HEADER TRANSCRIPTION 04-MAR-08 2RO1 TITLE NMR SOLUTION STRUCTURES OF HUMAN KAP1 PHD FINGER-BROMODOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTION INTERMEDIARY FACTOR 1-BETA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 624-812; COMPND 5 SYNONYM: TIF1-BETA, TRIPARTITE MOTIF-CONTAINING PROTEIN 28, NUCLEAR COMPND 6 COREPRESSOR KAP-1, KRAB-ASSOCIATED PROTEIN 1, KAP-1, KRAB-INTERACTING COMPND 7 PROTEIN 1, KRIP-1, RING FINGER PROTEIN 96; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 GENE: TRIM28, KAP1, RNF96, TIF1B; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET15B KEYWDS KAP, TIF, PHD FINGER, BROMODOMAIN, SUMO, ACETYLATION, ALTERNATIVE KEYWDS 2 SPLICING, METAL-BINDING, NUCLEUS, PHOSPHOPROTEIN, REPRESSOR, KEYWDS 3 TRANSCRIPTION, TRANSCRIPTION REGULATION, ZINC, ZINC-FINGER EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR L.ZENG,K.L.YAP,A.V.IVANOV,X.WANG,S.MUJTABA,O.PLOTNIKOVA,F.J.RAUSCHER REVDAT 4 16-MAR-22 2RO1 1 REMARK LINK REVDAT 3 24-FEB-09 2RO1 1 VERSN REVDAT 2 17-JUN-08 2RO1 1 JRNL REVDAT 1 20-MAY-08 2RO1 0 JRNL AUTH L.ZENG,K.L.YAP,A.V.IVANOV,X.WANG,S.MUJTABA,O.PLOTNIKOVA, JRNL AUTH 2 F.J.RAUSCHER,M.M.ZHOU JRNL TITL STRUCTURAL INSIGHTS INTO HUMAN KAP1 PHD FINGER-BROMODOMAIN JRNL TITL 2 AND ITS ROLE IN GENE SILENCING JRNL REF NAT.STRUCT.MOL.BIOL. V. 15 626 2008 JRNL REFN ISSN 1545-9993 JRNL PMID 18488044 JRNL DOI 10.1038/NSMB.1416 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1, CNS 1.1 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES, READ (CNS), REMARK 3 BRUNGER, ADAMS, CLORE, GROS, NILGES, READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2RO1 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-MAR-08. REMARK 100 THE DEPOSITION ID IS D_1000150079. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 0.2 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5MM [U-100% 13C; U-100% 15N] REMARK 210 PROTEIN, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D 1H-15N TOCSY; 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX; AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ARIA 2.1 REMARK 210 METHOD USED : SIMULATED ANNEALING, TORSION REMARK 210 ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL 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 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 H SER A 683 H LEU A 684 1.32 REMARK 500 O CYS A 628 H GLN A 632 1.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 9 TYR A 755 CG TYR A 755 CD1 -0.085 REMARK 500 12 TYR A 755 CG TYR A 755 CD1 -0.078 REMARK 500 20 TYR A 755 CZ TYR A 755 CE2 -0.082 REMARK 500 REMARK 500 REMARK: NULL 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 TYR A 755 CB - CG - CD2 ANGL. DEV. = -4.9 DEGREES REMARK 500 1 PHE A 761 CB - CG - CD1 ANGL. DEV. = -4.7 DEGREES REMARK 500 2 PHE A 772 CB - CG - CD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 2 PHE A 772 CB - CG - CD1 ANGL. DEV. = 4.7 DEGREES REMARK 500 3 PHE A 772 CB - CG - CD2 ANGL. DEV. = -5.4 DEGREES REMARK 500 3 PHE A 772 CB - CG - CD1 ANGL. DEV. = 4.3 DEGREES REMARK 500 5 TYR A 755 CB - CG - CD2 ANGL. DEV. = -4.6 DEGREES REMARK 500 5 PHE A 772 CB - CG - CD2 ANGL. DEV. = -4.7 DEGREES REMARK 500 5 PHE A 792 CB - CG - CD1 ANGL. DEV. = -4.3 DEGREES REMARK 500 6 TYR A 755 CB - CG - CD2 ANGL. DEV. = -5.0 DEGREES REMARK 500 6 PHE A 792 CB - CG - CD1 ANGL. DEV. = -4.7 DEGREES REMARK 500 7 PRO A 660 C - N - CA ANGL. DEV. = 10.0 DEGREES REMARK 500 7 TYR A 755 CB - CG - CD2 ANGL. DEV. = -5.2 DEGREES REMARK 500 7 TYR A 755 CB - CG - CD1 ANGL. DEV. = 3.9 DEGREES REMARK 500 7 PHE A 761 CB - CG - CD2 ANGL. DEV. = -4.6 DEGREES REMARK 500 7 PHE A 772 CB - CG - CD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 7 PHE A 772 CB - CG - CD1 ANGL. DEV. = 4.6 DEGREES REMARK 500 8 PRO A 753 N - CA - CB ANGL. DEV. = -8.9 DEGREES REMARK 500 8 PHE A 772 CB - CG - CD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 8 PHE A 772 CB - CG - CD1 ANGL. DEV. = 5.3 DEGREES REMARK 500 8 PHE A 792 CB - CG - CD1 ANGL. DEV. = -4.5 DEGREES REMARK 500 9 PHE A 792 CB - CG - CD1 ANGL. DEV. = -4.2 DEGREES REMARK 500 10 PRO A 753 N - CA - CB ANGL. DEV. = -8.9 DEGREES REMARK 500 10 PHE A 792 CB - CG - CD1 ANGL. DEV. = -4.9 DEGREES REMARK 500 11 PRO A 753 N - CA - CB ANGL. DEV. = -7.6 DEGREES REMARK 500 11 PHE A 772 CB - CG - CD2 ANGL. DEV. = -6.1 DEGREES REMARK 500 11 PHE A 772 CB - CG - CD1 ANGL. DEV. = 4.7 DEGREES REMARK 500 12 PRO A 753 N - CA - CB ANGL. DEV. = -8.3 DEGREES REMARK 500 12 PHE A 772 CB - CG - CD2 ANGL. DEV. = -4.4 DEGREES REMARK 500 12 PHE A 792 CB - CG - CD1 ANGL. DEV. = -4.4 DEGREES REMARK 500 13 TYR A 755 CB - CG - CD2 ANGL. DEV. = -4.9 DEGREES REMARK 500 13 PHE A 792 CB - CG - CD1 ANGL. DEV. = -5.0 DEGREES REMARK 500 14 TYR A 755 CB - CG - CD2 ANGL. DEV. = -3.8 DEGREES REMARK 500 15 TYR A 755 CB - CG - CD2 ANGL. DEV. = -4.7 DEGREES REMARK 500 15 PHE A 772 CB - CG - CD2 ANGL. DEV. = -4.9 DEGREES REMARK 500 16 VAL A 659 N - CA - CB ANGL. DEV. = -13.5 DEGREES REMARK 500 16 PRO A 753 N - CA - CB ANGL. DEV. = -9.3 DEGREES REMARK 500 17 PHE A 792 CB - CG - CD1 ANGL. DEV. = -4.6 DEGREES REMARK 500 18 PRO A 753 N - CA - CB ANGL. DEV. = -9.3 DEGREES REMARK 500 18 PHE A 792 CB - CG - CD2 ANGL. DEV. = 4.4 DEGREES REMARK 500 18 PHE A 792 CB - CG - CD1 ANGL. DEV. = -5.8 DEGREES REMARK 500 20 TYR A 755 CB - CG - CD1 ANGL. DEV. = 3.7 DEGREES REMARK 500 20 PHE A 792 CB - CG - CD1 ANGL. DEV. = -5.3 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 ILE A 627 117.56 34.78 REMARK 500 1 CYS A 628 80.73 -56.03 REMARK 500 1 ARG A 629 -44.96 -15.58 REMARK 500 1 VAL A 630 -74.70 -51.90 REMARK 500 1 ASP A 636 42.41 -79.36 REMARK 500 1 CYS A 640 104.90 -59.74 REMARK 500 1 ASN A 641 -9.77 -50.40 REMARK 500 1 GLU A 644 -3.69 49.90 REMARK 500 1 PHE A 645 92.81 -55.36 REMARK 500 1 HIS A 648 4.27 -61.56 REMARK 500 1 LEU A 649 -62.60 74.49 REMARK 500 1 ALA A 655 121.15 61.98 REMARK 500 1 LEU A 656 -172.02 -49.89 REMARK 500 1 ASP A 658 107.10 145.90 REMARK 500 1 VAL A 659 110.60 18.46 REMARK 500 1 PRO A 660 32.95 -74.95 REMARK 500 1 TRP A 664 176.67 -58.86 REMARK 500 1 SER A 665 79.66 -160.10 REMARK 500 1 CYS A 666 -165.42 37.83 REMARK 500 1 VAL A 671 -173.77 53.58 REMARK 500 1 LEU A 672 142.65 -32.98 REMARK 500 1 LEU A 675 -5.21 -50.32 REMARK 500 1 GLU A 677 -80.06 59.85 REMARK 500 1 GLU A 678 -155.29 -70.27 REMARK 500 1 SER A 681 20.07 -178.65 REMARK 500 1 SER A 683 -13.04 -172.94 REMARK 500 1 LEU A 684 -61.54 69.93 REMARK 500 1 ASP A 685 123.50 173.40 REMARK 500 1 ASP A 688 128.72 -178.22 REMARK 500 1 SER A 689 -48.67 -152.13 REMARK 500 1 THR A 690 -21.76 -145.57 REMARK 500 1 VAL A 693 -38.20 -161.32 REMARK 500 1 LYS A 695 -88.49 -68.56 REMARK 500 1 SER A 697 144.35 64.82 REMARK 500 1 VAL A 707 -71.61 -94.97 REMARK 500 1 LEU A 708 -39.48 -36.06 REMARK 500 1 HIS A 721 -34.11 -37.36 REMARK 500 1 ASP A 726 -77.19 6.75 REMARK 500 1 SER A 727 -87.39 60.63 REMARK 500 1 THR A 728 41.08 -146.83 REMARK 500 1 PHE A 729 102.58 -163.35 REMARK 500 1 SER A 730 -31.36 -166.05 REMARK 500 1 ASP A 732 19.21 -160.52 REMARK 500 1 THR A 737 -26.50 -155.56 REMARK 500 1 LEU A 738 -165.46 43.19 REMARK 500 1 ASP A 739 166.18 172.75 REMARK 500 1 LEU A 751 -95.93 -60.23 REMARK 500 1 SER A 752 -48.48 -177.14 REMARK 500 1 PRO A 754 138.43 -12.48 REMARK 500 1 TYR A 755 -146.91 -68.02 REMARK 500 REMARK 500 THIS ENTRY HAS 1231 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 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 628 SG REMARK 620 2 CYS A 631 SG 110.3 REMARK 620 3 HIS A 648 ND1 102.9 112.1 REMARK 620 4 CYS A 651 SG 108.6 110.8 111.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 640 SG REMARK 620 2 CYS A 643 SG 107.8 REMARK 620 3 CYS A 666 SG 107.7 109.1 REMARK 620 4 CYS A 669 SG 109.4 112.2 110.5 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 301 DBREF 2RO1 A 624 812 UNP Q13263 TIF1B_HUMAN 624 812 SEQRES 1 A 189 SER ALA THR ILE CYS ARG VAL CYS GLN LYS PRO GLY ASP SEQRES 2 A 189 LEU VAL MET CYS ASN GLN CYS GLU PHE CYS PHE HIS LEU SEQRES 3 A 189 ASP CYS HIS LEU PRO ALA LEU GLN ASP VAL PRO GLY GLU SEQRES 4 A 189 GLU TRP SER CYS SER LEU CYS HIS VAL LEU PRO ASP LEU SEQRES 5 A 189 LYS GLU GLU ASP GLY SER LEU SER LEU ASP GLY ALA ASP SEQRES 6 A 189 SER THR GLY VAL VAL ALA LYS LEU SER PRO ALA ASN GLN SEQRES 7 A 189 ARG LYS CYS GLU ARG VAL LEU LEU ALA LEU PHE CYS HIS SEQRES 8 A 189 GLU PRO CYS ARG PRO LEU HIS GLN LEU ALA THR ASP SER SEQRES 9 A 189 THR PHE SER LEU ASP GLN PRO GLY GLY THR LEU ASP LEU SEQRES 10 A 189 THR LEU ILE ARG ALA ARG LEU GLN GLU LYS LEU SER PRO SEQRES 11 A 189 PRO TYR SER SER PRO GLN GLU PHE ALA GLN ASP VAL GLY SEQRES 12 A 189 ARG MET PHE LYS GLN PHE ASN LYS LEU THR GLU ASP LYS SEQRES 13 A 189 ALA ASP VAL GLN SER ILE ILE GLY LEU GLN ARG PHE PHE SEQRES 14 A 189 GLU THR ARG MET ASN GLU ALA PHE GLY ASP THR LYS PHE SEQRES 15 A 189 SER ALA VAL LEU VAL GLU PRO HET ZN A 201 1 HET ZN A 301 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 SER A 697 HIS A 714 1 18 HELIX 2 2 PRO A 716 GLN A 722 1 7 HELIX 3 3 ASP A 739 GLU A 749 1 11 HELIX 4 4 SER A 757 THR A 776 1 20 HELIX 5 5 VAL A 782 PHE A 800 1 19 LINK ZN ZN A 201 SG CYS A 628 1555 1555 2.22 LINK ZN ZN A 201 SG CYS A 631 1555 1555 2.24 LINK ZN ZN A 201 ND1 HIS A 648 1555 1555 2.04 LINK ZN ZN A 201 SG CYS A 651 1555 1555 2.23 LINK ZN ZN A 301 SG CYS A 640 1555 1555 2.23 LINK ZN ZN A 301 SG CYS A 643 1555 1555 2.25 LINK ZN ZN A 301 SG CYS A 666 1555 1555 2.25 LINK ZN ZN A 301 SG CYS A 669 1555 1555 2.26 SITE 1 AC1 3 CYS A 628 CYS A 631 HIS A 648 SITE 1 AC2 4 CYS A 640 GLN A 642 CYS A 643 PHE A 645 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