[English] 日本語
Yorodumi
- PDB-7sme: p107 pocket domain complexed with HDAC1 peptide -

+
Open data


ID or keywords:

Loading...

-
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 / protein lysine delactylase activity / p75NTR negatively regulates cell cycle via SC1 / epidermal cell differentiation / histone decrotonylase activity / fungiform papilla formation ...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 / protein lysine delactylase activity / p75NTR negatively regulates cell cycle via SC1 / epidermal cell differentiation / histone decrotonylase activity / fungiform papilla formation / NuRD complex / negative regulation of androgen receptor signaling pathway / regulation of cell fate specification / negative regulation of stem cell population maintenance / endoderm development / histone deacetylase activity, hydrolytic mechanism / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / histone deacetylase / regulation of stem cell differentiation / protein deacetylation / Regulation of MITF-M-dependent genes involved in apoptosis / STAT3 nuclear events downstream of ALK signaling / Transcription of E2F targets under negative control by DREAM complex / protein lysine deacetylase activity / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / histone deacetylase activity / embryonic digit morphogenesis / positive regulation of intracellular estrogen receptor signaling pathway / DNA methylation-dependent constitutive heterochromatin formation / negative regulation of G1/S transition of mitotic cell cycle / Notch-HLH transcription pathway / negative regulation of gene expression, epigenetic / G1/S-Specific Transcription / Sin3-type complex / negative regulation of intrinsic apoptotic signaling pathway / histone deacetylase complex / odontogenesis of dentin-containing tooth / eyelid development in camera-type eye / positive regulation of stem cell population maintenance / E-box binding / oligodendrocyte differentiation / RNA Polymerase I Transcription Initiation / positive regulation of oligodendrocyte differentiation / negative regulation of cellular senescence / G0 and Early G1 / Regulation of MECP2 expression and activity / host-mediated suppression of viral transcription / hair follicle placode formation / NF-kappaB binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / RNA polymerase II core promoter sequence-specific DNA binding / core promoter sequence-specific DNA binding / heterochromatin / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / Nuclear events stimulated by ALK signaling in cancer / MECP2 regulates neuronal receptors and channels / Regulation of TP53 Activity through Acetylation / cellular response to platelet-derived growth factor stimulus / transcription repressor complex / negative regulation of canonical NF-kappaB signal transduction / positive regulation of smooth muscle cell proliferation / Transcriptional and post-translational regulation of MITF-M expression and activity / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / negative regulation of cell migration / SUMOylation of chromatin organization proteins / Regulation of PTEN gene transcription / transcription corepressor binding / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / Regulation of endogenous retroelements by KRAB-ZFP proteins / RNA polymerase II transcription regulatory region sequence-specific DNA binding / hippocampus development / Deactivation of the beta-catenin transactivating complex / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / promoter-specific chromatin binding / circadian regulation of gene expression / Downregulation of SMAD2/3:SMAD4 transcriptional activity / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / negative regulation of transforming growth factor beta receptor signaling pathway / negative regulation of canonical Wnt signaling pathway / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / NoRC negatively regulates rRNA expression / NOTCH1 Intracellular Domain Regulates Transcription / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / histone deacetylase binding / neuron differentiation / Cyclin D associated events in G1 / p53 binding / transcription corepressor activity / heterochromatin formation / Factors involved in megakaryocyte development and platelet production / chromatin organization / transcription regulator complex / DNA-binding transcription factor binding / Estrogen-dependent gene expression / Potential therapeutics for SARS / RNA polymerase II-specific DNA-binding transcription factor binding
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more