HEADER RNA BINDING PROTEIN 16-JAN-13 3ZJ1 TITLE STRUCTURE OF NAB2P TANDEM ZINC FINGER 12 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEAR POLYADENYLATED RNA-BINDING PROTEIN NAB2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ZINC FINGERS 1 AND 2, RESIDUES 253-333; 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 3ZJ1 1 AUTHOR JRNL REVDAT 2 30-OCT-13 3ZJ1 1 JRNL REVDAT 1 11-SEP-13 3ZJ1 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 3ZJ1 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-55425. 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-13C HSQC, HNCO, REMARK 210 HNCA, CBCA(CO)HN, H(C)CH-TOCSY, REMARK 210 15N HSQC- NOESY, NOESY, TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ, 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE, DMX 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 1 ARG A 313 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 ARG A 313 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 6 ARG A 315 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 8 ARG A 315 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 10 ARG A 321 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 12 ARG A 313 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 16 ARG A 313 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 ARG A 261 125.25 71.51 REMARK 500 1 HIS A 267 34.64 -83.52 REMARK 500 1 ARG A 272 -33.46 176.25 REMARK 500 1 SER A 273 -1.71 -146.81 REMARK 500 1 ASN A 288 20.11 -78.68 REMARK 500 1 THR A 295 -31.27 -138.54 REMARK 500 1 PRO A 301 48.48 -76.20 REMARK 500 1 ASN A 302 -59.20 -161.02 REMARK 500 1 LYS A 329 14.03 59.74 REMARK 500 2 ARG A 261 123.01 62.09 REMARK 500 2 HIS A 267 34.40 -84.17 REMARK 500 2 ARG A 272 -33.95 175.81 REMARK 500 2 SER A 273 -2.20 -149.17 REMARK 500 2 ASN A 288 22.36 -79.58 REMARK 500 2 THR A 295 -29.05 -140.14 REMARK 500 2 ASN A 302 -65.57 -167.32 REMARK 500 2 ASP A 304 20.89 -77.23 REMARK 500 3 ARG A 261 158.09 59.14 REMARK 500 3 HIS A 267 39.03 -85.96 REMARK 500 3 PRO A 301 48.51 -77.41 REMARK 500 3 ASN A 302 -62.99 -164.04 REMARK 500 3 ALA A 328 147.98 79.95 REMARK 500 4 THR A 256 114.04 75.17 REMARK 500 4 LYS A 258 -176.64 -69.27 REMARK 500 4 ARG A 261 118.33 64.70 REMARK 500 4 HIS A 267 41.24 -85.39 REMARK 500 4 ASN A 288 20.43 -78.71 REMARK 500 4 ASN A 302 -66.25 -162.70 REMARK 500 4 ALA A 328 -152.87 -145.52 REMARK 500 5 SER A 252 165.94 71.15 REMARK 500 5 GLU A 259 -146.56 -104.57 REMARK 500 5 ARG A 261 123.25 65.72 REMARK 500 5 HIS A 267 35.95 -84.84 REMARK 500 5 ASN A 288 31.18 -84.18 REMARK 500 5 THR A 295 -35.59 -161.58 REMARK 500 5 ASN A 302 -67.40 -163.94 REMARK 500 5 ALA A 327 -133.42 -96.09 REMARK 500 6 SER A 252 168.77 69.64 REMARK 500 6 LYS A 258 -161.90 -69.37 REMARK 500 6 GLU A 259 -153.36 -74.68 REMARK 500 6 ARG A 261 123.14 64.08 REMARK 500 6 HIS A 267 38.82 -84.93 REMARK 500 6 THR A 295 -32.57 -137.63 REMARK 500 6 ASN A 302 -52.08 -164.57 REMARK 500 6 GLU A 303 -64.25 -96.20 REMARK 500 6 ASP A 304 23.36 -75.60 REMARK 500 6 LYS A 329 -30.95 -143.59 REMARK 500 7 THR A 254 155.59 68.89 REMARK 500 7 ARG A 261 121.43 64.47 REMARK 500 7 HIS A 267 33.43 -83.65 REMARK 500 REMARK 500 THIS ENTRY HAS 165 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 12 ARG A 261 0.08 SIDE CHAIN REMARK 500 17 ARG A 313 0.09 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 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 268 SG REMARK 620 2 CYS A 262 SG 113.0 REMARK 620 3 CYS A 274 SG 114.0 112.7 REMARK 620 4 HIS A 278 NE2 104.2 104.8 107.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 1 ZN A 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 289 SG REMARK 620 2 HIS A 300 NE2 105.7 REMARK 620 3 CYS A 283 SG 115.1 104.5 REMARK 620 4 CYS A 296 SG 111.5 103.9 114.7 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ZJ2 RELATED DB: PDB REMARK 900 STRUCTURE OF NAB2P TANDEM ZINC FINGER 34 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE TWO N-TERMINAL RESIDUES (GS) ARE NOT FROM WILD TYPE REMARK 999 SEQUENCE DBREF 3ZJ1 A 253 333 UNP P32505 NAB2_YEAST 253 333 SEQADV 3ZJ1 GLY A 251 UNP P32505 EXPRESSION TAG SEQADV 3ZJ1 SER A 252 UNP P32505 EXPRESSION TAG SEQRES 1 A 83 GLY SER PHE THR PRO THR LYS LYS GLU GLY ARG CYS ARG SEQRES 2 A 83 LEU PHE PRO HIS CYS PRO LEU GLY ARG SER CYS PRO HIS SEQRES 3 A 83 ALA HIS PRO THR LYS VAL CYS ASN GLU TYR PRO ASN CYS SEQRES 4 A 83 PRO LYS PRO PRO GLY THR CYS GLU PHE LEU HIS PRO ASN SEQRES 5 A 83 GLU ASP GLU GLU LEU MET LYS GLU MET GLU ARG THR ARG SEQRES 6 A 83 GLU GLU PHE GLN LYS ARG LYS ALA ASP LEU LEU ALA ALA SEQRES 7 A 83 LYS ARG LYS PRO VAL HET ZN A 401 1 HET ZN A 402 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 ASP A 304 ALA A 327 1 24 LINK ZN ZN A 401 SG CYS A 268 1555 1555 2.46 LINK ZN ZN A 401 SG CYS A 262 1555 1555 2.45 LINK ZN ZN A 401 SG CYS A 274 1555 1555 2.44 LINK ZN ZN A 401 NE2 HIS A 278 1555 1555 2.33 LINK ZN ZN A 402 NE2 HIS A 300 1555 1555 2.30 LINK ZN ZN A 402 SG CYS A 283 1555 1555 2.43 LINK ZN ZN A 402 SG CYS A 296 1555 1555 2.45 LINK ZN ZN A 402 SG CYS A 289 1555 1555 2.44 CISPEP 1 PHE A 265 PRO A 266 1 6.17 CISPEP 2 TYR A 286 PRO A 287 1 2.10 CISPEP 3 PHE A 265 PRO A 266 2 5.08 CISPEP 4 TYR A 286 PRO A 287 2 3.27 CISPEP 5 PHE A 265 PRO A 266 3 2.17 CISPEP 6 TYR A 286 PRO A 287 3 3.56 CISPEP 7 PHE A 265 PRO A 266 4 2.33 CISPEP 8 TYR A 286 PRO A 287 4 3.19 CISPEP 9 PHE A 265 PRO A 266 5 4.87 CISPEP 10 TYR A 286 PRO A 287 5 2.79 CISPEP 11 PHE A 265 PRO A 266 6 5.26 CISPEP 12 TYR A 286 PRO A 287 6 2.44 CISPEP 13 PHE A 265 PRO A 266 7 3.76 CISPEP 14 TYR A 286 PRO A 287 7 2.32 CISPEP 15 PHE A 265 PRO A 266 8 7.72 CISPEP 16 TYR A 286 PRO A 287 8 2.76 CISPEP 17 PHE A 265 PRO A 266 9 4.28 CISPEP 18 TYR A 286 PRO A 287 9 3.27 CISPEP 19 PHE A 265 PRO A 266 10 5.66 CISPEP 20 TYR A 286 PRO A 287 10 2.95 CISPEP 21 PHE A 265 PRO A 266 11 5.05 CISPEP 22 TYR A 286 PRO A 287 11 3.58 CISPEP 23 PHE A 265 PRO A 266 12 2.86 CISPEP 24 TYR A 286 PRO A 287 12 3.82 CISPEP 25 PHE A 265 PRO A 266 13 11.46 CISPEP 26 TYR A 286 PRO A 287 13 0.74 CISPEP 27 PHE A 265 PRO A 266 14 7.50 CISPEP 28 TYR A 286 PRO A 287 14 1.69 CISPEP 29 PHE A 265 PRO A 266 15 4.69 CISPEP 30 TYR A 286 PRO A 287 15 1.85 CISPEP 31 PHE A 265 PRO A 266 16 5.29 CISPEP 32 TYR A 286 PRO A 287 16 2.53 CISPEP 33 PHE A 265 PRO A 266 17 7.80 CISPEP 34 TYR A 286 PRO A 287 17 2.95 CISPEP 35 PHE A 265 PRO A 266 18 5.37 CISPEP 36 TYR A 286 PRO A 287 18 -0.38 CISPEP 37 PHE A 265 PRO A 266 19 4.36 CISPEP 38 TYR A 286 PRO A 287 19 4.79 CISPEP 39 PHE A 265 PRO A 266 20 3.97 CISPEP 40 TYR A 286 PRO A 287 20 1.82 SITE 1 AC1 4 CYS A 262 CYS A 268 CYS A 274 HIS A 278 SITE 1 AC2 4 CYS A 283 CYS A 289 CYS A 296 HIS A 300 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