 REMARK 500 1 SER A 40 76.99 -119.32 REMARK 500 1 GLU A 41 -164.37 49.13 REMARK 500 1 PRO A 45 -167.03 -69.72 REMARK 500 1 LEU A 54 -167.44 -74.96 REMARK 500 1 LYS A 70 -81.37 -65.49 REMARK 500 1 VAL A 82 -7.98 -58.34 REMARK 500 1 ASN A 84 32.48 74.89 REMARK 500 1 GLU A 87 -75.08 -51.78 REMARK 500 1 LEU A 97 75.46 66.93 REMARK 500 2 MET A 3 -74.63 -129.60 REMARK 500 2 ALA A 4 142.49 -170.97 REMARK 500 2 MET A 5 128.50 -176.39 REMARK 500 2 ALA A 6 124.19 -178.94 REMARK 500 2 GLU A 41 -173.28 -67.74 REMARK 500 2 PRO A 45 -176.90 -69.75 REMARK 500 2 LYS A 70 -76.67 -60.11 REMARK 500 2 VAL A 82 -5.89 -59.26 REMARK 500 2 GLU A 87 -75.30 -51.56 REMARK 500 2 LEU A 97 106.08 66.45 REMARK 500 3 ALA A 4 76.30 -101.51 REMARK 500 3 LYS A 7 66.78 -173.40 REMARK 500 3 ARG A 9 -76.08 -94.60 REMARK 500 3 TYR A 67 -39.93 -135.79 REMARK 500 3 LYS A 70 -74.14 -59.32 REMARK 500 3 GLU A 87 -84.15 -53.08 REMARK 500 3 LEU A 97 116.04 65.41 REMARK 500 3 ARG A 101 43.18 -98.69 REMARK 500 4 ALA A 2 155.46 64.57 REMARK 500 4 MET A 3 26.12 -142.32 REMARK 500 4 ALA A 4 56.41 -109.01 REMARK 500 4 ALA A 6 -154.40 38.42 REMARK 500 4 LYS A 7 -55.25 -149.17 REMARK 500 4 ALA A 8 107.11 -171.57 REMARK 500 4 LYS A 10 54.47 -141.84 REMARK 500 4 PRO A 11 78.97 -69.79 REMARK 500 4 SER A 40 -162.33 -105.82 REMARK 500 4 PRO A 45 -167.18 -69.83 REMARK 500 4 LEU A 54 -170.55 -68.36 REMARK 500 4 TYR A 67 -39.76 -135.06 REMARK 500 4 LYS A 70 -74.91 -58.74 REMARK 500 4 GLU A 87 -80.25 -53.17 REMARK 500 4 LEU A 97 93.67 64.03 REMARK 500 5 ALA A 2 132.44 67.05 REMARK 500 5 MET A 3 69.87 -150.56 REMARK 500 5 ALA A 6 141.27 -170.12 REMARK 500 5 LEU A 39 -116.53 -122.51 REMARK 500 REMARK 500 THIS ENTRY HAS 210 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 18242 RELATED DB: BMRB DBREF 2M5V A 3 102 UNP Q86W26 NAL10_HUMAN 1 100 SEQADV 2M5V GLY A 1 UNP Q86W26 EXPRESSION TAG SEQADV 2M5V ALA A 2 UNP Q86W26 EXPRESSION TAG SEQRES 1 A 102 GLY ALA MET ALA MET ALA LYS ALA ARG LYS PRO ARG GLU SEQRES 2 A 102 ALA LEU LEU TRP ALA LEU SER ASP LEU GLU GLU ASN ASP SEQRES 3 A 102 PHE LYS LYS LEU LYS PHE TYR LEU ARG ASP MET THR LEU SEQRES 4 A 102 SER GLU GLY GLN PRO PRO LEU ALA ARG GLY GLU LEU GLU SEQRES 5 A 102 GLY LEU ILE PRO VAL ASP LEU ALA GLU LEU LEU ILE SER SEQRES 6 A 102 LYS TYR GLY GLU LYS GLU ALA VAL LYS VAL VAL LEU LYS SEQRES 7 A 102 GLY LEU LYS VAL MET ASN LEU LEU GLU LEU VAL ASP GLN SEQRES 8 A 102 LEU SER HIS ILE CYS LEU HIS ASP TYR ARG GLU HELIX 1 1 LYS A 10 LEU A 22 1 13 HELIX 2 2 GLU A 23 LEU A 39 1 17 HELIX 3 3 ALA A 47 LEU A 51 5 5 HELIX 4 4 ILE A 55 TYR A 67 1 13 HELIX 5 5 GLY A 68 VAL A 82 1 15 HELIX 6 6 LEU A 85 CYS A 96 1 12 HELIX 7 7 LEU A 97 ARG A 101 5 5 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