PDB Short entry for 1J4W HEADER TRANSCRIPTION/DNA 30-NOV-01 1J4W TITLE COMPLEX OF THE KH3 AND KH4 DOMAINS OF FBP WITH A SINGLE_STRANDED 29MER TITLE 2 DNA OLIGONUCLEOTIDE FROM THE FUSE ELEMENT OF THE C-MYC ONCOGENE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'- COMPND 3 D(*GP*TP*A*TP*AP*TP*TP*CP*CP*CP*TP*CP*GP*GP*G*AP*TP*TP*TP*TP*TP*TP*AP COMPND 4 *TP*TP*TP*TP*GP*T)-3'); COMPND 5 CHAIN: B; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: FROM THE FUSE ELEMENT OF THE C-MYC ONCOGENE; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: FUSE BINDING PROTEIN; COMPND 10 CHAIN: A; COMPND 11 FRAGMENT: RESIDUES 278-447, NUMBERERED 5-174. KH3 AND KH4 DOMAINS.; COMPND 12 SYNONYM: FBP, FAR UPSTREAM BINDING ELEMENT PROTEIN; COMPND 13 ENGINEERED: YES; COMPND 14 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 5 ORGANISM_COMMON: HUMAN; SOURCE 6 ORGANISM_TAXID: 9606; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BE23; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS SINGLE-STRANDED DNA BINDING PROTEIN, TRANSCRIPTION FACTOR, FBP, FUSE KEYWDS 2 ELEMENT, C-MYC ONCOGENE, TRANSCRIPTION-DNA COMPLEX EXPDTA SOLUTION NMR AUTHOR G.M.CLORE,D.T.BRADDOCK REVDAT 4 27-DEC-23 1J4W 1 REMARK REVDAT 3 27-OCT-21 1J4W 1 REMARK SEQADV REVDAT 2 24-FEB-09 1J4W 1 VERSN REVDAT 1 06-MAR-02 1J4W 0 JRNL AUTH D.T.BRADDOCK,J.M.LOUIS,J.L.BABER,D.LEVENS,G.M.CLORE JRNL TITL STRUCTURE AND DYNAMICS OF KH DOMAINS FROM FBP BOUND TO JRNL TITL 2 SINGLE-STRANDED DNA. JRNL REF NATURE V. 415 1051 2002 JRNL REFN ISSN 0028-0836 JRNL PMID 11875576 JRNL DOI 10.1038/4151051A REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH (HTTP://NMR.CIT.NIH.GOV/XPLOR_NIH) REMARK 3 AUTHORS : CLORE, KUSZEWSKI, SCHWIETERS, TJANDRA REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES WERE CALCULATED BY SIMULATED ANNEALING IN TORSION REMARK 3 ANGLE SPACE (SCHWIETERS AND CLORE (2001) J MAGN RESON 152, 288-302) REMARK 3 AGAINST A TARGET FUNCTION COMPRISING THE EXPERIMENTAL NMR REMARK 3 RESTRAINTS (NOE-DERIVED INTERPROTON DISTANCE, TORSION ANGLE, 3J REMARK 3 COUPLING, 13CALPHA/13CBETA SHIFTS AND DIPOLAR COUPLINGS). THE NON- REMARK 3 BONDED CONTACTS IN THE TARGET FUNCTION ARE REPRESENTED BY A REMARK 3 QUARTIC VAN DER WAALS REPULSION TERM, SUPPLEMENTED BY TORSION REMARK 3 ANGLE (KUSZEWSKI ET AL. J. MAGN. RESON 125, 171-177 (1997)) BASE- REMARK 3 BASE POSITIONAL (KUSZEWSKI ET AL. J AM CHEM SOC 123, 3903-3918 REMARK 3 (2001)) DATABASE POTENTIALS OF MEAN FORCE. REMARK 3 REMARK 3 IN THIS ENTRY THE LAST NUMERICAL COLUMN IS THE RMS OF REMARK 3 THE 80 INDIVIDUAL SIMULATED ANNEALING STRUCTURES (FOR REMARK 3 EACH HALF OF THE COMPLEX) ABOUT THE MEAN COORDINATE REMARK 3 POSITIONS: RESIDUES 75-103 OF THE PROTEIN ARE REMARK 3 DISORDERED IN THE COMPLEX. ALTHOUGH THE SINGLE-STRANDED REMARK 3 DNA IS B-LIKE, THE COORDINATES OF THOSE PORTIONS OF THE REMARK 3 SS-DNA NOT IN CONTACT WITH THE PROTEIN COULD NOT BE REMARK 3 ACCURATELY DETERMINED (BASES 201-203, 212-215 AND REMARK 3 223-229). THEREFORE THE COORDINATES ARE PRESENTED IN REMARK 3 TWO HALVES: THE KH3 HALF OF THE COMPLEX (RESIDUES 1-74 REMARK 3 OF THE PROTEIN AND BASES 216-222 OF THE SS-DNA) AND THE REMARK 3 KH4 HALF OF THE COMPLEX (RESIDUES 104-174 OF THE REMARK 3 PROTEIN AND BASES 204-211 OF THE SS-DNA). THE REMARK 3 COORDINATE ACCURACY IS CALCULATED FOR THE TWO HALVES OF REMARK 3 THE COMPLEX SEPARATELY. THE APPROXIMATE ORIENTATION OF REMARK 3 AND SEPARATION BETWEEN THE TWO DOMAINS COULD BE DERIVED REMARK 3 FROM ANALYSIS OF HETERONUCLEAR RELAXATION MEASUREMENTS. REMARK 3 THE ORIENTATIONS OF THE TWO HALVES OF THE COMPLEX IN REMARK 3 THESE COORDINATES REFLECTS THE RESULTS OF THE REMARK 3 RELAXATION MEASUREMENTS. THE AVERAGE ORIENTATION OF THE REMARK 3 TWO HALVES OF THE COMPLEX IS PARALLEL WITH AN AVERAGE REMARK 3 INTERHELICAL ANGLE OF ABOUT 1 DEGREE BETWEEN THE THIRD REMARK 3 HELIX OF EACH DOMAIN. THE OVERALL ROTATIONAL REMARK 3 CORRELATION TIME OF THE COMPLEX IS 21.5 NS WITH A REMARK 3 DIFFUSION ANISOTROPY OF 1.85. THE TIME SCALE FOR THE REMARK 3 INTERDOMAIN MOTIONS IS AROUND 4 NS AND THE TWO DOMAINS REMARK 3 WOBBLE INDEPENDENTLY IN CONES WITH SEMI-ANGLES OF ABOUT REMARK 3 30 DEGREES. THE OVERALL LENGTH OF THE COMPLEX IS ABOUT REMARK 3 100 ANGSTROMS AND THE SEPARATION BETWEEN THE TWO HALVES REMARK 3 OF THE COMPLEX IS AROUND 35 ANGSTROMS. THE RESTRAINED REMARK 3 REGULARIZED MEAN STRUCTURE FOR THE TWO HALVES OF THE REMARK 3 COMPLEX IS OBTAINED BY RESTRAINED REGULARIZATION OF THE REMARK 3 AVERAGE COORDINATES AGAINST THE SAME TARGET FUNCTION REMARK 3 USED TO CALCULATE THE SIMULATED ANNEALING STRUCTURES. REMARK 3 REMARK 3 SOLVED BY MULTI HETERONUCLEAR NMR AND IS BASED ON REMARK 3 3153 EXPERIMENTAL NMR RESTRAINTS REMARK 3 KH3 HALF KH4 HALF REMARK 3 DISTANCES 1095 949 REMARK 3 TORSION ANGLES 244 261 REMARK 3 3JHNA COUPLINGS 33 36 REMARK 3 13CA/CB SHIFTS 120 121 REMARK 3 1DNH DIPOLARS 61 61 REMARK 3 1DNC' DIPOLARS 47 39 REMARK 3 2DHNC' DIPOLARS 46 40 REMARK 3 REMARK 3 BREAKDOWN OF INTRAMOLECULAR PROTEIN DISTANCE RESTRAINTS REMARK 3 INTRARESIDUE 157 169 REMARK 3 SEQUENTIAL 274 216 REMARK 3 MEDIUM RANGE 247 155 REMARK 3 LONG RANGE 260 216 REMARK 3 BACKBONE H-BONDS 33 36 REMARK 3 REMARK 3 INTRA-DNA DISTANCES 41 53 REMARK 3 INTERMOLECULAR DISTANCES 50 68 REMARK 4 REMARK 4 1J4W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-DEC-01. REMARK 100 THE DEPOSITION ID IS D_1000001616. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 6.80 REMARK 210 IONIC STRENGTH : 50 MM SODIUM PHOSPHATE REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : (1) TRIPLE RESONANCE FOR REMARK 210 ASSIGNMENT OF PROTEIN. (2) REMARK 210 QUANTITATIVE J CORRELATION FOR REMARK 210 COUPLING CONSTANTS. (3) 3D; 4D REMARK 210 HETERONUCLEAR SEPARATED; REMARK 210 FILTERED NOE EXPTS. (4) 2D 12C- REMARK 210 FILTERED EXPERIMENTS FOR DNA REMARK 210 ASSIGNMENTS. (5) IPAP EXPTS FOR REMARK 210 DIPOLAR COUPLINGS WERE MEASURED REMARK 210 IN A LIQUID CRYSTALLINE MEDIUM REMARK 210 OF PHAGE FD (25 MG/ML) REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 750 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DMX AND DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XPLOR_NIH REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 80 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : REGULARIZED MEAN STRUCTURE REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 RES C SSSEQI REMARK 465 DG B 201 REMARK 465 DT B 202 REMARK 465 DA B 203 REMARK 465 DC B 212 REMARK 465 DG B 213 REMARK 465 DG B 214 REMARK 465 DG B 215 REMARK 465 DA B 223 REMARK 465 DT B 224 REMARK 465 DT B 225 REMARK 465 DT B 226 REMARK 465 DT B 227 REMARK 465 DG B 228 REMARK 465 DT B 229 REMARK 465 ALA A 75 REMARK 465 GLY A 76 REMARK 465 ASN A 77 REMARK 465 PRO A 78 REMARK 465 GLY A 79 REMARK 465 GLY A 80 REMARK 465 PRO A 81 REMARK 465 GLY A 82 REMARK 465 PRO A 83 REMARK 465 GLY A 84 REMARK 465 GLY A 85 REMARK 465 ARG A 86 REMARK 465 GLY A 87 REMARK 465 ARG A 88 REMARK 465 GLY A 89 REMARK 465 ARG A 90 REMARK 465 GLY A 91 REMARK 465 GLN A 92 REMARK 465 GLY A 93 REMARK 465 ASN A 94 REMARK 465 TRP A 95 REMARK 465 ASN A 96 REMARK 465 MET A 97 REMARK 465 GLY A 98 REMARK 465 PRO A 99 REMARK 465 PRO A 100 REMARK 465 GLY A 101 REMARK 465 GLY A 102 REMARK 465 LEU A 103 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (RES=RESIDUE NAME; REMARK 470 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 470 RES CSSEQI ATOMS REMARK 470 DT B 204 P OP1 OP2 O5' REMARK 470 DA B 216 P OP1 OP2 O5' 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 O ILE A 28 H ALA A 32 1.55 REMARK 500 O GLU A 171 H ILE A 174 1.56 REMARK 500 O ILE A 25 H GLN A 29 1.59 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 PRO A 40 160.84 -38.22 REMARK 500 THR A 44 -12.62 60.49 REMARK 500 PRO A 46 49.99 -77.68 REMARK 500 PRO A 143 109.50 -48.58 REMARK 500 GLU A 171 -79.42 -53.94 REMARK 500 GLU A 172 -17.46 -34.42 REMARK 500 REMARK 500 REMARK: NULL DBREF 1J4W A 5 174 UNP Q96AE4 FUBP1_HUMAN 278 447 DBREF 1J4W B 201 229 PDB 1J4W 1J4W 201 229 SEQADV 1J4W GLY A 1 UNP Q96AE4 CLONING ARTIFACT SEQADV 1J4W SER A 2 UNP Q96AE4 CLONING ARTIFACT SEQADV 1J4W HIS A 3 UNP Q96AE4 CLONING ARTIFACT SEQADV 1J4W MET A 4 UNP Q96AE4 CLONING ARTIFACT SEQADV 1J4W ALA A 59 UNP Q96AE4 CYS 332 ENGINEERED MUTATION SEQRES 1 B 29 DG DT DA DT DA DT DT DC DC DC DT DC DG SEQRES 2 B 29 DG DG DA DT DT DT DT DT DT DA DT DT DT SEQRES 3 B 29 DT DG DT SEQRES 1 A 174 GLY SER HIS MET ILE ASP VAL PRO ILE PRO ARG PHE ALA SEQRES 2 A 174 VAL GLY ILE VAL ILE GLY ARG ASN GLY GLU MET ILE LYS SEQRES 3 A 174 LYS ILE GLN ASN ASP ALA GLY VAL ARG ILE GLN PHE LYS SEQRES 4 A 174 PRO ASP ASP GLY THR THR PRO GLU ARG ILE ALA GLN ILE SEQRES 5 A 174 THR GLY PRO PRO ASP ARG ALA GLN HIS ALA ALA GLU ILE SEQRES 6 A 174 ILE THR ASP LEU LEU ARG SER VAL GLN ALA GLY ASN PRO SEQRES 7 A 174 GLY GLY PRO GLY PRO GLY GLY ARG GLY ARG GLY ARG GLY SEQRES 8 A 174 GLN GLY ASN TRP ASN MET GLY PRO PRO GLY GLY LEU GLN SEQRES 9 A 174 GLU PHE ASN PHE ILE VAL PRO THR GLY LYS THR GLY LEU SEQRES 10 A 174 ILE ILE GLY LYS GLY GLY GLU THR ILE LYS SER ILE SER SEQRES 11 A 174 GLN GLN SER GLY ALA ARG ILE GLU LEU GLN ARG ASN PRO SEQRES 12 A 174 PRO PRO ASN ALA ASP PRO ASN MET LYS LEU PHE THR ILE SEQRES 13 A 174 ARG GLY THR PRO GLN GLN ILE ASP TYR ALA ARG GLN LEU SEQRES 14 A 174 ILE GLU GLU LYS ILE HELIX 1 1 ARG A 11 GLY A 19 1 9 HELIX 2 2 GLY A 22 GLY A 33 1 12 HELIX 3 3 PRO A 55 GLN A 74 1 20 HELIX 4 4 LYS A 114 GLY A 120 1 7 HELIX 5 5 GLY A 123 GLY A 134 1 12 HELIX 6 6 THR A 159 ILE A 174 1 16 SHEET 1 A 3 HIS A 3 PRO A 10 0 SHEET 2 A 3 GLU A 47 GLY A 54 -1 O ALA A 50 N VAL A 7 SHEET 3 A 3 ARG A 35 LYS A 39 -1 N GLN A 37 O GLN A 51 SHEET 1 B 3 GLU A 105 PRO A 111 0 SHEET 2 B 3 MET A 151 ARG A 157 -1 O PHE A 154 N PHE A 108 SHEET 3 B 3 ARG A 136 GLN A 140 -1 N ARG A 136 O ARG A 157 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