HEADER TRANSCRIPTION 11-APR-14 4CYK TITLE STRUCTURAL BASIS FOR BINDING OF PAN3 TO PAN2 AND ITS FUNCTION IN MRNA TITLE 2 RECRUITMENT AND DEADENYLATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: PAB-DEPENDENT POLY(A)-SPECIFIC RIBONUCLEASE SUBUNIT PAN3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-41; COMPND 5 SYNONYM: PAB1P-DEPENDENT POLY(A)-NUCLEASE, PAN3P; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI B41; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 869694; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PRSETA; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PHLTV KEYWDS TRANSCRIPTION, PAN3P, PAN2P, POLYA, RNA, DEADENYLATION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.WOLF,E.VALKOV,M.D.ALLEN,B.MEINEKE,Y.GORDIYENKO,S.H.MCLAUGHLIN, AUTHOR 2 T.M.OLSEN,C.V.ROBINSON,M.BYCROFT,M.STEWART,L.A.PASSMORE REVDAT 7 23-JUN-21 4CYK 1 REMARK LINK REVDAT 6 27-APR-16 4CYK 1 ATOM TER HETATM CONECT REVDAT 6 2 1 MASTER REVDAT 5 30-JUL-14 4CYK 1 JRNL REVDAT 4 11-JUN-14 4CYK 1 JRNL REVDAT 3 04-JUN-14 4CYK 1 ATOM REVDAT 2 28-MAY-14 4CYK 1 ATOM REVDAT 1 21-MAY-14 4CYK 0 JRNL AUTH J.WOLF,E.VALKOV,M.D.ALLEN,B.MEINEKE,Y.GORDIYENKO, JRNL AUTH 2 S.H.MCLAUGHLIN,T.M.OLSEN,C.V.ROBINSON,M.BYCROFT,M.STEWART, JRNL AUTH 3 L.A.PASSMORE JRNL TITL STRUCTURAL BASIS FOR PAN3 BINDING TO PAN2 AND ITS FUNCTION JRNL TITL 2 IN MRNA RECRUITMENT AND DEADENYLATION. JRNL REF EMBO J. V. 33 1514 2014 JRNL REFN ISSN 0261-4189 JRNL PMID 24872509 JRNL DOI 10.15252/EMBJ.201488373 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE, REMARK 3 SIMONSON,WARREN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT DETAILS CAN BE FOUND IN THE REMARK 3 JRNL CITATION ABOVE. REMARK 4 REMARK 4 4CYK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-APR-14. REMARK 100 THE DEPOSITION ID IS D_1290060303. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.0 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 90% WATER / 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CNS REMARK 210 METHOD USED : CNS 1.2 REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 20 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : NO VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING HOMONUCLEAR AND TRIPLE REMARK 210 -RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED PROTEIN 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 PHE A 32 154.06 107.50 REMARK 500 2 ASP A 2 -70.68 -124.40 REMARK 500 2 PHE A 32 155.13 107.38 REMARK 500 2 THR A 38 153.45 61.21 REMARK 500 2 THR A 39 102.98 61.09 REMARK 500 3 ASP A 2 41.56 -104.22 REMARK 500 3 LYS A 3 90.55 -59.14 REMARK 500 3 PHE A 32 154.65 108.53 REMARK 500 3 ASP A 36 176.14 59.49 REMARK 500 3 ASN A 37 -48.00 -143.64 REMARK 500 4 PHE A 32 154.28 105.68 REMARK 500 4 ASP A 36 33.28 -98.12 REMARK 500 5 PHE A 32 155.61 107.81 REMARK 500 5 ASP A 36 161.80 59.98 REMARK 500 5 THR A 38 32.49 -98.21 REMARK 500 6 ASP A 2 -43.89 -165.96 REMARK 500 6 PHE A 32 153.80 108.33 REMARK 500 7 PHE A 32 157.20 106.56 REMARK 500 7 HIS A 34 79.08 -105.13 REMARK 500 8 ASP A 2 -40.07 -175.56 REMARK 500 8 PHE A 32 153.73 106.89 REMARK 500 8 ASN A 37 101.49 -56.98 REMARK 500 8 THR A 38 78.94 -163.88 REMARK 500 8 ALA A 40 81.90 59.78 REMARK 500 9 PHE A 32 154.37 109.06 REMARK 500 9 ASP A 36 -175.77 -62.08 REMARK 500 9 ALA A 40 31.19 -153.24 REMARK 500 10 ASP A 2 -77.98 -80.40 REMARK 500 10 PHE A 32 156.10 107.51 REMARK 500 10 THR A 39 -67.69 -140.93 REMARK 500 11 PHE A 32 154.08 107.48 REMARK 500 11 ASP A 36 -48.85 -130.66 REMARK 500 12 PHE A 32 154.60 108.97 REMARK 500 12 THR A 39 37.59 -97.89 REMARK 500 13 PHE A 32 154.29 106.55 REMARK 500 13 THR A 38 86.28 -65.11 REMARK 500 13 ALA A 40 -70.90 -158.92 REMARK 500 14 ASP A 2 -46.88 -142.19 REMARK 500 14 PHE A 32 156.90 108.01 REMARK 500 14 HIS A 34 78.81 -101.63 REMARK 500 14 ASN A 37 121.17 62.39 REMARK 500 15 PHE A 32 154.53 107.77 REMARK 500 15 ALA A 40 95.22 67.84 REMARK 500 16 ASP A 2 -47.58 -137.81 REMARK 500 16 PHE A 32 153.02 109.45 REMARK 500 16 ASN A 37 58.98 -152.30 REMARK 500 17 PHE A 32 153.80 107.31 REMARK 500 17 ASP A 36 162.18 61.43 REMARK 500 17 ASN A 37 154.14 61.39 REMARK 500 17 THR A 38 -67.18 -158.33 REMARK 500 REMARK 500 THIS ENTRY HAS 59 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 42 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 14 SG REMARK 620 2 CYS A 23 SG 117.7 REMARK 620 3 CYS A 30 SG 115.3 109.5 REMARK 620 4 HIS A 34 NE2 94.4 101.7 117.0 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 42 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 19959 RELATED DB: BMRB DBREF 4CYK A 1 41 UNP P36102 PAN3_YEAST 1 41 SEQRES 1 A 41 MET ASP LYS ILE ASN PRO ASP TRP ALA LYS ASP ILE PRO SEQRES 2 A 41 CYS ARG ASN ILE THR ILE TYR GLY TYR CYS LYS LYS GLU SEQRES 3 A 41 LYS GLU GLY CYS PRO PHE LYS HIS SER ASP ASN THR THR SEQRES 4 A 41 ALA THR HET ZN A 42 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ HELIX 1 1 ASN A 5 LYS A 10 1 6 HELIX 2 2 CYS A 14 TYR A 20 1 7 HELIX 3 3 CYS A 23 GLU A 28 5 6 LINK SG CYS A 14 ZN ZN A 42 1555 1555 2.35 LINK SG CYS A 23 ZN ZN A 42 1555 1555 2.29 LINK SG CYS A 30 ZN ZN A 42 1555 1555 2.28 LINK NE2 HIS A 34 ZN ZN A 42 1555 1555 2.03 SITE 1 AC1 4 CYS A 14 CYS A 23 CYS A 30 HIS A 34 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