[English] 日本語
Yorodumi
- PDB-7smd: p107 pocket domain complexed with EID1 peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7smd
Titlep107 pocket domain complexed with EID1 peptide
Components
  • EP300-interacting inhibitor of differentiation 1
  • Retinoblastoma-like protein 1
KeywordsCELL CYCLE / Transcription / cyclin box pocket transcriptional regulator
Function / homology
Function and homology information


regulation of lipid kinase activity / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Transcription of E2F targets under negative control by DREAM complex / negative regulation of G1/S transition of mitotic cell cycle / histone acetyltransferase binding / G1/S-Specific Transcription / negative regulation of cellular senescence / G0 and Early G1 / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / RNA polymerase II transcription regulatory region sequence-specific DNA binding ...regulation of lipid kinase activity / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Transcription of E2F targets under negative control by DREAM complex / negative regulation of G1/S transition of mitotic cell cycle / histone acetyltransferase binding / G1/S-Specific Transcription / negative regulation of cellular senescence / G0 and Early G1 / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / RNA polymerase II transcription regulatory region sequence-specific DNA binding / promoter-specific chromatin binding / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / cytoplasmic ribonucleoprotein granule / Cyclin D associated events in G1 / transcription corepressor activity / chromatin organization / transcription regulator complex / cell differentiation / negative regulation of gene expression / negative regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / nucleoplasm
Similarity search - Function
EP300-interacting inhibitor of differentiation / 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) ...EP300-interacting inhibitor of differentiation / 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 / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily
Similarity search - Domain/homology
Retinoblastoma-like protein 1 / EP300-interacting inhibitor of differentiation 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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: EP300-interacting inhibitor of differentiation 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0944
Polymers44,9022
Non-polymers1922
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-29 kcal/mol
Surface area17810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.741, 75.868, 71.973
Angle α, β, γ (deg.)90.00, 108.48, 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 EP300-interacting inhibitor of differentiation 1 / 21 kDa pRb-associated protein / CREBBP/EP300 inhibitory protein 1 / E1A-like inhibitor of ...21 kDa pRb-associated protein / CREBBP/EP300 inhibitory protein 1 / E1A-like inhibitor of differentiation 1 / EID-1


Mass: 1635.769 Da / Num. of mol.: 1 / Fragment: UNP residues 174-187 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9Y6B2
#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.: 58 / 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: 2.85 Å3/Da / Density % sol: 56.8 %
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-D / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.15→33.92 Å / Num. obs: 27480 / % possible obs: 99.6 % / Redundancy: 3.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.074 / Net I/σ(I): 11.5
Reflection shellResolution: 2.15→2.22 Å / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2385 / CC1/2: 0.69

-
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: 2.15→33.92 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2594 1313 4.78 %
Rwork0.2274 --
obs0.229 27466 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→33.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2882 0 10 59 2951
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0222949
X-RAY DIFFRACTIONf_angle_d2.2363992
X-RAY DIFFRACTIONf_dihedral_angle_d10.611385
X-RAY DIFFRACTIONf_chiral_restr0.1455
X-RAY DIFFRACTIONf_plane_restr0.014503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.240.31271580.29952873X-RAY DIFFRACTION100
2.24-2.340.3111300.27522890X-RAY DIFFRACTION100
2.34-2.460.25121590.26192881X-RAY DIFFRACTION100
2.46-2.620.30181370.23692906X-RAY DIFFRACTION100
2.62-2.820.27121520.22862899X-RAY DIFFRACTION100
2.82-3.10.2471410.22512895X-RAY DIFFRACTION100
3.1-3.550.25841380.22242918X-RAY DIFFRACTION100
3.55-4.470.23331350.20522942X-RAY DIFFRACTION100
4.47-33.920.26161630.22752949X-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