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- PDB-1j5k: COMPLEX OF THE KH3 DOMAIN OF HNRNP K WITH A SINGLE_STRANDED 10MER... -

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Basic information

Entry
Database: PDB / ID: 1j5k
TitleCOMPLEX OF THE KH3 DOMAIN OF HNRNP K WITH A SINGLE_STRANDED 10MER DNA OLIGONUCLEOTIDE
Components
  • 5'-D(*AP*TP*AP*T*TP*CP*CP*CP*TP*C)-3'
  • Heterogeneous nuclear ribonucleoprotein K
KeywordsTRANSCRIPTION/DNA / SINGLE-STRANDED DNA BINDING PROTEIN / TRANSCRIPTION FACTOR / HNRNP K / CT ELEMENT / C-MYC ONCOGENE / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of low-density lipoprotein particle clearance / random inactivation of X chromosome / regulatory ncRNA-mediated heterochromatin formation / regulation of mRNA splicing, via spliceosome / SUMOylation of RNA binding proteins / podosome / positive regulation of low-density lipoprotein receptor activity / negative regulation of mRNA splicing, via spliceosome / Processing of Capped Intron-Containing Pre-mRNA ...regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of low-density lipoprotein particle clearance / random inactivation of X chromosome / regulatory ncRNA-mediated heterochromatin formation / regulation of mRNA splicing, via spliceosome / SUMOylation of RNA binding proteins / podosome / positive regulation of low-density lipoprotein receptor activity / negative regulation of mRNA splicing, via spliceosome / Processing of Capped Intron-Containing Pre-mRNA / RNA processing / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / HCMV Late Events / cell projection / mRNA splicing, via spliceosome / positive regulation of receptor-mediated endocytosis / cytoplasmic stress granule / cadherin binding / ribonucleoprotein complex / protein domain specific binding / focal adhesion / negative regulation of DNA-templated transcription / mRNA binding / chromatin / negative regulation of apoptotic process / regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / membrane / nucleus / cytoplasm
Similarity search - Function
ROK, N-terminal / ROKNT (NUC014) domain / K Homology domain, type 1 / KH domain / K Homology domain, type 1 / Ribosomal Protein S8; Chain: A, domain 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain ...ROK, N-terminal / ROKNT (NUC014) domain / K Homology domain, type 1 / KH domain / K Homology domain, type 1 / Ribosomal Protein S8; Chain: A, domain 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / Heterogeneous nuclear ribonucleoprotein K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsClore, G.M. / Braddock, D.T.
CitationJournal: EMBO J. / Year: 2002
Title: Molecular basis of sequence-specific single-stranded DNA recognition by KH domains: solution structure of a complex between hnRNP K KH3 and single-stranded DNA.
Authors: Braddock, D.T. / Baber, J.L. / Levens, D. / Clore, G.M.
History
DepositionMay 13, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: 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

Downloads & links

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Assembly

Deposited unit
B: 5'-D(*AP*TP*AP*T*TP*CP*CP*CP*TP*C)-3'
A: Heterogeneous nuclear ribonucleoprotein K


Theoretical massNumber of molelcules
Total (without water)12,6122
Polymers12,6122
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 125REGULARIZED MEAN STRUCTURE
Representative

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Components

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


Mass: 2954.955 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein Heterogeneous nuclear ribonucleoprotein K / HNRNP K / DC-stretch binding protein / CSBP / Transformation upregulated nuclear protein / TUNP


Mass: 9656.836 Da / Num. of mol.: 1 / Fragment: KH3 domain, RESIDUES 379-463, NUMBERED 5-89
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: P61978

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: (5) IPAP EXPTS FOR DIPOLAR COUPLINGS WERE MEASURED IN A LIQUID CRYSTALLINE MEDIUM OF PHAGE PF1 (18 MG/ML), 5% C12E5 POLYETHYLENE GLYCOL/HEXANOL (MOLAR RATIO OF SURFACTANT TO ALCOHOL 0.96)
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111(1) TRIPLE RESONANCE FOR ASSIGNMENT OF PROTEIN
121(2) QUANTITATIVE J CORRELATION FOR COUPLING CONSTANTS
131(3) 3D, 4D HETERONUCLEAR SEPARATED, FILTERED NOE EXPTS
141(4) 2D 12C-FILTERED EXPERIMENTS FOR DNA ASSIGNMENTS
151(5) IPAP EXPTS FOR DIPOLAR COUPLINGS

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Sample preparation

Sample conditionsIonic strength: 50 mM SODIUM PHOSPHATE / pH: 6.8 / Temperature: 308 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker DRXBrukerDRX7502
Bruker DRXBrukerDRX8003

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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, 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)) AND 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 125 INDIVIDUAL SIMULATED ANNEALING STRUCTURES ABOUT THE MEAN COORDINATE POSITIONS: RESIDUES 1-9 and 86-89 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 101-104 and 110). THEREFORE ONLY THE COORDINATES OF RESIDUES 10-85 AND NUCLEOTIDES 105-109 ARE PRESENTED. SOLVED BY MULTI HETERONUCLEAR NMR AND IS BASED ON 1986 EXPERIMENTAL NMR RESTRAINTS DISTANCES 1289 TORSION ANGLES 266 13CA/CB SHIFTS 144 1DNH DIPOLARS IN PEG/HEXANOL 63 1DNC' DIPOLARS IN PEG/HEXANOL 44 2DHNC' DIPOLARS IN PEG/HEXANOL 40 1DNH DIPOLARS IN PHAGE PF1 56 1DNC' DIPOLARS IN PHAGE PF1 42 2DHNC' DIPOLARS IN PHAGE PF1 42 BREAKDOWN OF INTRAMOLECULAR PROTEIN DISTANCE RESTRAINTS INTRARESIDUE 315 SEQUENTIAL 282 MEDIUM RANGE 197 LONG RANGE 300 BACKBONE H-BONDS 54 RESTRAINTS FOR 27 H-BONDS INTRA-DNA DISTANCES 68 INTERMOLECULAR DISTANCES 73
NMR ensembleConformer selection criteria: REGULARIZED MEAN STRUCTURE / Conformers calculated total number: 125 / Conformers submitted total number: 1

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