HEADER SIGNALING PROTEIN, PROTEIN BINDING 12-JAN-14 2MJM TITLE THE SOLUTION NMR STRUCTURE OF THE NLRC5 CASPASE RECRUITMENT DOMAIN TITLE 2 (CARD) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN NLRC5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: NLRC5 CASPASE RECRUITMENT DOMAIN (UNP RESIDUES 1-96); COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: NLRC5; 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: PGEX-6P-1 KEYWDS NLRC5, CARD, RIG-I, PROTEIN BINDING, DEATH FOLD, PROTEIN-PROTEIN KEYWDS 2 INTERACTION, INFLAMMATION, INNATE IMMUNE SYSTEM, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR P.G.M.GUTTE,O.ZERBE REVDAT 2 14-JUN-23 2MJM 1 REMARK SEQADV REVDAT 1 03-SEP-14 2MJM 0 JRNL AUTH P.G.GUTTE,S.JURT,M.G.GRUTTER,O.ZERBE JRNL TITL UNUSUAL STRUCTURAL FEATURES REVEALED BY THE SOLUTION NMR JRNL TITL 2 STRUCTURE OF THE NLRC5 CASPASE RECRUITMENT DOMAIN. JRNL REF BIOCHEMISTRY V. 53 3106 2014 JRNL REFN ISSN 0006-2960 JRNL PMID 24815518 JRNL DOI 10.1021/BI500177X REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 2.1, CHARMM REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), B. R. BROOKS, C. L. REMARK 3 BROOKS III, D. M. YORK, AND M. KARPLUS (CHARMM) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: RESTRAINED MOLECULAR DYNAMICS IN REMARK 3 EXPLICIT SOLVENT REMARK 4 REMARK 4 2MJM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000103692. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 6.2 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 600 UM [U-100% 13C; U-100% 15N] REMARK 210 PROTEIN, 20 MM MES, 100 MM REMARK 210 SODIUM CHLORIDE, 50 MM POTASSIUM REMARK 210 CHLORIDE, 2 MM TCEP, 95% H2O/5% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D CBCA(CO)NH; 3D REMARK 210 HNCACB; 3D HCCH-TOCSY; 3D 1H-13C REMARK 210 NOESY ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 3D HNCO; HB(CBCGCD)HD REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA 1.8.6, UNIO'10, CYANA 2.1 REMARK 210 METHOD USED : MOLECULAR DYNAMICS 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 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 16 VAL A 95 CB VAL A 95 CG1 -0.132 REMARK 500 16 VAL A 95 CB VAL A 95 CG2 -0.128 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 7 24.85 -74.80 REMARK 500 1 ASN A 15 -44.50 -145.72 REMARK 500 1 MET A 44 99.24 -43.33 REMARK 500 1 PRO A 52 -145.93 -64.16 REMARK 500 1 SER A 53 38.37 -74.73 REMARK 500 1 ASP A 85 -46.84 72.12 REMARK 500 1 ASP A 89 -50.77 173.96 REMARK 500 2 PRO A 2 99.35 -56.22 REMARK 500 2 LEU A 3 -73.59 -115.64 REMARK 500 2 LEU A 13 122.31 -35.21 REMARK 500 2 ASN A 15 -72.58 -128.70 REMARK 500 2 ASN A 29 52.85 -145.49 REMARK 500 2 MET A 44 91.06 41.70 REMARK 500 2 ASP A 45 59.54 -98.11 REMARK 500 2 ASP A 47 37.61 -80.45 REMARK 500 2 PRO A 52 -169.87 -66.45 REMARK 500 2 SER A 53 38.55 -78.18 REMARK 500 2 PRO A 87 100.31 -22.93 REMARK 500 2 MET A 90 32.35 -143.46 REMARK 500 3 LEU A 3 160.50 70.97 REMARK 500 3 SER A 5 96.96 66.69 REMARK 500 3 ASP A 7 24.25 -141.82 REMARK 500 3 LEU A 13 141.10 -176.45 REMARK 500 3 MET A 44 91.50 28.75 REMARK 500 3 PRO A 52 -151.43 -61.04 REMARK 500 3 SER A 53 37.18 -75.33 REMARK 500 3 ASP A 89 -45.14 70.13 REMARK 500 3 MET A 90 40.38 -87.95 REMARK 500 3 PRO A 100 36.78 -82.37 REMARK 500 4 SER A 5 97.48 64.29 REMARK 500 4 LEU A 13 171.72 67.05 REMARK 500 4 MET A 44 110.00 -37.66 REMARK 500 4 ASP A 45 56.56 -113.31 REMARK 500 4 CYS A 48 39.25 -81.51 REMARK 500 4 PRO A 52 -141.48 -69.22 REMARK 500 4 SER A 53 38.36 -75.78 REMARK 500 4 ASP A 85 71.15 55.74 REMARK 500 5 ASP A 7 25.22 -73.59 REMARK 500 5 LEU A 13 -51.85 64.15 REMARK 500 5 ASN A 14 -80.59 -126.42 REMARK 500 5 ASN A 15 84.67 67.99 REMARK 500 5 MET A 44 92.63 41.32 REMARK 500 5 ASP A 45 56.80 -99.12 REMARK 500 5 PRO A 52 -149.45 -76.83 REMARK 500 5 SER A 53 38.65 -76.00 REMARK 500 5 ASP A 85 -151.64 -138.30 REMARK 500 5 ASP A 89 83.63 53.48 REMARK 500 5 MET A 90 32.25 -156.12 REMARK 500 6 LEU A 13 -168.91 63.10 REMARK 500 6 MET A 44 92.12 41.96 REMARK 500 REMARK 500 THIS ENTRY HAS 185 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 3 ARG A 24 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19732 RELATED DB: BMRB DBREF 2MJM A 6 101 UNP C3VPR6 NLRC5_MOUSE 1 96 SEQADV 2MJM GLY A 1 UNP C3VPR6 EXPRESSION TAG SEQADV 2MJM PRO A 2 UNP C3VPR6 EXPRESSION TAG SEQADV 2MJM LEU A 3 UNP C3VPR6 EXPRESSION TAG SEQADV 2MJM GLY A 4 UNP C3VPR6 EXPRESSION TAG SEQADV 2MJM SER A 5 UNP C3VPR6 EXPRESSION TAG SEQRES 1 A 101 GLY PRO LEU GLY SER MET ASP ALA GLU SER ILE ARG LEU SEQRES 2 A 101 ASN ASN GLU ASN LEU TRP ALA TRP LEU VAL ARG LEU LEU SEQRES 3 A 101 SER LYS ASN PRO GLU TRP LEU SER ALA LYS LEU ARG SER SEQRES 4 A 101 PHE LEU PRO THR MET ASP LEU ASP CYS SER TYR GLU PRO SEQRES 5 A 101 SER ASN PRO GLU VAL ILE HIS ARG GLN LEU ASN ARG LEU SEQRES 6 A 101 PHE ALA GLN GLY MET ALA THR TRP LYS SER PHE ILE ASN SEQRES 7 A 101 ASP LEU CYS PHE GLU LEU ASP VAL PRO LEU ASP MET GLU SEQRES 8 A 101 ILE PRO LEU VAL SER ILE TRP GLY PRO ARG HELIX 1 1 MET A 6 SER A 10 5 5 HELIX 2 2 ASN A 15 LYS A 28 1 14 HELIX 3 3 ASN A 29 LEU A 41 1 13 HELIX 4 4 ASN A 54 GLY A 69 1 16 HELIX 5 5 GLY A 69 LEU A 84 1 16 HELIX 6 6 MET A 90 SER A 96 1 7 HELIX 7 7 ILE A 97 GLY A 99 5 3 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