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- PDB-8ez6: The DBC1/SIRT1 Interaction is Choreographed by Post-translational... -

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Basic information

Entry
Database: PDB / ID: 8ez6
TitleThe DBC1/SIRT1 Interaction is Choreographed by Post-translational Modification
ComponentsCell cycle and apoptosis regulator protein 2
KeywordsGENE REGULATION / DBC1 / S1-like / insulin signaling / liver metabolism / chaperone
Function / homology
Function and homology information


DBIRD complex / regulation of protein deacetylation / positive regulation of DNA damage checkpoint / adenyl-nucleotide exchange factor activity / mitochondrial fragmentation involved in apoptotic process / negative regulation of catalytic activity / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / enzyme inhibitor activity / RNA polymerase II complex binding / Regulation of HSF1-mediated heat shock response ...DBIRD complex / regulation of protein deacetylation / positive regulation of DNA damage checkpoint / adenyl-nucleotide exchange factor activity / mitochondrial fragmentation involved in apoptotic process / negative regulation of catalytic activity / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage / enzyme inhibitor activity / RNA polymerase II complex binding / Regulation of HSF1-mediated heat shock response / response to UV / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / RNA splicing / regulation of DNA-templated transcription elongation / regulation of protein stability / regulation of circadian rhythm / negative regulation of cell growth / Wnt signaling pathway / mRNA processing / spindle / unfolded protein binding / positive regulation of canonical Wnt signaling pathway / rhythmic process / cell cycle / mitochondrial matrix / positive regulation of apoptotic process / negative regulation of DNA-templated transcription / DNA damage response / chromatin / enzyme binding / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
S1-like RNA binding domain / Cell cycle and apoptosis regulator protein / DBC1/CARP1 catalytically inactive NUDIX hydrolase domain / LAIKA domain / BURAN domain / DBC1 / S1-like / LAIKA domain / BURAN domain / DBC1 / EF-hand domain pair
Similarity search - Domain/homology
Cell cycle and apoptosis regulator protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKrzysiak, T.C. / Gronenborn, A.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK114855 United States
CitationJournal: Protein Sci. / Year: 2024
Title: Inhibitory protein-protein interactions of the SIRT1 deacetylase are choreographed by post-translational modification.
Authors: Krzysiak, T.C. / Choi, Y.J. / Kim, Y.J. / Yang, Y. / DeHaven, C. / Thompson, L. / Ponticelli, R. / Mermigos, M.M. / Thomas, L. / Marquez, A. / Sipula, I. / Kemper, J.K. / Jurczak, M. / ...Authors: Krzysiak, T.C. / Choi, Y.J. / Kim, Y.J. / Yang, Y. / DeHaven, C. / Thompson, L. / Ponticelli, R. / Mermigos, M.M. / Thomas, L. / Marquez, A. / Sipula, I. / Kemper, J.K. / Jurczak, M. / Thomas, G. / Gronenborn, A.M.
History
DepositionOct 31, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year
Revision 1.2Apr 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell cycle and apoptosis regulator protein 2
B: Cell cycle and apoptosis regulator protein 2


Theoretical massNumber of molelcules
Total (without water)16,0002
Polymers16,0002
Non-polymers00
Water82946
1
A: Cell cycle and apoptosis regulator protein 2


Theoretical massNumber of molelcules
Total (without water)8,0001
Polymers8,0001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cell cycle and apoptosis regulator protein 2


Theoretical massNumber of molelcules
Total (without water)8,0001
Polymers8,0001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.388, 50.822, 62.066
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Cell cycle and apoptosis regulator protein 2 / Cell division cycle and apoptosis regulator protein 2 / DBIRD complex subunit KIAA1967 / Deleted in ...Cell division cycle and apoptosis regulator protein 2 / DBIRD complex subunit KIAA1967 / Deleted in breast cancer gene 1 protein / DBC-1 / DBC.1 / NET35 / p30 DBC


Mass: 8000.075 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CCAR2, DBC1, KIAA1967 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N163
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.84 Å3/Da / Density % sol: 33.25 %
Crystal growTemperature: 298 K / Method: microbatch / Details: 0.1M sodium acetate pH 4.6, 2M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Dec 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→39.32 Å / Num. obs: 8285 / % possible obs: 97.9 % / Redundancy: 13.59 % / Biso Wilson estimate: 20.73 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 37.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 13.69 % / Rmerge(I) obs: 0.127 / Num. unique obs: 602 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158_4158refinement
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WFQ

1wfq


Resolution: 2→39.32 Å / SU ML: 0.2205 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 22.3753
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2382 826 10 %
Rwork0.2018 7431 -
obs0.2053 8257 97.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.22 Å2
Refinement stepCycle: LAST / Resolution: 2→39.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1023 0 0 46 1069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01041045
X-RAY DIFFRACTIONf_angle_d1.27721419
X-RAY DIFFRACTIONf_chiral_restr0.0824164
X-RAY DIFFRACTIONf_plane_restr0.0066180
X-RAY DIFFRACTIONf_dihedral_angle_d13.0664375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.130.261330.21791195X-RAY DIFFRACTION96.51
2.13-2.290.26641320.19771193X-RAY DIFFRACTION96.79
2.29-2.520.22991360.21391228X-RAY DIFFRACTION97.92
2.52-2.880.27231370.22211225X-RAY DIFFRACTION98.13
2.88-3.630.2161400.19341261X-RAY DIFFRACTION99.01
3.63-39.320.22961480.19211329X-RAY DIFFRACTION99.13

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