PDB Short entry for 5AGQ HEADER TRANSCRIPTION 03-FEB-15 5AGQ TITLE SOLUTION STRUCTURE OF THE TAM DOMAIN OF HUMAN TIP5 BAZ2A INVOLVED IN TITLE 2 EPIGENETIC REGULATION OF RRNA GENES COMPND MOL_ID: 1; COMPND 2 MOLECULE: BROMODOMAIN ADJACENT TO ZINC FINGER DOMAIN PROTEIN 2A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TAM DOMAIN, RESIDUES 543-650; COMPND 5 SYNONYM: TRANSCRIPTION TERMINATION FACTOR I-INTERACTING PROTEIN 5, COMPND 6 TTF-I-INTERACTING PROTEIN 5, TIP5, HWALP3, HUMAN TIP5 BAZ2A; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS TRANSCRIPTION, TAM DOMAIN, TIP5/BAZ2A, PROTEIN RNA INTERACTION, KEYWDS 2 EPIGENETICS, RRNA GENE SILENCING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR I.ANOSOVA,S.MELNIK,K.TRIPSIANES,F.KATEB,I.GRUMMT,M.SATTLER REVDAT 5 14-JUN-23 5AGQ 1 REMARK REVDAT 4 23-OCT-19 5AGQ 1 REMARK ATOM REVDAT 3 10-JUN-15 5AGQ 1 JRNL REVDAT 2 13-MAY-15 5AGQ 1 JRNL REVDAT 1 06-MAY-15 5AGQ 0 JRNL AUTH I.ANOSOVA,S.MELNIK,K.TRIPSIANES,F.KATEB,I.GRUMMT,M.SATTLER JRNL TITL A NOVEL RNA BINDING SURFACE OF THE TAM DOMAIN OF TIP5/BAZ2A JRNL TITL 2 MEDIATES EPIGENETIC REGULATION OF RRNA GENES. JRNL REF NUCLEIC ACIDS RES. V. 43 5208 2015 JRNL REFN ISSN 0305-1048 JRNL PMID 25916849 JRNL DOI 10.1093/NAR/GKV365 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE, REMARK 3 JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON, REMARK 3 WARREN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5AGQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 03-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1290062809. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293.0 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : 1.0 ATM REMARK 210 SAMPLE CONTENTS : 20MM SODIUM PHOSPHATE PH 7. 0, REMARK 210 50MM NACL, 1MM DTT, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 15N-HSQC; 13C-HSQC; HNCACB; REMARK 210 HN(CO)CACB; CC(CO)NH- TOCSY; REMARK 210 HCCH-TOCSY; 15N- EDITED 3D NOESY; REMARK 210 13C- EDITED 3D NOESY REMARK 210 (ALIPHATICS); 13C-EDITED 3D REMARK 210 NOESY (AROMATICS) REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY, CYANA 3.0 REMARK 210 METHOD USED : ARIA2, CNS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : BEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY ON 13C, 15N-LABELED TIP5-TAM DOMAIN. THE SOLUTION REMARK 210 STRUCTURE WAS DEFINED BASED ON 2732 DISTANCE RESTRAINTS, DERIVED REMARK 210 FROM CYANA 3.0, TORSION ANGLE RESTRAINTS AND TWO SETS OF RDCS REMARK 210 FROM TWO DIFFERENT ALIGNMENT MEDIA. VALIDATION PERFORMED WITH REMARK 210 ICING WEB, PROCHECK AND WHATCHECK. 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 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 1-20 REMARK 465 RES C SSSEQI REMARK 465 GLY A 512 REMARK 465 ALA A 513 REMARK 465 MET A 514 REMARK 465 GLU A 515 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 VAL A 591 -71.20 -101.77 REMARK 500 2 CYS A 556 -22.77 -141.14 REMARK 500 2 VAL A 591 -72.47 -106.98 REMARK 500 3 VAL A 591 -72.60 -109.74 REMARK 500 4 CYS A 556 -24.27 -143.86 REMARK 500 4 ASN A 573 -168.72 -117.37 REMARK 500 4 VAL A 591 -70.31 -104.81 REMARK 500 5 CYS A 556 -24.89 -143.41 REMARK 500 6 HIS A 531 -99.99 -94.66 REMARK 500 6 ASN A 573 -162.93 -117.57 REMARK 500 6 VAL A 591 -72.07 -107.60 REMARK 500 8 HIS A 576 -34.30 -137.14 REMARK 500 8 VAL A 591 -69.68 -102.82 REMARK 500 9 VAL A 591 -68.08 -104.98 REMARK 500 10 VAL A 591 -73.05 -104.96 REMARK 500 11 ARG A 518 117.58 68.00 REMARK 500 11 VAL A 591 -70.74 -105.43 REMARK 500 12 VAL A 591 -71.71 -106.39 REMARK 500 14 ASN A 573 -167.08 -123.10 REMARK 500 15 VAL A 591 -71.16 -105.29 REMARK 500 16 LYS A 561 13.36 -140.63 REMARK 500 16 VAL A 591 -69.10 -108.52 REMARK 500 17 VAL A 591 -70.69 -101.17 REMARK 500 18 VAL A 591 -70.59 -106.45 REMARK 500 19 VAL A 591 -72.49 -104.97 REMARK 500 20 VAL A 591 -69.29 -109.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 26517 RELATED DB: BMRB REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUE NUMBERING ACCORDING TO ISOFORM 1. N-TERMINAL REMARK 999 RESIDUES GLY-ALA-MET-GLU ARE ADDED BY CLONING AND REMAIN REMARK 999 AFTER EXPRESSION TAG REMOVAL WITH TOBACCO ETCH VIRUS (TEV) REMARK 999 PROTEASE. DBREF 5AGQ A 516 623 UNP Q9UIF9 BAZ2A_HUMAN 543 650 SEQADV 5AGQ GLY A 512 UNP Q9UIF9 EXPRESSION TAG SEQADV 5AGQ ALA A 513 UNP Q9UIF9 EXPRESSION TAG SEQADV 5AGQ MET A 514 UNP Q9UIF9 EXPRESSION TAG SEQADV 5AGQ GLU A 515 UNP Q9UIF9 EXPRESSION TAG SEQADV 5AGQ SER A 624 UNP Q9UIF9 CLONING ARTIFACT SEQRES 1 A 113 GLY ALA MET GLU ARG ARG ARG ILE ALA THR PRO GLU GLU SEQRES 2 A 113 VAL ARG LEU PRO LEU GLN HIS GLY TRP ARG ARG GLU VAL SEQRES 3 A 113 ARG ILE LYS LYS GLY SER HIS ARG TRP GLN GLY GLU THR SEQRES 4 A 113 TRP TYR TYR GLY PRO CYS GLY LYS ARG MET LYS GLN PHE SEQRES 5 A 113 PRO GLU VAL ILE LYS TYR LEU SER ARG ASN VAL VAL HIS SEQRES 6 A 113 SER VAL ARG ARG GLU HIS PHE SER PHE SER PRO ARG MET SEQRES 7 A 113 PRO VAL GLY ASP PHE PHE GLU GLU ARG ASP THR PRO GLU SEQRES 8 A 113 GLY LEU GLN TRP VAL GLN LEU SER ALA GLU GLU ILE PRO SEQRES 9 A 113 SER ARG ILE GLN ALA ILE THR GLY SER HELIX 1 1 THR A 521 GLY A 532 1 12 HELIX 2 2 GLN A 562 ASN A 573 1 12 HELIX 3 3 ARG A 579 PHE A 583 5 5 HELIX 4 4 GLU A 613 THR A 622 1 10 SHEET 1 AA 5 ARG A 559 MET A 560 0 SHEET 2 AA 5 TRP A 546 TYR A 553 -1 O TYR A 552 N MET A 560 SHEET 3 AA 5 ARG A 534 LYS A 541 -1 O ARG A 534 N TYR A 553 SHEET 4 AA 5 ASP A 593 THR A 600 1 O ASP A 593 N VAL A 537 SHEET 5 AA 5 GLY A 603 LEU A 609 -1 O GLY A 603 N THR A 600 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