HEADER NUCLEIC ACID BINDING PROTEIN/RNA 22-APR-04 1T2R TITLE STRUCTURAL BASIS FOR 3' END RECOGNITION OF NUCLEIC ACIDS BY THE TITLE 2 DROSOPHILA ARGONAUTE 2 PAZ DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-R(*CP*UP*CP*AP*C)-3'; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ARGONAUTE 2; COMPND 7 CHAIN: A; COMPND 8 FRAGMENT: PAZ DOMAIN, RESIDUES 605-723; COMPND 9 SYNONYM: CG7439 PROTEIN; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 5 ORGANISM_COMMON: FRUIT FLY; SOURCE 6 ORGANISM_TAXID: 7227; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PETM60 KEYWDS NUCLEIC ACID BINDING PROTEIN, RNA, NUCLEIC ACID BINDING PROTEIN-RNA KEYWDS 2 COMPLEX EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR A.LINGEL,B.SIMON,E.IZAURRALDE,M.SATTLER REVDAT 3 02-MAR-22 1T2R 1 REMARK SEQADV REVDAT 2 24-FEB-09 1T2R 1 VERSN REVDAT 1 01-JUN-04 1T2R 0 JRNL AUTH A.LINGEL,B.SIMON,E.IZAURRALDE,M.SATTLER JRNL TITL NUCLEIC ACID 3'-END RECOGNITION BY THE ARGONAUTE2 PAZ JRNL TITL 2 DOMAIN. JRNL REF NAT.STRUCT.MOL.BIOL. V. 11 576 2004 JRNL REFN ISSN 1545-9993 JRNL PMID 15156196 JRNL DOI 10.1038/NSMB777 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.LINGEL,B.SIMON,E.IZAURRALDE,M.SATTLER REMARK 1 TITL STRUCTURE AND NUCLEIC-ACID BINDING OF THE DROSOPHILA REMARK 1 TITL 2 ARGONAUTE 2 PAZ DOMAIN REMARK 1 REF NATURE V. 426 465 2003 REMARK 1 REFN ISSN 0028-0836 REMARK 1 DOI 10.1038/NATURE02123 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : NILGES, BRUNGER ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE EXPERIMENTALLY DETERMINED DISTANCE RESTRAINTS WERE APPLIED IN REMARK 3 A MIXED TORSION AND CARTESIA DY REMARK 3 NAMICS SIMULATED ANNEALING PROTOCOL. THE FINAL STRUCTURE ENSEMBLE REMARK 3 WAS REFINED IN A SHELL OF WATER REMARK 3 MOLECULES. REMARK 4 REMARK 4 1T2R COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-APR-04. REMARK 100 THE DEPOSITION ID IS D_1000022238. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 295 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.2-1.0 MM 15N OR 15N,13C REMARK 210 -LABELED PROTEIN, 0.1-2.5 MM REMARK 210 UNLABELED DNA, 50 MM SODIUM REMARK 210 PHOSPHATE BUFFER, 0.2 MM DTT REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : TRIPLE RESONANCE; NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEW, ARIA/CNS REMARK 210 METHOD USED : MOLECULAR DYNAMICS SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 150 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST ENERGIES 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-10 REMARK 465 RES C SSSEQI REMARK 465 C B 201 REMARK 465 U B 202 REMARK 465 C B 203 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 O3' C B 205 H LEU A 110 1.52 REMARK 500 OE1 GLU A 34 HH12 ARG A 64 1.60 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 5 TYR A 90 CE1 TYR A 90 CZ 0.175 REMARK 500 5 TYR A 90 CZ TYR A 90 CE2 -0.182 REMARK 500 9 TYR A 90 CE1 TYR A 90 CZ 0.092 REMARK 500 9 TYR A 90 CZ TYR A 90 CE2 -0.092 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 MET A 3 44.07 -85.02 REMARK 500 1 ARG A 38 86.65 -69.50 REMARK 500 1 VAL A 102 -166.34 -115.70 REMARK 500 2 VAL A 102 -162.38 -116.75 REMARK 500 3 ARG A 38 94.59 -66.91 REMARK 500 3 VAL A 102 -168.96 -123.52 REMARK 500 4 ALA A 18 -151.21 -148.37 REMARK 500 4 VAL A 102 -166.00 -113.69 REMARK 500 5 MET A 3 30.16 -140.59 REMARK 500 5 ALA A 18 -159.73 -114.80 REMARK 500 5 VAL A 102 -165.10 -126.92 REMARK 500 6 VAL A 102 -166.23 -124.87 REMARK 500 7 MET A 3 40.18 -101.73 REMARK 500 7 ARG A 38 99.62 -67.37 REMARK 500 7 HIS A 98 108.82 62.54 REMARK 500 8 ARG A 38 99.25 -66.61 REMARK 500 8 VAL A 102 -162.40 -107.42 REMARK 500 10 ARG A 38 93.81 -66.75 REMARK 500 10 VAL A 102 -164.19 -127.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1T2S RELATED DB: PDB REMARK 900 RELATED ID: 1UPO RELATED DB: PDB DBREF 1T2R A 5 123 UNP Q9VUQ5 AGO2_DROME 605 723 DBREF 1T2R B 201 205 PDB 1T2R 1T2R 201 205 SEQADV 1T2R GLY A 1 UNP Q9VUQ5 CLONING ARTIFACT SEQADV 1T2R ALA A 2 UNP Q9VUQ5 CLONING ARTIFACT SEQADV 1T2R MET A 3 UNP Q9VUQ5 CLONING ARTIFACT SEQADV 1T2R ALA A 4 UNP Q9VUQ5 CLONING ARTIFACT SEQRES 1 B 5 C U C A C SEQRES 1 A 123 GLY ALA MET ALA MET PRO MET ILE GLU TYR LEU GLU ARG SEQRES 2 A 123 PHE SER LEU LYS ALA LYS ILE ASN ASN THR THR ASN LEU SEQRES 3 A 123 ASP TYR SER ARG ARG PHE LEU GLU PRO PHE LEU ARG GLY SEQRES 4 A 123 ILE ASN VAL VAL TYR THR PRO PRO GLN SER PHE GLN SER SEQRES 5 A 123 ALA PRO ARG VAL TYR ARG VAL ASN GLY LEU SER ARG ALA SEQRES 6 A 123 PRO ALA SER SER GLU THR PHE GLU HIS ASP GLY LYS LYS SEQRES 7 A 123 VAL THR ILE ALA SER TYR PHE HIS SER ARG ASN TYR PRO SEQRES 8 A 123 LEU LYS PHE PRO GLN LEU HIS CYS LEU ASN VAL GLY SER SEQRES 9 A 123 SER ILE LYS SER ILE LEU LEU PRO ILE GLU LEU CYS SER SEQRES 10 A 123 ILE GLU GLU GLY GLN ALA HELIX 1 1 MET A 7 SER A 15 1 9 HELIX 2 2 LEU A 26 ARG A 31 1 6 HELIX 3 3 LEU A 33 ARG A 38 1 6 HELIX 4 4 PRO A 47 GLN A 51 5 5 HELIX 5 5 PRO A 66 SER A 69 5 4 HELIX 6 6 ILE A 81 ARG A 88 1 8 HELIX 7 7 PRO A 112 GLU A 114 5 3 SHEET 1 A 4 ALA A 4 PRO A 6 0 SHEET 2 A 4 CYS A 116 GLU A 119 -1 O ILE A 118 N MET A 5 SHEET 3 A 4 ILE A 40 TYR A 44 -1 N VAL A 43 O SER A 117 SHEET 4 A 4 ARG A 55 VAL A 59 -1 O ARG A 55 N TYR A 44 SHEET 1 B 3 GLY A 61 LEU A 62 0 SHEET 2 B 3 LEU A 100 GLY A 103 -1 O ASN A 101 N GLY A 61 SHEET 3 B 3 SER A 108 LEU A 111 -1 O LEU A 111 N LEU A 100 SHEET 1 C 2 THR A 71 HIS A 74 0 SHEET 2 C 2 LYS A 77 THR A 80 -1 O VAL A 79 N PHE A 72 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