HEADER RNA BINDING PROTEIN 16-JAN-13 3ZJ2 TITLE STRUCTURE OF NAB2P TANDEM ZINC FINGER 34 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEAR POLYADENYLATED RNA-BINDING PROTEIN NAB2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ZINC FINGERS 3 AND 4, RESIDUES 333-401; COMPND 5 SYNONYM: NAB2P; 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; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET28 KEYWDS RNA BINDING PROTEIN, CCCH-TYPE ZINC FINGER, MRNA EXPORT, POLY(A) KEYWDS 2 LENGTH CONTROL, POLYADENOSINE RNA BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.MARTINEZ-LUMBRERAS,C.M.SANTIVERI,Y.MIRASSOU,S.ZORRILLA, AUTHOR 2 J.M.PEREZ- CANADILLAS REVDAT 3 09-JUL-14 3ZJ2 1 AUTHOR JRNL REVDAT 2 30-OCT-13 3ZJ2 1 JRNL REVDAT 1 11-SEP-13 3ZJ2 0 JRNL AUTH S.MARTINEZ-LUMBRERAS,C.M.SANTIVERI,Y.MIRASSOU,S.ZORRILLA, JRNL AUTH 2 J.M.PEREZ-CANADILLAS JRNL TITL TWO SINGULAR TYPES OF CCCH TANDEM ZINC FINGER IN NAB2P JRNL TITL 2 CONTRIBUTE TO POLYADENOSINE RNA RECOGNITION. JRNL REF STRUCTURE V. 21 1800 2013 JRNL REFN ISSN 0969-2126 JRNL PMID 23994011 JRNL DOI 10.1016/J.STR.2013.07.019 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 7.0 REMARK 3 AUTHORS : CASE, D.A. ET AL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT PROTOCOL AS DESCRIBED IN THE REMARK 3 PRIMARY CITATION REMARK 4 REMARK 4 3ZJ2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-JUL-13. REMARK 100 THE PDBE ID CODE IS EBI-55434. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298.0 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 25MM REMARK 210 PRESSURE : 1.0 ATM REMARK 210 SAMPLE CONTENTS : 90% H2O/10% D2O, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 1H-15N HSQC, 1H-15N HMBC, 1H-13C REMARK 210 HSQC, HNCO, HN(CA) CO, HNCA, REMARK 210 HNCACB, CBCA(CO) HN, H(C)CH- REMARK 210 TOCSY, (H)CCH- TOCSY, (HB) REMARK 210 CB(CGCD) HD ARO, (HB)CB(CGCDCE)HE REMARK 210 ARO, 15N HSQC-NOESY, NOESY AND REMARK 210 TOCSY, (H)CCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ, 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, ANALYSIS, CYANA, AMBER REMARK 210 METHOD USED : CYANA, AMBER REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : LOWEST TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NONE 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: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 3 ARG A 383 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 7 ARG A 383 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES 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 GLN A 334 25.12 -79.55 REMARK 500 1 ASN A 360 115.02 -171.34 REMARK 500 1 ASN A 374 -112.29 40.99 REMARK 500 1 ARG A 383 32.04 -143.90 REMARK 500 1 SER A 387 -178.37 -68.86 REMARK 500 1 GLU A 394 86.94 -170.86 REMARK 500 1 VAL A 395 20.93 -75.70 REMARK 500 1 SER A 399 -39.14 73.95 REMARK 500 2 ASN A 360 111.39 -166.44 REMARK 500 2 LEU A 368 68.12 -100.04 REMARK 500 2 ASN A 374 -121.68 51.49 REMARK 500 2 ARG A 383 43.12 -146.59 REMARK 500 2 GLU A 394 89.15 -169.02 REMARK 500 3 ASN A 360 98.88 -164.23 REMARK 500 3 LEU A 368 49.84 -93.99 REMARK 500 3 ASN A 374 -112.27 47.57 REMARK 500 3 ARG A 383 50.71 -146.17 REMARK 500 3 LYS A 393 -71.83 -83.85 REMARK 500 3 GLU A 394 21.20 -161.14 REMARK 500 3 ILE A 398 19.76 58.40 REMARK 500 3 GLN A 400 152.27 64.55 REMARK 500 4 ASN A 360 110.71 -167.55 REMARK 500 4 LEU A 368 58.55 -107.51 REMARK 500 4 ASN A 374 -109.41 44.38 REMARK 500 4 ARG A 383 35.47 -141.69 REMARK 500 4 GLU A 394 71.56 -155.74 REMARK 500 4 LYS A 396 129.94 69.29 REMARK 500 5 GLN A 334 23.39 -146.80 REMARK 500 5 ASN A 360 117.55 -172.83 REMARK 500 5 LEU A 368 70.75 -100.70 REMARK 500 5 ASN A 374 -117.96 48.26 REMARK 500 5 GLU A 394 42.83 -155.62 REMARK 500 6 SER A 332 -169.57 -164.08 REMARK 500 6 ASN A 360 115.46 -169.48 REMARK 500 6 LEU A 368 47.29 -107.57 REMARK 500 6 ASN A 374 -118.95 50.71 REMARK 500 6 ARG A 383 33.49 -141.69 REMARK 500 6 GLU A 394 87.26 -169.29 REMARK 500 7 LYS A 341 -19.15 57.90 REMARK 500 7 ASN A 360 108.70 -165.98 REMARK 500 7 ASN A 374 -112.93 49.33 REMARK 500 7 ARG A 383 41.91 -147.66 REMARK 500 7 LYS A 393 -60.58 -90.10 REMARK 500 7 GLU A 394 75.73 -169.64 REMARK 500 8 VAL A 333 18.30 -145.67 REMARK 500 8 ASN A 360 103.95 -167.09 REMARK 500 8 LEU A 368 71.48 -101.11 REMARK 500 8 ASN A 374 -118.51 51.72 REMARK 500 8 ARG A 383 38.96 -150.01 REMARK 500 8 LYS A 396 64.90 39.62 REMARK 500 REMARK 500 THIS ENTRY HAS 141 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 383 0.10 SIDE CHAIN 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 1 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 355 NE2 REMARK 620 2 CYS A 340 SG 103.8 REMARK 620 3 CYS A 351 SG 101.6 115.4 REMARK 620 4 CYS A 346 SG 105.4 111.7 116.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 ZN A 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 371 SG REMARK 620 2 CYS A 382 SG 110.5 REMARK 620 3 CYS A 377 SG 112.4 113.4 REMARK 620 4 HIS A 386 NE2 102.8 103.7 113.3 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ZJ1 RELATED DB: PDB REMARK 900 STRUCTURE OF NAB2P TANDEM ZINC FINGER 12 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE TWO N-TERMINAL RESIDUES (GS) ARE NOT FROM WILD TYPE REMARK 999 SEQUENCE DBREF 3ZJ2 A 333 401 UNP P32505 NAB2_YEAST 333 401 SEQADV 3ZJ2 GLY A 331 UNP P32505 EXPRESSION TAG SEQADV 3ZJ2 SER A 332 UNP P32505 EXPRESSION TAG SEQRES 1 A 71 GLY SER VAL GLN THR GLY ILE VAL LEU CYS LYS PHE GLY SEQRES 2 A 71 ALA LEU CYS SER ASN PRO SER CYS PRO PHE GLY HIS PRO SEQRES 3 A 71 THR PRO ALA ASN GLU ASP ALA LYS VAL ILE ASP LEU MET SEQRES 4 A 71 TRP CYS ASP LYS ASN LEU THR CYS ASP ASN PRO GLU CYS SEQRES 5 A 71 ARG LYS ALA HIS SER SER LEU SER LYS ILE LYS GLU VAL SEQRES 6 A 71 LYS PRO ILE SER GLN LYS HET ZN A 501 1 HET ZN A 502 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 PHE A 342 CYS A 346 5 5 HELIX 2 2 LYS A 373 CYS A 377 5 5 HELIX 3 3 LEU A 389 GLU A 394 1 6 LINK ZN ZN A 501 NE2 HIS A 355 1555 1555 2.33 LINK ZN ZN A 501 SG CYS A 340 1555 1555 2.46 LINK ZN ZN A 501 SG CYS A 351 1555 1555 2.47 LINK ZN ZN A 501 SG CYS A 346 1555 1555 2.44 LINK ZN ZN A 502 SG CYS A 382 1555 1555 2.45 LINK ZN ZN A 502 SG CYS A 377 1555 1555 2.44 LINK ZN ZN A 502 NE2 HIS A 386 1555 1555 2.38 LINK ZN ZN A 502 SG CYS A 371 1555 1555 2.40 SITE 1 AC1 4 CYS A 340 CYS A 346 CYS A 351 HIS A 355 SITE 1 AC2 4 CYS A 371 CYS A 377 CYS A 382 HIS A 386 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