HEADER HYDROLASE 17-MAR-09 2RQA TITLE SOLUTION STRUCTURE OF LGP2 CTD COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-DEPENDENT RNA HELICASE DHX58; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 546-678; COMPND 5 SYNONYM: ATP-DEPENDENT HELICASE LGP2, PROTEIN D11LGP2 HOMOLOG; COMPND 6 EC: 3.6.1.-; 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: DHX58, D11LGP2E, LGP2; 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, ATP-BINDING, COILED COIL, CYTOPLASM, HELICASE, KEYWDS 2 HYDROLASE, IMMUNE RESPONSE, INNATE IMMUNITY, NUCLEOTIDE-BINDING, KEYWDS 3 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 20-NOV-24 2RQA 1 REMARK REVDAT 3 16-MAR-22 2RQA 1 REMARK SEQADV REVDAT 2 07-JUL-09 2RQA 1 JRNL REVDAT 1 05-MAY-09 2RQA 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 2RQA 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_1000150156. 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 LGP2, 50MM TRIS-2, 250MM SODIUM REMARK 210 CHLORIDE-3, 1MM DTT-4, 90% H2O/ REMARK 210 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: 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: 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 PRO A 543 -166.02 -75.01 REMARK 500 1 MET A 545 95.91 -37.80 REMARK 500 1 ILE A 557 -33.86 -35.58 REMARK 500 1 MET A 560 49.26 76.92 REMARK 500 1 ALA A 562 104.32 83.26 REMARK 500 1 ASN A 581 129.84 179.51 REMARK 500 1 SER A 591 174.57 -56.06 REMARK 500 1 ASP A 593 152.95 -44.93 REMARK 500 1 PRO A 594 -89.64 -74.99 REMARK 500 1 CYS A 615 -74.03 -124.29 REMARK 500 1 GLU A 617 102.65 -42.73 REMARK 500 1 SER A 627 40.62 85.11 REMARK 500 1 VAL A 655 128.83 -39.94 REMARK 500 1 ASP A 663 93.52 -69.99 REMARK 500 2 PRO A 543 -165.16 -75.02 REMARK 500 2 MET A 545 74.84 -110.97 REMARK 500 2 ILE A 557 -37.54 -32.21 REMARK 500 2 CYS A 559 -70.35 -73.80 REMARK 500 2 MET A 560 43.92 78.17 REMARK 500 2 ALA A 562 108.72 65.91 REMARK 500 2 THR A 575 -71.59 -131.35 REMARK 500 2 ASN A 581 128.72 178.81 REMARK 500 2 PRO A 594 -89.56 -75.03 REMARK 500 2 CYS A 615 -74.33 -129.80 REMARK 500 2 GLU A 617 103.37 -42.50 REMARK 500 2 SER A 627 40.39 81.33 REMARK 500 2 ARG A 646 155.15 -39.55 REMARK 500 3 ILE A 557 -33.92 -35.67 REMARK 500 3 CYS A 559 -70.31 -74.03 REMARK 500 3 MET A 560 48.35 77.31 REMARK 500 3 ALA A 562 102.35 82.46 REMARK 500 3 GLU A 573 24.11 46.86 REMARK 500 3 THR A 575 -76.51 -36.23 REMARK 500 3 ASN A 581 141.28 176.49 REMARK 500 3 PRO A 594 -89.71 -74.90 REMARK 500 3 ASN A 598 -64.64 -91.29 REMARK 500 3 LYS A 602 -62.00 -108.99 REMARK 500 3 CYS A 615 -75.02 -125.35 REMARK 500 3 GLU A 617 102.37 -42.78 REMARK 500 3 SER A 627 39.67 86.02 REMARK 500 4 MET A 545 68.06 -101.49 REMARK 500 4 ILE A 557 -35.62 -34.40 REMARK 500 4 CYS A 559 -71.61 -71.01 REMARK 500 4 MET A 560 42.15 77.36 REMARK 500 4 ALA A 562 100.61 84.09 REMARK 500 4 ASN A 581 130.74 173.35 REMARK 500 4 PRO A 594 -76.71 -75.01 REMARK 500 4 LYS A 602 -62.84 -105.94 REMARK 500 4 CYS A 615 -75.54 -123.22 REMARK 500 4 GLU A 617 102.58 -42.61 REMARK 500 REMARK 500 THIS ENTRY HAS 277 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 A 679 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 556 SG REMARK 620 2 CYS A 559 SG 90.1 REMARK 620 3 CYS A 612 SG 87.2 101.1 REMARK 620 4 CYS A 615 SG 92.1 19.7 120.8 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 679 DBREF 2RQA A 546 678 UNP Q96C10 DHX58_HUMAN 546 678 SEQADV 2RQA GLY A 542 UNP Q96C10 EXPRESSION TAG SEQADV 2RQA PRO A 543 UNP Q96C10 EXPRESSION TAG SEQADV 2RQA HIS A 544 UNP Q96C10 EXPRESSION TAG SEQADV 2RQA MET A 545 UNP Q96C10 EXPRESSION TAG SEQRES 1 A 137 GLY PRO HIS MET GLN PHE PRO VAL GLU HIS VAL GLN LEU SEQRES 2 A 137 LEU CYS ILE ASN CYS MET VAL ALA VAL GLY HIS GLY SER SEQRES 3 A 137 ASP LEU ARG LYS VAL GLU GLY THR HIS HIS VAL ASN VAL SEQRES 4 A 137 ASN PRO ASN PHE SER ASN TYR TYR ASN VAL SER ARG ASP SEQRES 5 A 137 PRO VAL VAL ILE ASN LYS VAL PHE LYS ASP TRP LYS PRO SEQRES 6 A 137 GLY GLY VAL ILE SER CYS ARG ASN CYS GLY GLU VAL TRP SEQRES 7 A 137 GLY LEU GLN MET ILE TYR LYS SER VAL LYS LEU PRO VAL SEQRES 8 A 137 LEU LYS VAL ARG SER MET LEU LEU GLU THR PRO GLN GLY SEQRES 9 A 137 ARG ILE GLN ALA LYS LYS TRP SER ARG VAL PRO PHE SER SEQRES 10 A 137 VAL PRO ASP PHE ASP PHE LEU GLN HIS CYS ALA GLU ASN SEQRES 11 A 137 LEU SER ASP LEU SER LEU ASP HET ZN A 679 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 PRO A 582 TYR A 587 5 6 HELIX 2 2 ASP A 663 LEU A 672 1 10 SHEET 1 A 3 GLY A 564 HIS A 565 0 SHEET 2 A 3 GLN A 553 CYS A 556 -1 N LEU A 554 O GLY A 564 SHEET 3 A 3 MET A 638 GLU A 641 -1 O LEU A 639 N LEU A 555 SHEET 1 B 2 LEU A 569 VAL A 572 0 SHEET 2 B 2 HIS A 576 ASN A 579 -1 O VAL A 578 N ARG A 570 SHEET 1 C 3 LYS A 605 PRO A 606 0 SHEET 2 C 3 LEU A 621 ILE A 624 -1 O ILE A 624 N LYS A 605 SHEET 3 C 3 LYS A 629 VAL A 632 -1 O LEU A 630 N MET A 623 SSBOND 1 CYS A 559 CYS A 615 1555 1555 0.80 LINK SG CYS A 556 ZN ZN A 679 1555 1555 2.73 LINK SG CYS A 559 ZN ZN A 679 1555 1555 2.35 LINK SG CYS A 612 ZN ZN A 679 1555 1555 2.34 LINK SG CYS A 615 ZN ZN A 679 1555 1555 2.34 SITE 1 AC1 5 CYS A 556 CYS A 559 CYS A 612 CYS A 615 SITE 2 AC1 5 GLY A 616 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