10 20 30 40 50 60 70 80 1WZH - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSCRIPTION/DNA 05-MAR-05 1WZH
TITLE MODEL FOR BINDING OF E2F8 DBDS TO E2F CONSENSUS SEQUENCE TITLE 2 BASED UPON STRUCTURAL HOMOLOGY TO E2F4/DP2
COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIKEN CDNA 4432406C08; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: DNA BINDING DOMAIN TWO; COMPND 5 SYNONYM: E2F8 DBD2; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'- COMPND 8 D(P*TP*TP*TP*TP*CP*GP*CP*GP*CP*GP*GP*TP*TP*TP*T)-3'; COMPND 9 CHAIN: D; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: 5'- COMPND 12 D(P*AP*AP*AP*AP*CP*CP*GP*CP*GP*CP*GP*AP*AP*AP*A)-3'; COMPND 13 CHAIN: E; COMPND 14 MOL_ID: 4; COMPND 15 MOLECULE: RIKEN CDNA 4432406C08; COMPND 16 CHAIN: F; COMPND 17 FRAGMENT: DNA BINDING DOMAIN ONE; COMPND 18 SYNONYM: E2F8 DBD1
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 MOL_ID: 2; SOURCE 5 MOL_ID: 3; SOURCE 6 MOL_ID: 4; SOURCE 7 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 8 ORGANISM_COMMON: MOUSE
KEYWDS WINGED HELIX-TURN-HELIX, DNA BINDING DOMAINS
EXPDTA THEORETICAL MODEL
AUTHOR B.MAITI,J.LI,A.DE BRUIN,F.GORDON,C.TIMMERS,R.OPAVSKY, AUTHOR 2 K.PATIL,J.TUTTLE,W.CLEGHORN,G.LEONE
REVDAT 2 21-JUN-05 1WZH 1 JRNL REVDAT 1 29-MAR-05 1WZH 0
JRNL AUTH B.MAITI,J.LI,A.DE BRUIN,F.GORDON,C.TIMMERS, JRNL AUTH 2 R.OPAVSKY,K.PATIL,J.TUTTLE,W.CLEGHORN,G.LEONE JRNL TITL CLONING AND CHARACTERIZATION OF MOUSE E2F8, A JRNL TITL 2 NOVEL MAMMALIAN E2F FAMILY MEMBER CAPABLE OF JRNL TITL 3 BLOCKING CELLULAR PROLIFERATION JRNL REF J.BIOL.CHEM. V. 280 18211 2005 JRNL REFN ASTM JBCHA3 US ISSN 0021-9258
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SWISS PDBVIEWER 3.7 REMARK 3 AUTHORS : NICOLAS GUEX , ALEXANDRE DIEMAND , MANUEL C. REMARK 3 PEITSCH , TORSTEN SCHWEDE REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1WZH COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-MAR-2005. REMARK 100 THE RCSB ID CODE IS RCSB024188.
REMARK 105 REMARK 105 THE PROTEIN DATA BANK HAS ADOPTED THE SACCHARIDE CHEMISTS REMARK 105 NOMENCLATURE FOR ATOMS OF THE DEOXYRIBOSE/RIBOSE MOIETY REMARK 105 RATHER THAN THAT OF THE NUCLEOSIDE CHEMISTS. THE RING REMARK 105 OXYGEN ATOM IS LABELLED O4* INSTEAD OF O1*.
REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: SOLVED CRYSTAL STRUCTURE OF E2F4/DP HETERODIMER BOUND REMARK 220 TO E2F CONSENSUS SEQUENCE (ZHENG, N., FRAENKEL, E., REMARK 220 PABO, C. O., PAVLETICH, N. P.: STRUCTURAL BASIS OF DNA REMARK 220 RECOGNITION BY THE HETERODIMERIC CELL CYCLE REMARK 220 TRANSCRIPTION FACTOR E2F-DP. GENES DEV 13 PP. 666 (1999) REMARK 220 ). 1CF7 WAS USED FOR HOMOLOGY MODELING OF E2F8 BINDING REMARK 220 DOMAINS
REMARK 225 REMARK 225 THEORETICAL MODEL REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE. REMARK 225 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND REMARK 225 SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE REMARK 225 RECORDS ARE MEANINGLESS.
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 REMARK 500 O5* A E 604 CD1 ILE F 141 0.83 REMARK 500 O1P C E 605 CG ASP F 140 1.37 REMARK 500 O1P C E 605 CB ASP F 140 1.39 REMARK 500 O1P G E 607 OG SER A 265 1.41 REMARK 500 O1P C E 605 OD2 ASP F 140 1.46 REMARK 500 P C E 605 CB ASP F 140 1.51 REMARK 500 O2P C E 605 CB ASP F 140 1.59 REMARK 500 O2P C E 606 NH2 ARG F 172 1.66 REMARK 500 C5* A E 604 CD1 ILE F 141 1.79 REMARK 500 O5* C E 605 OD1 ASP F 140 1.79 REMARK 500 P C E 605 CG ASP F 140 1.80 REMARK 500 NH1 ARG A 267 OE1 GLU F 165 1.89 REMARK 500 O2P C E 605 CA ASP F 140 1.94 REMARK 500 O5* C E 605 CG ASP F 140 1.94 REMARK 500 P A E 604 CD1 ILE F 141 1.99 REMARK 500 O ARG A 267 OG SER F 166 2.05 REMARK 500 P C E 606 NH2 ARG F 172 2.12 REMARK 500 N7 G D 508 CD ARG F 155 2.16 REMARK 500 O2P C E 605 N ILE F 141 2.19 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),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 LYS A 292 CE LYS A 292 NZ -0.111 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ILE A 293 CB - CG1 - CD1 ANGL. DEV. = 16.4 DEGREES REMARK 500 ILE A 318 CB - CG1 - CD1 ANGL. DEV. = 13.8 DEGREES 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 M RES CSSEQI PSI PHI REMARK 500 SER A 265 156.79 81.88 REMARK 500 THR A 281 -75.10 69.12 REMARK 500 LYS A 307 -52.63 91.08 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU A 301 ASP A 302 -142.14
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1CF7 RELATED DB: PDB REMARK 900 THE COORDINATES FOR DNA WERE TAKEN FROM 1CF7
DBREF 1WZH A 263 341 GB 38087952 XP_149937 263 341 DBREF 1WZH F 112 181 GB 38087952 XP_149937 112 181
SEQRES 1 A 79 ASP LYS SER LEU ARG VAL MET SER GLN LYS PHE VAL MET SEQRES 2 A 79 LEU PHE LEU VAL SER THR PRO GLN ILE VAL SER LEU GLU SEQRES 3 A 79 ILE ALA ALA LYS ILE LEU ILE GLY GLU ASP HIS VAL GLU SEQRES 4 A 79 ASP LEU ASP LYS SER LYS TYR LYS THR LYS ILE ARG ARG SEQRES 5 A 79 LEU TYR ASP ILE ALA ASN VAL LEU SER SER LEU ASP LEU SEQRES 6 A 79 ILE LYS LYS VAL HIS VAL THR GLU GLU ARG GLY ARG LYS SEQRES 7 A 79 PRO SEQRES 1 D 15 T T T T C G C G C G G T T SEQRES 2 D 15 T T SEQRES 1 E 15 A A A A C C G C G C G A A SEQRES 2 E 15 A A SEQRES 1 F 70 SER ARG LYS GLU LYS SER LEU GLY LEU LEU CYS HIS LYS SEQRES 2 F 70 PHE LEU ALA ARG TYR PRO LYS TYR PRO ASN PRO ALA VAL SEQRES 3 F 70 ASN ASN ASP ILE CYS LEU ASP GLU VAL ALA GLU GLU LEU SEQRES 4 F 70 ASN VAL GLU ARG ARG ARG ILE TYR ASP ILE VAL ASN VAL SEQRES 5 F 70 LEU GLU SER LEU HIS MET VAL SER ARG LEU ALA LYS ASN SEQRES 6 F 70 ARG TYR THR TRP HIS
HELIX 1 1 LYS A 264 THR A 281 1 18 HELIX 2 2 ILE A 284 GLU A 297 1 14 HELIX 3 3 ASP A 304 LEU A 325 1 22 HELIX 4 4 SER F 112 SER F 117 1 6 HELIX 5 5 SER F 117 TYR F 132 1 16 HELIX 6 6 LEU F 143 LEU F 150 1 8 HELIX 7 7 GLU F 153 HIS F 168 1 16
SHEET 1 A 2 PRO A 282 GLN A 283 0 SHEET 2 A 2 GLU A 335 GLU A 336 -1 O GLU A 335 N GLN A 283 SHEET 1 B 3 ALA F 136 VAL F 137 0 SHEET 2 B 3 ARG F 177 TRP F 180 -1 O TYR F 178 N VAL F 137 SHEET 3 B 3 VAL F 170 ALA F 174 -1 N SER F 171 O THR F 179
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