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- PDB-2cka: Solution structures of the BRK domains of the human Chromo Helica... -

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Basic information

Entry
Database: PDB / ID: 2cka
TitleSolution structures of the BRK domains of the human Chromo Helicase Domain 7 and 8, reveals structural similarity with GYF domain suggesting a role in protein interaction
ComponentsCHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 8
KeywordsHYDROLASE / BRK DOMAIN / TRANSCRIPTION ELONGATION / CHROMATIN REMODELING / PROTEIN-PROTEIN INTERACTION / TRANSCRIPTION / HELICASE / NUCLEAR PROTEIN / CHROMATIN REGULATOR
Function / homology
Function and homology information


negative regulation of fibroblast apoptotic process / ATP-dependent chromatin remodeler activity / digestive tract development / positive regulation of transcription by RNA polymerase III / social behavior / MLL1 complex / prepulse inhibition / : / Deactivation of the beta-catenin transactivating complex / negative regulation of canonical Wnt signaling pathway ...negative regulation of fibroblast apoptotic process / ATP-dependent chromatin remodeler activity / digestive tract development / positive regulation of transcription by RNA polymerase III / social behavior / MLL1 complex / prepulse inhibition / : / Deactivation of the beta-catenin transactivating complex / negative regulation of canonical Wnt signaling pathway / brain development / beta-catenin binding / Wnt signaling pathway / mRNA processing / p53 binding / DNA helicase / histone binding / in utero embryonic development / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / chromatin remodeling / negative regulation of DNA-templated transcription / chromatin binding / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
Chromodomain-helicase-DNA-binding protein 8 / Ribosomal Protein L9; domain 1 - #120 / : / : / Chromodomain-helicase-DNA-binding protein 6-9, tri-helical / BRK domain / Ribosomal Protein L9; domain 1 / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases ...Chromodomain-helicase-DNA-binding protein 8 / Ribosomal Protein L9; domain 1 - #120 / : / : / Chromodomain-helicase-DNA-binding protein 6-9, tri-helical / BRK domain / Ribosomal Protein L9; domain 1 / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like domain superfamily / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chromodomain-helicase-DNA-binding protein 8
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodSOLUTION NMR / CANDID IN CYANA
AuthorsAb, E. / de Jong, R.N. / Diercks, T. / Xiaoyun, J. / Daniels, M. / Kaptein, R. / Folkers, G.E.
CitationJournal: To be Published
Title: Solution Structures of the Brk Domains of the Human Chromo Helicase Domain 7 and 8, Reveals Structural Similarity with Gyf Domain Suggesting a Role in Protein Interaction
Authors: Ab, E. / De Jong, R.N. / Diercks, T. / Xiaoyun, J. / Daniels, M. / Kaptein, R. / Folkers, G.E.
History
DepositionApr 14, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 15, 2020Group: Data collection / Other / Category: pdbx_database_status / pdbx_nmr_software
Item: _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name
Revision 1.4Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.5Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 8


Theoretical massNumber of molelcules
Total (without water)11,0601
Polymers11,0601
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 / 50LEAST RESTRAINT VIOLATION
RepresentativeModel #1

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Components

#1: Protein CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 8 / ATP-DEPENDENT HELICASE CHD8 / CHD-8 / HELICASE WITH SNF2 DOMAIN 1


Mass: 11059.638 Da / Num. of mol.: 1 / Fragment: BRK DOMAIN, RESIDUES 2012-2085
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: SELF MADE CDNA LIBRARY OF MULTIPLE HUMAN CARCINOMA CELL LINES
Plasmid: PHISLIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA
References: UniProt: Q9HCK8, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCO
121HN(CA)CO
131HN(CA)CB
141CBCA(CO)NH
151HBHA(CO)NH
161HNCAHA
171CC(CO)NH
181CCH-COSY
191(H)CCH- TOCSY
1101HNH-NOESY
1111HCH- NOESY
1121CNH-NOESY
1131HH- NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED CHD8 2012-2085

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Sample preparation

DetailsContents: 95% H2O/5% D2O
Sample conditionsIonic strength: 150 mM / pH: 7 / Pressure: 1.0 atm / Temperature: 298.0 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
Sparkystructure solution
RefinementMethod: CANDID IN CYANA / Software ordinal: 1
Details: EFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 50 / Conformers submitted total number: 20

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