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- PDB-7sme: p107 pocket domain complexed with HDAC1 peptide -

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Basic information

Entry
Database: PDB / ID: 7sme
Titlep107 pocket domain complexed with HDAC1 peptide
Components
  • Histone deacetylase 1
  • Retinoblastoma-like protein 1
KeywordsCELL CYCLE / Transcription / cyclin box pocket transcriptional regulator
Function / homology
Function and homology information


Loss of MECP2 binding ability to 5mC-DNA / Krueppel-associated box domain binding / regulation of lipid kinase activity / Repression of WNT target genes / MECP2 regulates transcription of neuronal ligands / p75NTR negatively regulates cell cycle via SC1 / epidermal cell differentiation / histone decrotonylase activity / fungiform papilla formation / negative regulation of androgen receptor signaling pathway ...Loss of MECP2 binding ability to 5mC-DNA / Krueppel-associated box domain binding / regulation of lipid kinase activity / Repression of WNT target genes / MECP2 regulates transcription of neuronal ligands / p75NTR negatively regulates cell cycle via SC1 / epidermal cell differentiation / histone decrotonylase activity / fungiform papilla formation / negative regulation of androgen receptor signaling pathway / regulation of cell fate specification / negative regulation of stem cell population maintenance / endoderm development / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / regulation of stem cell differentiation / NuRD complex / DNA methylation-dependent heterochromatin formation / protein deacetylation / Transcription of E2F targets under negative control by DREAM complex / STAT3 nuclear events downstream of ALK signaling / histone deacetylase / protein lysine deacetylase activity / positive regulation of signaling receptor activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / embryonic digit morphogenesis / negative regulation of gene expression, epigenetic / negative regulation of G1/S transition of mitotic cell cycle / positive regulation of oligodendrocyte differentiation / histone deacetylase activity / Sin3-type complex / positive regulation of stem cell population maintenance / G1/S-Specific Transcription / cellular response to platelet-derived growth factor stimulus / Notch-HLH transcription pathway / eyelid development in camera-type eye / oligodendrocyte differentiation / E-box binding / odontogenesis of dentin-containing tooth / negative regulation of cellular senescence / RNA Polymerase I Transcription Initiation / histone deacetylase complex / hair follicle placode formation / Regulation of MECP2 expression and activity / G0 and Early G1 / NF-kappaB binding / negative regulation by host of viral transcription / RNA polymerase II core promoter sequence-specific DNA binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / heterochromatin / Nuclear events stimulated by ALK signaling in cancer / MECP2 regulates neuronal receptors and channels / core promoter sequence-specific DNA binding / negative regulation of intrinsic apoptotic signaling pathway / negative regulation of canonical NF-kappaB signal transduction / Regulation of TP53 Activity through Acetylation / transcription repressor complex / SUMOylation of chromatin organization proteins / negative regulation of cell migration / transcription corepressor binding / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Regulation of PTEN gene transcription / HDACs deacetylate histones / Deactivation of the beta-catenin transactivating complex / hippocampus development / promoter-specific chromatin binding / Downregulation of SMAD2/3:SMAD4 transcriptional activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / positive regulation of smooth muscle cell proliferation / Formation of the beta-catenin:TCF transactivating complex / negative regulation of transforming growth factor beta receptor signaling pathway / circadian regulation of gene expression / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / negative regulation of canonical Wnt signaling pathway / neuron differentiation / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / histone deacetylase binding / transcription corepressor activity / Cyclin D associated events in G1 / p53 binding / chromatin organization / Factors involved in megakaryocyte development and platelet production / DNA-binding transcription factor binding / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / Potential therapeutics for SARS / cell differentiation / chromatin remodeling / cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / negative regulation of DNA-templated transcription / neuronal cell body / positive regulation of cell population proliferation / positive regulation of gene expression
Similarity search - Function
Rb C-terminal domain / Retinoblastoma-associated protein, B-box / Retinoblastoma-associated protein, A-box / Retinoblastoma-associated protein, C-terminal / Retinoblastoma-associated protein, N-terminal / Retinoblastoma protein family / Retinoblastoma-associated protein B domain / Retinoblastoma-associated protein A domain / Domain of unknown function (DUF3452) / Domain of unknown function (DUF3452) ...Rb C-terminal domain / Retinoblastoma-associated protein, B-box / Retinoblastoma-associated protein, A-box / Retinoblastoma-associated protein, C-terminal / Retinoblastoma-associated protein, N-terminal / Retinoblastoma protein family / Retinoblastoma-associated protein B domain / Retinoblastoma-associated protein A domain / Domain of unknown function (DUF3452) / Domain of unknown function (DUF3452) / Retinoblastoma-associated protein A domain / Rb C-terminal domain / Histone deacetylase / Histone deacetylase family / Histone deacetylase domain / Histone deacetylase domain superfamily / Histone deacetylase domain / Ureohydrolase domain superfamily / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily
Similarity search - Domain/homology
Retinoblastoma-like protein 1 / Histone deacetylase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsPutta, S. / Fernandez, S.M. / Tripathi, S.M. / Muller, G.A. / Rubin, S.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124148 United States
CitationJournal: Structure / Year: 2022
Title: Structural basis for tunable affinity and specificity of LxCxE-dependent protein interactions with the retinoblastoma protein family.
Authors: Putta, S. / Alvarez, L. / Ludtke, S. / Sehr, P. / Muller, G.A. / Fernandez, S.M. / Tripathi, S. / Lewis, J. / Gibson, T.J. / Chemes, L.B. / Rubin, S.M.
History
DepositionOct 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Retinoblastoma-like protein 1
B: Histone deacetylase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6574
Polymers44,4652
Non-polymers1922
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-32 kcal/mol
Surface area16850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.910, 75.170, 71.737
Angle α, β, γ (deg.)90.00, 109.86, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Retinoblastoma-like protein 1 / 107 kDa retinoblastoma-associated protein / p107 / pRb1


Mass: 43265.965 Da / Num. of mol.: 1 / Fragment: UNP residues 391-601,780-887,924-972
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBL1 / Production host: Escherichia coli (E. coli) / References: UniProt: P28749
#2: Protein/peptide Histone deacetylase 1 / HD1 / Protein deacetylase HDAC1 / Protein decrotonylase HDAC1


Mass: 1199.268 Da / Num. of mol.: 1 / Fragment: UNP residues 413-422 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q13547, histone deacetylase, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.97 Å3/Da / Density % sol: 58.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 100 mM MES, pH 6.5, 4% PEG400, 1.6 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.64→46.98 Å / Num. obs: 14817 / % possible obs: 99.6 % / Redundancy: 7.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.18 / Net I/σ(I): 7.8
Reflection shellResolution: 2.64→2.76 Å / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 1937 / CC1/2: 0.89

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4YOS

4yos


Resolution: 2.64→46.98 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 28.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2771 709 4.81 %
Rwork0.2241 --
obs0.2266 14739 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.64→46.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2842 0 10 33 2885
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132910
X-RAY DIFFRACTIONf_angle_d2.0753940
X-RAY DIFFRACTIONf_dihedral_angle_d10.655380
X-RAY DIFFRACTIONf_chiral_restr0.118448
X-RAY DIFFRACTIONf_plane_restr0.014496
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.64-2.840.33091510.26022789X-RAY DIFFRACTION100
2.84-3.130.32451310.24322826X-RAY DIFFRACTION100
3.13-3.580.29961560.24512770X-RAY DIFFRACTION100
3.58-4.510.24361360.21462780X-RAY DIFFRACTION98
4.51-46.980.26811350.20692865X-RAY DIFFRACTION100

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