HEADER HYDROLASE 17-MAR-09 2RQB TITLE SOLUTION STRUCTURE OF MDA5 CTD COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTERFERON-INDUCED HELICASE C DOMAIN-CONTAINING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 896-1025; COMPND 5 SYNONYM: INTERFERON-INDUCED WITH HELICASE C DOMAIN PROTEIN 1, COMPND 6 HELICASE WITH 2 CARD DOMAINS, HELICARD, MELANOMA DIFFERENTIATION- COMPND 7 ASSOCIATED PROTEIN 5, MDA-5, RNA HELICASE-DEAD BOX PROTEIN 116, COMPND 8 MURABUTIDE DOWN-REGULATED PROTEIN; COMPND 9 EC: 3.6.1.-; COMPND 10 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: IFIH1, MDA5, RH116; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-1 KEYWDS RNA BINDING PROTEIN, HYDROLASE, ALTERNATIVE SPLICING, ANTIVIRAL KEYWDS 2 DEFENSE, ATP-BINDING, CYTOPLASM, DIABETES MELLITUS, HELICASE, HOST- KEYWDS 3 VIRUS INTERACTION, IMMUNE RESPONSE, INNATE IMMUNITY, NUCLEOTIDE- KEYWDS 4 BINDING, NUCLEUS, PHOSPHOPROTEIN, POLYMORPHISM, RNA-BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.TAKAHASI,H.KUMETA,N.TSUDUKI,R.NARITA,T.SHIGEMOTO,R.HIRAI, AUTHOR 2 M.YONEYAMA,M.HORIUCHI,K.OGURA,T.FUJITA,I.FUYUHIKO REVDAT 4 30-OCT-24 2RQB 1 REMARK REVDAT 3 16-MAR-22 2RQB 1 REMARK SEQADV REVDAT 2 07-JUL-09 2RQB 1 JRNL REVDAT 1 05-MAY-09 2RQB 0 JRNL AUTH K.TAKAHASI,H.KUMETA,N.TSUDUKI,R.NARITA,T.SHIGEMOTO,R.HIRAI, JRNL AUTH 2 M.YONEYAMA,M.HORIUCHI,K.OGURA,T.FUJITA,F.INAGAKI JRNL TITL SOLUTION STRUCTURES OF CYTOSOLIC RNA SENSOR MDA5 AND LGP2 JRNL TITL 2 C-TERMINAL DOMAINS: IDENTIFICATION OF THE RNA RECOGNITION JRNL TITL 3 LOOP IN RIG-I-LIKE RECEPTORS JRNL REF J.BIOL.CHEM. V. 284 17465 2009 JRNL REFN ISSN 0021-9258 JRNL PMID 19380577 JRNL DOI 10.1074/JBC.M109.007179 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA, CYANA REMARK 3 AUTHORS : GUNTERT, MUMENTHALER, WUTHRICH (CYANA), GUNTERT, REMARK 3 MUMENTHALER, WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2RQB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000150157. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 0.25 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM [U-100% 13C; U-100% 15N] REMARK 210 MDA5, 20MM BIS-TRIS-2, 250MM REMARK 210 SODIUM CHLORIDE-3, 10MM DTT-4, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCA(CO)NH; 3D C(CO)NH; 3D REMARK 210 HNCO; 3D HNCA; 3D HNCACB; 3D REMARK 210 HBHA(CO)NH; 3D HN(CO)CA; 3D REMARK 210 H(CCO)NH; 3D HCCH-TOCSY; 3D HNHA; REMARK 210 3D 1H-15N NOESY; 3D 1H-15N REMARK 210 TOCSY; 3D HN(COCA)CB REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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 SER A 895 -73.98 -118.16 REMARK 500 1 CYS A 910 -101.12 -99.14 REMARK 500 1 SER A 911 42.89 154.56 REMARK 500 1 ASP A 919 30.62 -93.06 REMARK 500 1 MET A 931 46.92 -83.27 REMARK 500 1 LEU A 947 -76.50 -104.13 REMARK 500 1 LYS A 950 -75.44 -76.75 REMARK 500 1 CYS A 951 95.66 -55.88 REMARK 500 1 ALA A 952 -177.89 -176.27 REMARK 500 1 CYS A 962 -174.57 -62.88 REMARK 500 1 ALA A 967 97.58 -50.44 REMARK 500 1 SER A 995 90.57 -69.97 REMARK 500 1 PRO A1011 -165.04 -75.00 REMARK 500 1 PHE A1021 -30.42 -38.00 REMARK 500 1 SER A1022 106.75 -40.80 REMARK 500 2 SER A 895 46.88 -98.17 REMARK 500 2 ASN A 898 45.11 -91.10 REMARK 500 2 CYS A 910 -101.99 -99.90 REMARK 500 2 SER A 911 42.63 155.83 REMARK 500 2 LYS A 925 28.39 43.05 REMARK 500 2 MET A 931 46.58 -84.19 REMARK 500 2 LYS A 950 -79.77 -100.76 REMARK 500 2 CYS A 951 95.43 -49.81 REMARK 500 2 ALA A 952 -177.23 -176.07 REMARK 500 2 CYS A 962 -174.46 -61.90 REMARK 500 2 ALA A 967 99.10 -51.03 REMARK 500 2 SER A 995 91.76 -64.58 REMARK 500 2 PRO A1011 -165.70 -74.97 REMARK 500 2 SER A1022 46.50 -88.15 REMARK 500 2 GLU A1024 170.62 -57.29 REMARK 500 3 SER A 895 -176.53 -170.91 REMARK 500 3 TYR A 896 -174.57 -52.10 REMARK 500 3 CYS A 910 -101.33 -98.87 REMARK 500 3 SER A 911 42.06 154.08 REMARK 500 3 ASP A 919 31.41 -93.98 REMARK 500 3 LYS A 925 27.85 46.50 REMARK 500 3 MET A 931 47.53 -82.50 REMARK 500 3 GLU A 943 104.61 -46.56 REMARK 500 3 LYS A 950 -78.70 -97.17 REMARK 500 3 CYS A 951 95.78 -49.29 REMARK 500 3 ALA A 952 -178.89 -176.27 REMARK 500 3 CYS A 962 -174.54 -67.65 REMARK 500 3 ALA A 967 95.13 -54.43 REMARK 500 3 PRO A1011 -169.64 -75.04 REMARK 500 3 LEU A1020 -72.47 -82.26 REMARK 500 3 GLU A1024 176.86 -48.37 REMARK 500 4 CYS A 910 -100.60 -97.41 REMARK 500 4 SER A 911 42.47 153.93 REMARK 500 4 ASP A 919 31.28 -92.85 REMARK 500 4 GLU A 924 29.56 40.94 REMARK 500 REMARK 500 THIS ENTRY HAS 315 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 ZN A1026 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 907 SG REMARK 620 2 CYS A 910 SG 131.9 REMARK 620 3 CYS A 962 SG 74.6 152.4 REMARK 620 4 CYS A 964 SG 170.2 49.7 102.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1026 DBREF 2RQB A 896 1025 UNP Q9BYX4 IFIH1_HUMAN 896 1025 SEQADV 2RQB GLY A 891 UNP Q9BYX4 EXPRESSION TAG SEQADV 2RQB PRO A 892 UNP Q9BYX4 EXPRESSION TAG SEQADV 2RQB LEU A 893 UNP Q9BYX4 EXPRESSION TAG SEQADV 2RQB GLY A 894 UNP Q9BYX4 EXPRESSION TAG SEQADV 2RQB SER A 895 UNP Q9BYX4 EXPRESSION TAG SEQRES 1 A 135 GLY PRO LEU GLY SER TYR LYS ASN ASN PRO SER LEU ILE SEQRES 2 A 135 THR PHE LEU CYS LYS ASN CYS SER VAL LEU ALA CYS SER SEQRES 3 A 135 GLY GLU ASP ILE HIS VAL ILE GLU LYS MET HIS HIS VAL SEQRES 4 A 135 ASN MET THR PRO GLU PHE LYS GLU LEU TYR ILE VAL ARG SEQRES 5 A 135 GLU ASN LYS ALA LEU GLN LYS LYS CYS ALA ASP TYR GLN SEQRES 6 A 135 ILE ASN GLY GLU ILE ILE CYS LYS CYS GLY GLN ALA TRP SEQRES 7 A 135 GLY THR MET MET VAL HIS LYS GLY LEU ASP LEU PRO CYS SEQRES 8 A 135 LEU LYS ILE ARG ASN PHE VAL VAL VAL PHE LYS ASN ASN SEQRES 9 A 135 SER THR LYS LYS GLN TYR LYS LYS TRP VAL GLU LEU PRO SEQRES 10 A 135 ILE THR PHE PRO ASN LEU ASP TYR SER GLU CYS CYS LEU SEQRES 11 A 135 PHE SER ASP GLU ASP HET ZN A1026 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 PRO A 933 LEU A 938 5 6 HELIX 2 2 LYS A 1002 LEU A 1006 5 5 HELIX 3 3 ASP A 1014 CYS A 1018 5 5 SHEET 1 A 4 CYS A 915 SER A 916 0 SHEET 2 A 4 ILE A 903 CYS A 907 -1 N PHE A 905 O CYS A 915 SHEET 3 A 4 PHE A 987 PHE A 991 -1 O VAL A 988 N LEU A 906 SHEET 4 A 4 THR A 996 LYS A 998 -1 O LYS A 998 N VAL A 989 SHEET 1 B 2 HIS A 921 ILE A 923 0 SHEET 2 B 2 HIS A 927 VAL A 929 -1 N HIS A 927 O ILE A 923 SHEET 1 C 2 ILE A 940 ARG A 942 0 SHEET 2 C 2 GLU A 959 ILE A 961 -1 O ILE A 961 N ILE A 940 SHEET 1 D 3 GLN A 955 ILE A 956 0 SHEET 2 D 3 GLY A 969 VAL A 973 -1 O VAL A 973 N GLN A 955 SHEET 3 D 3 LEU A 979 LEU A 982 -1 O CYS A 981 N THR A 970 SSBOND 1 CYS A 910 CYS A 964 1555 1555 2.04 LINK SG CYS A 907 ZN ZN A1026 1555 1555 2.73 LINK SG CYS A 910 ZN ZN A1026 1555 1555 2.46 LINK SG CYS A 962 ZN ZN A1026 1555 1555 2.45 LINK SG CYS A 964 ZN ZN A1026 1555 1555 2.39 SITE 1 AC1 4 CYS A 907 CYS A 910 CYS A 962 CYS A 964 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