[English] 日本語
Yorodumi
- PDB-9laf: Crystal structure of Elongin BC-EPOP peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9laf
TitleCrystal structure of Elongin BC-EPOP peptide
Components
  • Elongin BC and Polycomb repressive complex 2-associated protein
  • Elongin-B
  • Elongin-C
KeywordsTRANSCRIPTION / EPOP / Elongin B / Elongin C
Function / homology
Function and homology information


neuron fate commitment / ESC/E(Z) complex / target-directed miRNA degradation / VCB complex / elongin complex / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / transcription elongation-coupled chromatin remodeling / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery ...neuron fate commitment / ESC/E(Z) complex / target-directed miRNA degradation / VCB complex / elongin complex / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / transcription elongation-coupled chromatin remodeling / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / transcription corepressor binding / stem cell differentiation / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / Vif-mediated degradation of APOBEC3G / Inactivation of CSF3 (G-CSF) signaling / Evasion by RSV of host interferon responses / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Regulation of expression of SLITs and ROBOs / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / chromosome / protein-containing complex assembly / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / protein ubiquitination / ubiquitin protein ligase binding / chromatin binding / regulation of transcription by RNA polymerase II / protein-containing complex binding / nucleoplasm / cytosol
Similarity search - Function
Elongin BC and Polycomb repressive complex 2-associated protein EPOP / Elongin BC and Polycomb repressive complex 2-associated protein / : / Elongin-C / Elongin B / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily ...Elongin BC and Polycomb repressive complex 2-associated protein EPOP / Elongin BC and Polycomb repressive complex 2-associated protein / : / Elongin-C / Elongin B / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Elongin BC and Polycomb repressive complex 2-associated protein / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsKim, S. / Lee, B.I.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
Other government2310200
Other government2510731
National Research Foundation (NRF, Korea)RS-2023-NR076355 Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2025
Title: Structural analysis of EPOP BC-box binding to the elongin BC complex.
Authors: Kim, S. / Yeo, H. / Lee, B.I.
History
DepositionJan 2, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 21, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Elongin-B
C: Elongin-C
A: Elongin BC and Polycomb repressive complex 2-associated protein


Theoretical massNumber of molelcules
Total (without water)25,5513
Polymers25,5513
Non-polymers00
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-22 kcal/mol
Surface area10110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.151, 156.613, 36.817
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Components on special symmetry positions
IDModelComponents
11B-208-

HOH

-
Components

#1: Protein Elongin-B / EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / ...EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / Transcription elongation factor B polypeptide 2


Mass: 11748.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOB, TCEB2 / Plasmid: pACYCDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15370
#2: Protein Elongin-C / EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / ...EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / Transcription elongation factor B polypeptide 1


Mass: 10843.420 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOC, TCEB1 / Plasmid: pACYCDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q15369
#3: Protein/peptide Elongin BC and Polycomb repressive complex 2-associated protein / Proline-rich protein 28


Mass: 2959.478 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPOP, C17orf96, PRR28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A6NHQ4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.39 Å3/Da / Density % sol: 68.39 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 15% v/v 2-Propanol, 0.1 M Sodium citrate tribasic dihydrate pH 5.0, 10% w/v Polyethylene glycol 10,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 11, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 19316 / % possible obs: 98.4 % / Redundancy: 5.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.094 / Net I/σ(I): 16.25
Reflection shellResolution: 2.15→2.19 Å / Num. unique obs: 788 / CC1/2: 0.878

-
Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.14→47.88 Å / SU ML: 0.1948 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.6697
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2308 1907 10.01 %
Rwork0.1925 17139 -
obs0.1964 19046 96.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.41 Å2
Refinement stepCycle: LAST / Resolution: 2.14→47.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1540 0 0 104 1644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00731566
X-RAY DIFFRACTIONf_angle_d0.80042108
X-RAY DIFFRACTIONf_chiral_restr0.0523245
X-RAY DIFFRACTIONf_plane_restr0.0067266
X-RAY DIFFRACTIONf_dihedral_angle_d15.8645586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.14-2.20.25811020.2092914X-RAY DIFFRACTION74.05
2.2-2.260.26631300.19591170X-RAY DIFFRACTION95.24
2.26-2.320.2391370.1861234X-RAY DIFFRACTION98.14
2.32-2.40.2341360.19681223X-RAY DIFFRACTION98.84
2.4-2.480.23791360.19671230X-RAY DIFFRACTION99.13
2.48-2.580.23891370.19321221X-RAY DIFFRACTION98.26
2.58-2.70.24491400.20811257X-RAY DIFFRACTION99.79
2.7-2.840.2231400.19341263X-RAY DIFFRACTION99.79
2.84-3.020.26321380.2111237X-RAY DIFFRACTION99.28
3.02-3.250.24811360.20461231X-RAY DIFFRACTION98.7
3.25-3.580.23811410.19621268X-RAY DIFFRACTION99.58
3.58-4.10.22151430.16921277X-RAY DIFFRACTION98.2
4.1-5.160.18771400.16661268X-RAY DIFFRACTION98.6
5.17-47.880.22911510.21441346X-RAY DIFFRACTION97.72

+
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