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- PDB-1j4w: COMPLEX OF THE KH3 and KH4 DOMAINS OF FBP WITH A SINGLE_STRANDED ... -

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Basic information

Entry
Database: PDB / ID: 1j4w
TitleCOMPLEX OF THE KH3 and KH4 DOMAINS OF FBP WITH A SINGLE_STRANDED 29mer DNA OLIGONUCLEOTIDE FROM THE FUSE ELEMENT OF THE C-MYC ONCOGENE
Components
  • DNA (5'-D(*GP*TP*A*TP*AP*TP*TP*CP*CP*CP*TP*CP*GP*GP*G*AP*TP*TP*TP*TP*TP*TP*AP*TP*TP*TP*TP*GP*T)-3')
  • FUSE binding protein
KeywordsTRANSCRIPTION/DNA / SINGLE-STRANDED DNA BINDING PROTEIN / TRANSCRIPTION FACTOR / FBP / FUSE ELEMENT / C-MYC ONCOGENE / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


single-stranded DNA binding / regulation of gene expression / mRNA binding / positive regulation of gene expression / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
: / : / : / : / Far upstream element-binding protein, C-terminal / Domain of unknown function (DUF1897) / K Homology domain, type 1 / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. ...: / : / : / : / Far upstream element-binding protein, C-terminal / Domain of unknown function (DUF1897) / K Homology domain, type 1 / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / Ribosomal Protein S8; Chain: A, domain 1 / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Far upstream element-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsClore, G.M. / Braddock, D.T.
CitationJournal: Nature / Year: 2002
Title: Structure and dynamics of KH domains from FBP bound to single-stranded DNA.
Authors: Braddock, D.T. / Louis, J.M. / Baber, J.L. / Levens, D. / Clore, G.M.
History
DepositionNov 30, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: DNA (5'-D(*GP*TP*A*TP*AP*TP*TP*CP*CP*CP*TP*CP*GP*GP*G*AP*TP*TP*TP*TP*TP*TP*AP*TP*TP*TP*TP*GP*T)-3')
A: FUSE binding protein


Theoretical massNumber of molelcules
Total (without water)27,5162
Polymers27,5162
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 80REGULARIZED MEAN STRUCTURE
Representative

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Components

#1: DNA chain DNA (5'-D(*GP*TP*A*TP*AP*TP*TP*CP*CP*CP*TP*CP*GP*GP*G*AP*TP*TP*TP*TP*TP*TP*AP*TP*TP*TP*TP*GP*T)-3')


Mass: 8877.711 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: FROM THE FUSE ELEMENT OF THE C-MYC ONCOGENE
#2: Protein FUSE binding protein / FBP / FAR UPSTREAM BINDING ELEMENT PROTEIN


Mass: 18638.188 Da / Num. of mol.: 1
Fragment: RESIDUES 278-447, NUMBERERED 5-174. KH3 AND KH4 DOMAINS.
Mutation: C59A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BE23 / References: UniProt: Q96AE4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111(1) TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN. (2) QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS. (3) 3D
1214D HETERONUCLEAR SEPARATED
131FILTERED NOE EXPTS. (4) 2D 12C-FILTERED EXPERIMENTS FOR DNA ASSIGNMENTS. (5) IPAP EXPTS FOR DIPOLAR COUPLINGS WERE MEASURED IN A LIQUID CRYSTALLINE MEDIUM OF PHAGE FD (25 MG/ML)

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Sample preparation

Sample conditionsIonic strength: 50 mM SODIUM PHOSPHATE / pH: 6.80 / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMX AND DRXBrukerDMX AND DRX6001
Bruker DMX AND DRXBrukerDMX AND DRX7502
Bruker DMX AND DRXBrukerDMX AND DRX8003

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR NIH(HTTP://NMR.CIT.NIH.GOV/XPLOR_NIH)CLORE, KUSZEWSKI, SCHWIETERS, TJANDRArefinement
XPLOR_NIHstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: THE STRUCTURES WERE CALCULATED BY SIMULATED ANNEALING IN TORSION ANGLE SPACE (SCHWIETERS AND CLORE (2001) J MAGN RESON 152, 288-302) AGAINST A TARGET FUNCTION COMPRISING THE EXPERIMENTAL NMR ...Details: THE STRUCTURES WERE CALCULATED BY SIMULATED ANNEALING IN TORSION ANGLE SPACE (SCHWIETERS AND CLORE (2001) J MAGN RESON 152, 288-302) AGAINST A TARGET FUNCTION COMPRISING THE EXPERIMENTAL NMR RESTRAINTS (NOE-DERIVED INTERPROTON DISTANCE, TORSION ANGLE, 3J COUPLING, 13CALPHA/13CBETA SHIFTS AND DIPOLAR COUPLINGS). THE NON-BONDED CONTACTS IN THE TARGET FUNCTION ARE REPRESENTED BY A QUARTIC VAN DER WAALS REPULSION TERM, SUPPLEMENTED BY TORSION ANGLE (KUSZEWSKI ET AL. J. MAGN. RESON 125, 171-177 (1997)) BASE-BASE POSITIONAL (KUSZEWSKI ET AL. J AM CHEM SOC 123, 3903-3918 (2001)) DATABASE POTENTIALS OF MEAN FORCE. IN THIS ENTRY THE LAST NUMERICAL COLUMN IS THE RMS OF THE 80 INDIVIDUAL SIMULATED ANNEALING STRUCTURES (FOR EACH HALF OF THE COMPLEX) ABOUT THE MEAN COORDINATE POSITIONS: RESIDUES 75-103 OF THE PROTEIN ARE DISORDERED IN THE COMPLEX. ALTHOUGH THE SINGLE-STRANDED DNA IS B-LIKE, THE COORDINATES OF THOSE PORTIONS OF THE SS-DNA NOT IN CONTACT WITH THE PROTEIN COULD NOT BE ACCURATELY DETERMINED (BASES 201-203, 212-215 AND 223-229). THEREFORE THE COORDINATES ARE PRESENTED IN TWO HALVES: THE KH3 HALF OF THE COMPLEX (RESIDUES 1-74 OF THE PROTEIN AND BASES 216-222 OF THE SS-DNA) AND THE KH4 HALF OF THE COMPLEX (RESIDUES 104-174 OF THE PROTEIN AND BASES 204-211 OF THE SS-DNA). THE COORDINATE ACCURACY IS CALCULATED FOR THE TWO HALVES OF THE COMPLEX SEPARATELY. THE APPROXIMATE ORIENTATION OF AND SEPARATION BETWEEN THE TWO DOMAINS COULD BE DERIVED FROM ANALYSIS OF HETERONUCLEAR RELAXATION MEASUREMENTS. THE ORIENTATIONS OF THE TWO HALVES OF THE COMPLEX IN THESE COORDINATES REFLECTS THE RESULTS OF THE RELAXATION MEASUREMENTS. THE AVERAGE ORIENTATION OF THE TWO HALVES OF THE COMPLEX IS PARALLEL WITH AN AVERAGE INTERHELICAL ANGLE OF ABOUT 1 DEGREE BETWEEN THE THIRD HELIX OF EACH DOMAIN. THE OVERALL ROTATIONAL CORRELATION TIME OF THE COMPLEX IS 21.5 NS WITH A DIFFUSION ANISOTROPY OF 1.85. THE TIME SCALE FOR THE INTERDOMAIN MOTIONS IS AROUND 4 NS AND THE TWO DOMAINS WOBBLE INDEPENDENTLY IN CONES WITH SEMI-ANGLES OF ABOUT 30 DEGREES. THE OVERALL LENGTH OF THE COMPLEX IS ABOUT 100 ANGSTROMS AND THE SEPARATION BETWEEN THE TWO HALVES OF THE COMPLEX IS AROUND 35 ANGSTROMS. THE RESTRAINED REGULARIZED MEAN STRUCTURE FOR THE TWO HALVES OF THE COMPLEX IS OBTAINED BY RESTRAINED REGULARIZATION OF THE AVERAGE COORDINATES AGAINST THE SAME TARGET FUNCTION USED TO CALCULATE THE SIMULATED ANNEALING STRUCTURES. SOLVED BY MULTI HETERONUCLEAR NMR AND IS BASED ON 3153 EXPERIMENTAL NMR RESTRAINTS KH3 HALF KH4 HALF DISTANCES 1095 949 TORSION ANGLES 244 261 3JHNA COUPLINGS 33 36 13CA/CB SHIFTS 120 121 1DNH DIPOLARS 61 61 1DNC' DIPOLARS 47 39 2DHNC' DIPOLARS 46 40 BREAKDOWN OF INTRAMOLECULAR PROTEIN DISTANCE RESTRAINTS INTRARESIDUE 157 169 SEQUENTIAL 274 216 MEDIUM RANGE 247 155 LONG RANGE 260 216 BACKBONE H-BONDS 33 36 INTRA-DNA DISTANCES 41 53 INTERMOLECULAR DISTANCES 50 68
NMR ensembleConformer selection criteria: REGULARIZED MEAN STRUCTURE / Conformers calculated total number: 80 / Conformers submitted total number: 1

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