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- PDB-2kzu: DAXX helical bundle (DHB) domain / Rassf1C complex -

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Basic information

Entry
Database: PDB / ID: 2kzu
TitleDAXX helical bundle (DHB) domain / Rassf1C complex
Components
  • Death-associated protein 6
  • Ras association (RalGDS/AF-6) domain family 1
KeywordsAPOPTOSIS / Fas death-domain associated protein / DAXX helical bundle domain / Ras-association domain family 1C protein / tumor suppressor
Function / homology
Function and homology information


cellular response to diamide / Defective Inhibition of DNA Recombination at Telomere Due to DAXX Mutations / Defective Inhibition of DNA Recombination at Telomere Due to ATRX Mutations / neuron intrinsic apoptotic signaling pathway in response to oxidative stress / cellular response to sodium arsenite / regulation of cell cycle G1/S phase transition / nuclear androgen receptor binding / cellular response to cadmium ion / androgen receptor signaling pathway / protein kinase activator activity ...cellular response to diamide / Defective Inhibition of DNA Recombination at Telomere Due to DAXX Mutations / Defective Inhibition of DNA Recombination at Telomere Due to ATRX Mutations / neuron intrinsic apoptotic signaling pathway in response to oxidative stress / cellular response to sodium arsenite / regulation of cell cycle G1/S phase transition / nuclear androgen receptor binding / cellular response to cadmium ion / androgen receptor signaling pathway / protein kinase activator activity / chromosome, centromeric region / extrinsic apoptotic signaling pathway via death domain receptors / regulation of protein ubiquitination / cellular response to unfolded protein / transcription regulator inhibitor activity / JNK cascade / cellular response to copper ion / heat shock protein binding / Inhibition of DNA recombination at telomere / SUMOylation of transcription cofactors / positive regulation of protein ubiquitination / molecular condensate scaffold activity / PML body / HCMV Early Events / spindle pole / transcription corepressor activity / p53 binding / Regulation of TP53 Degradation / nucleosome assembly / positive regulation of protein phosphorylation / cellular response to heat / microtubule cytoskeleton / regulation of gene expression / regulation of apoptotic process / RNA polymerase II-specific DNA-binding transcription factor binding / histone binding / microtubule / Ras protein signal transduction / transcription coactivator activity / regulation of cell cycle / protein stabilization / nuclear body / chromatin remodeling / negative regulation of gene expression / negative regulation of DNA-templated transcription / centrosome / ubiquitin protein ligase binding / DNA damage response / regulation of DNA-templated transcription / protein kinase binding / nucleolus / enzyme binding / protein homodimerization activity / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ras association domain-containing protein 1 / Daxx helical bundle domain / Ras association domain-containing protein 1-6 / Novel Ras effector 1 C-terminal SARAH (Sav/Rassf/Hpo) domain / Daxx, N-terminal Rassf1C-interacting domain / Daxx, N-terminal domain superfamily / Daxx, histone-binding domain / Daxx, histone-binding domain superfamily / Daxx N-terminal Rassf1C-interacting domain / Death domain-associated protein 6, histone binding domain ...Ras association domain-containing protein 1 / Daxx helical bundle domain / Ras association domain-containing protein 1-6 / Novel Ras effector 1 C-terminal SARAH (Sav/Rassf/Hpo) domain / Daxx, N-terminal Rassf1C-interacting domain / Daxx, N-terminal domain superfamily / Daxx, histone-binding domain / Daxx, histone-binding domain superfamily / Daxx N-terminal Rassf1C-interacting domain / Death domain-associated protein 6, histone binding domain / SARAH domain / SARAH domain profile. / Ras association (RalGDS/AF-6) domain / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras-associating (RA) domain / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / Helicase, Ruva Protein; domain 3 / Ubiquitin-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Death domain associated protein / Ras association domain-containing protein 1 / Ras association domain-containing protein 1 / Death domain-associated protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 9
AuthorsEscobar-Cabrera, E. / Lau, D.K.W. / Giovinazzi, S. / Ishov, A.M. / McIntosh, L.P.
CitationJournal: Structure / Year: 2010
Title: Structural Characterization of the DAXX N-Terminal Helical Bundle Domain and Its Complex with Rassf1C.
Authors: Escobar-Cabrera, E. / Lau, D.K. / Giovinazzi, S. / Ishov, A.M. / McIntosh, L.P.
History
DepositionJun 25, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _struct_ref_seq_dif.details
Revision 1.3Jun 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 1.4May 15, 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: Death-associated protein 6
B: Ras association (RalGDS/AF-6) domain family 1


Theoretical massNumber of molelcules
Total (without water)13,1002
Polymers13,1002
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)25 / 120structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Death-associated protein 6


Mass: 10950.833 Da / Num. of mol.: 1 / Fragment: UNP residues 55 to 144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: cloned with BamHI EcoRI
Gene: DAXX, DADB-159G18.9-007, DAMC-227D19.15-007, DAQB-126H3.2-007, XXbac-BCX165D10.3-007, XXbac-BPG185D15.6-007
Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q4VX54, UniProt: Q9UER7*PLUS
#2: Protein/peptide Ras association (RalGDS/AF-6) domain family 1 / Ras association (RalGDS/AF-6) domain family 1 / isoform CRA_a


Mass: 2149.166 Da / Num. of mol.: 1 / Fragment: UNP residues 23 to 38
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RASSF1, hCG_17462 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5TZT2, UniProt: Q9NS23*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-15N HSQC
1323D CBCA(CO)NH
1423D HN(CA)CB
1513D CBCA(CO)NH
1613D (H)CCH-TOCSY
1712D 1H-13C HSQC
181(H)CC(CO)NH-TOCSY
191HCC(CO)NH-TOCSY
1101(HB)CB(CGCD)HD
1111(HB)CB(CGCDCE)HE
11213D 1H-15N NOESY
11313D 1H-13C NOESY
114113C/15N isotope-filtered NOESY-HSQC
115213C/15N isotope-filtered NOESY-HSQC
11623D 1H-15N NOESY
11723D 1H-13C NOESY
11822D 1H-13C HSQC
1192(H)CC(CO)NH-TOCSY
1202HCC(CO)NH-TOCSY
1212(HB)CB(CGCD)HD
1222(HB)CB(CGCD)HD-TOCSY
12323D 1H-15N TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.1 mM [U-100% 13C; U-100% 15N] DAXX-1, 1.65 mM Rassf1C-2, 95% H2O/5% D2O95% H2O/5% D2O
21.8 mM DAXX-3, 1.2 mM [U-100% 13C; U-100% 15N] Rassf1C-4, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMDAXX-1[U-100% 13C; U-100% 15N]1
1.65 mMRassf1C-21
1.8 mMDAXX-32
1.2 mMRassf1C-4[U-100% 13C; U-100% 15N]2
Sample conditionsIonic strength: 0 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian Unity / Manufacturer: Varian / Model: UNITY / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.2Linge, O'Donoghue and Nilgesstructure solution
ARIA2.2Linge, O'Donoghue and Nilgesrefinement
ARIA2.2Linge, O'Donoghue and Nilgessemi automatic peak assignments
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 2287 / NOE intraresidue total count: 949 / NOE long range total count: 340 / NOE medium range total count: 409 / NOE sequential total count: 480 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 81 / Protein psi angle constraints total count: 81
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 120 / Conformers submitted total number: 25 / Maximum lower distance constraint violation: 0 Å / Maximum upper distance constraint violation: 0.22 Å

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