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- PDB-1khm: C-TERMINAL KH DOMAIN OF HNRNP K (KH3) -

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Basic information

Entry
Database: PDB / ID: 1khm
TitleC-TERMINAL KH DOMAIN OF HNRNP K (KH3)
ComponentsPROTEIN (HNRNP K)
KeywordsRNA BINDING PROTEIN / HNRNP K / KH DOMAIN / THREE-DIMENSIONAL STRUCTURE / C-MYC / DIPOLAR COUPLING / DNA-BINDING / RNA-BINDING
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 / 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 ...regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of low-density lipoprotein particle clearance / 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 / cytoplasmic stress granule / positive regulation of receptor-mediated endocytosis / ribonucleoprotein complex / cadherin binding / protein domain specific binding / focal adhesion / negative regulation of DNA-templated transcription / mRNA binding / chromatin / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / 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
Heterogeneous nuclear ribonucleoprotein K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsBaber, J. / Libutti, D. / Levens, D. / Tjandra, N.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: High precision solution structure of the C-terminal KH domain of heterogeneous nuclear ribonucleoprotein K, a c-myc transcription factor.
Authors: Baber, J.L. / Libutti, D. / Levens, D. / Tjandra, N.
History
DepositionJan 7, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
A: PROTEIN (HNRNP K)


Theoretical massNumber of molelcules
Total (without water)9,6991
Polymers9,6991
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)20 / 100LOWEST OVERALL ENERGY
Representative

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Components

#1: Protein PROTEIN (HNRNP K) / KH3


Mass: 9698.854 Da / Num. of mol.: 1
Fragment: C-TERMINAL KH DOMAIN, RESIDUES 379-463 OF FULL LENGTH HNRNP K
Mutation: G26R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX-4T-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61978

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR

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Sample preparation

Sample conditionsIonic strength: 5 mM / pH: 5.5 / Pressure: 1 atm / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: nmr

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NMR measurement

NMR spectrometerType: Bruker AMX600 / Manufacturer: Bruker / Model: AMX600 / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1BRUNGERrefinement
X-PLOR3.1BRUNGERstructure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
Details: THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129-136, USING THE PROGRAM XPLOR 3.1 ( BRUNGER) MODIFIED TO INCORPORATE DIPOLAR ...Details: THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129-136, USING THE PROGRAM XPLOR 3.1 ( BRUNGER) MODIFIED TO INCORPORATE DIPOLAR COUPLING RESTRAINTS (UNPUBLISHED). THE 3D STRUCTURE OF THE C-TERMINAL G26R MUTANT KH DOMAIN OF HNRNP K WAS SOLVED BY MULTI-DIMENSIONAL HETERONUCLEAR-EDITED AND -FILTERED NMR. IT IS BASED ON 1567 EXPERIMENTAL RESTRAINTS: 448 INTRARESIDUE, 322 SEQUENTIAL (|I-J|=1), 198 MEDIUM RANGE (1 < |I-J| >=5) AND 279 LONG RANGE (|I-J| >5) DISTANCE RESTRAINTS; 55 DISTANCE RESTRAINTS FOR 28 HYDROGEN BONDS; 49 DNH, 59 DCH, 48 DC'N, AND 53 DCAC' DIPOLAR COUPLING RESTRAINTS; 56 PHI-ANGLE RESTRAINTS FROM HN-HA COUPLING CONSTANTS. THE 20 STRUCTURES ARE ARRANGED IN ORDER OF INCREASING OVERALL ENERGY WITH MODEL 1 THE LOWEST. MODEL 9 HAS THE SMALLEST BACKBONE PAIRWISE RMS TO THE AVERAGE STRUCTURE.
NMR ensembleConformer selection criteria: LOWEST OVERALL ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 20

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