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
(ATOM LINES ARE NOT SHOWN.)
END