[English] 日本語
Yorodumi
- PDB-5jh5: Structural Basis for the Hierarchical Assembly of the Core of PRC1.1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jh5
TitleStructural Basis for the Hierarchical Assembly of the Core of PRC1.1
Components
  • BCL-6 corepressor-like protein 1
  • Lysine-specific demethylase 2B
  • Polycomb group RING finger protein 1
  • S-phase kinase-associated protein 1
KeywordsMETAL BINDING PROTEIN/TRANSCRIPTION / gene repression / complex / transcription regulation / transcription repressor / METAL BINDING PROTEIN-TRANSCRIPTION complex
Function / homology
Function and homology information


fourth ventricle development / initiation of neural tube closure / midbrain-hindbrain boundary morphogenesis / third ventricle development / [histone H3]-dimethyl-L-lysine36 demethylase / histone H3K36me/H3K36me2 demethylase activity / embryonic camera-type eye morphogenesis / lateral ventricle development / PRC1 complex / negative regulation of neural precursor cell proliferation ...fourth ventricle development / initiation of neural tube closure / midbrain-hindbrain boundary morphogenesis / third ventricle development / [histone H3]-dimethyl-L-lysine36 demethylase / histone H3K36me/H3K36me2 demethylase activity / embryonic camera-type eye morphogenesis / lateral ventricle development / PRC1 complex / negative regulation of neural precursor cell proliferation / F-box domain binding / hindbrain development / unmethylated CpG binding / PcG protein complex / histone H3K36 demethylase activity / positive regulation of ubiquitin protein ligase activity / Cul7-RING ubiquitin ligase complex / maintenance of protein location in nucleus / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / ubiquitin ligase complex scaffold activity / midbrain development / Prolactin receptor signaling / positive regulation of stem cell population maintenance / cullin family protein binding / histone demethylase activity / protein monoubiquitination / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / forebrain development / Nuclear events stimulated by ALK signaling in cancer / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / molecular function activator activity / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / transcription coregulator activity / Vpu mediated degradation of CD4 / Dectin-1 mediated noncanonical NF-kB signaling / promoter-specific chromatin binding / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Iron uptake and transport / Negative regulation of NOTCH4 signaling / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / HDMs demethylate histones / beta-catenin binding / Degradation of beta-catenin by the destruction complex / NOTCH1 Intracellular Domain Regulates Transcription / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / FCERI mediated NF-kB activation / Interleukin-1 signaling / Orc1 removal from chromatin / protein polyubiquitination / Regulation of RUNX2 expression and activity / transcription corepressor activity / Cyclin D associated events in G1 / : / Regulation of PLK1 Activity at G2/M Transition / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / chromatin organization / Neddylation / chromosome / positive regulation of cell growth / spermatogenesis / negative regulation of neuron apoptotic process / proteasome-mediated ubiquitin-dependent protein catabolic process / rRNA binding / protein ubiquitination / chromatin remodeling / protein domain specific binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / centrosome / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / nucleolus / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
BCL-6 corepressor, PCGF1 binding domain / PCGF Ub-like fold discriminator superfamily / : / BCORL-PCGF1-binding domain / PHD-finger / RAWUL domain / RAWUL domain RING finger- and WD40-associated ubiquitin-like / Jumonji, helical domain / Jumonji helical domain / : ...BCL-6 corepressor, PCGF1 binding domain / PCGF Ub-like fold discriminator superfamily / : / BCORL-PCGF1-binding domain / PHD-finger / RAWUL domain / RAWUL domain RING finger- and WD40-associated ubiquitin-like / Jumonji, helical domain / Jumonji helical domain / : / Leucine-rich repeat, cysteine-containing subtype / Cupin-like domain 8 / Cupin-like domain / Leucine-rich repeat - CC (cysteine-containing) subfamily / Zinc finger, C3HC4 type (RING finger) / F-box-like / SKP1 component, dimerisation / S-phase kinase-associated protein 1 / SKP1-like, dimerisation domain superfamily / Skp1 family, dimerisation domain / CXXC zinc finger domain / Zinc finger, CXXC-type / Zinc finger CXXC-type profile. / F-box domain / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / SKP1/BTB/POZ domain superfamily / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ring finger / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Leucine-rich repeat domain superfamily / Zinc finger, FYVE/PHD-type / Ankyrin repeat-containing domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin-like (UB roll) / Zinc finger, RING/FYVE/PHD-type / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
S-phase kinase-associated protein 1 / BCL-6 corepressor-like protein 1 / Lysine-specific demethylase 2B / Polycomb group RING finger protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.55 Å
AuthorsWong, S.J. / Taylor, A.B. / Hart, P.J. / Kim, C.A.
CitationJournal: Structure / Year: 2016
Title: KDM2B Recruitment of the Polycomb Group Complex, PRC1.1, Requires Cooperation between PCGF1 and BCORL1.
Authors: Wong, S.J. / Gearhart, M.D. / Taylor, A.B. / Nanyes, D.R. / Ha, D.J. / Robinson, A.K. / Artigas, J.A. / Lee, O.J. / Demeler, B. / Hart, P.J. / Bardwell, V.J. / Kim, C.A.
History
DepositionApr 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lysine-specific demethylase 2B
B: S-phase kinase-associated protein 1
C: Polycomb group RING finger protein 1
D: BCL-6 corepressor-like protein 1


Theoretical massNumber of molelcules
Total (without water)78,5554
Polymers78,5554
Non-polymers00
Water1,15364
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.049, 73.796, 123.014
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Lysine-specific demethylase 2B / CXXC-type zinc finger protein 2 / F-box and leucine-rich repeat protein 10 / F-box protein FBL10 / ...CXXC-type zinc finger protein 2 / F-box and leucine-rich repeat protein 10 / F-box protein FBL10 / F-box/LRR-repeat protein 10 / JmjC domain-containing histone demethylation protein 1B / Jumonji domain-containing EMSY-interactor methyltransferase motif protein / Protein JEMMA / Protein-containing CXXC domain 2 / [Histone-H3]-lysine-36 demethylase 1B


Mass: 32494.600 Da / Num. of mol.: 1 / Fragment: RESIDUES 1059-1336
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM2B, CXXC2, FBL10, FBXL10, JHDM1B, PCCX2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8NHM5, [histone H3]-dimethyl-L-lysine36 demethylase
#2: Protein S-phase kinase-associated protein 1 / Cyclin-A/CDK2-associated protein p19 / p19A / Organ of Corti protein 2 / OCP-2 / Organ of Corti ...Cyclin-A/CDK2-associated protein p19 / p19A / Organ of Corti protein 2 / OCP-2 / Organ of Corti protein II / OCP-II / RNA polymerase II elongation factor-like protein / SIII / Transcription elongation factor B polypeptide 1-like / p19skp1


Mass: 18689.455 Da / Num. of mol.: 1 / Fragment: Residues 2-163
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SKP1, EMC19, OCP2, SKP1A, TCEB1L / Production host: Escherichia coli (E. coli) / References: UniProt: P63208
#3: Protein Polycomb group RING finger protein 1 / Nervous system Polycomb-1 / NSPc1 / RING finger protein 68


Mass: 13205.894 Da / Num. of mol.: 1 / Fragment: RESIDUES 150-255
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCGF1, NSPC1, RNF68 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BSM1
#4: Protein BCL-6 corepressor-like protein 1 / BCoR-like protein 1


Mass: 14164.601 Da / Num. of mol.: 1 / Fragment: RESIDUES 1594-1711
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BCORL1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5H9F3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 39.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.25
Details: 100 mM HEPES, 10 % 2-methyl-2,4-pentanediol, 10 mM NaCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.97962 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jul 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97962 Å / Relative weight: 1
ReflectionResolution: 2.55→63.282 Å / Num. obs: 21463 / % possible obs: 99.9 % / Redundancy: 7 % / Biso Wilson estimate: 44.86 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.114 / Net I/σ(I): 15.5
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 2 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
XDSdata reduction
XDSdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.55→63.282 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 28.71
RfactorNum. reflection% reflection
Rfree0.2573 1999 9.32 %
Rwork0.2062 --
obs0.211 21412 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.55→63.282 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4951 0 0 64 5015
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045049
X-RAY DIFFRACTIONf_angle_d0.676824
X-RAY DIFFRACTIONf_dihedral_angle_d16.2781921
X-RAY DIFFRACTIONf_chiral_restr0.063776
X-RAY DIFFRACTIONf_plane_restr0.004861
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.58230.39851320.33961316X-RAY DIFFRACTION96
2.5823-2.61630.34161360.32621310X-RAY DIFFRACTION97
2.6163-2.65210.39971110.31711334X-RAY DIFFRACTION99
2.6521-2.690.34071540.28471329X-RAY DIFFRACTION99
2.69-2.73020.35931380.27731366X-RAY DIFFRACTION100
2.7302-2.77280.34211360.25461318X-RAY DIFFRACTION100
2.7728-2.81830.32891570.24441368X-RAY DIFFRACTION100
2.8183-2.86690.39051460.26681316X-RAY DIFFRACTION100
2.8669-2.9190.38071300.26421383X-RAY DIFFRACTION100
2.919-2.97520.33181340.25071323X-RAY DIFFRACTION100
2.9752-3.03590.30141410.23821342X-RAY DIFFRACTION100
3.0359-3.10190.30121430.23631356X-RAY DIFFRACTION100
3.1019-3.1740.33891320.22281365X-RAY DIFFRACTION100
3.174-3.25340.29541360.22131342X-RAY DIFFRACTION100
3.2534-3.34140.29921460.22481337X-RAY DIFFRACTION100
3.3414-3.43970.28151170.2321328X-RAY DIFFRACTION99
3.4397-3.55070.27791480.21451362X-RAY DIFFRACTION100
3.5507-3.67760.25561310.20231355X-RAY DIFFRACTION100
3.6776-3.82480.27951410.18931335X-RAY DIFFRACTION100
3.8248-3.99890.21931470.1831331X-RAY DIFFRACTION99
3.9989-4.20970.23841380.16471351X-RAY DIFFRACTION100
4.2097-4.47340.2121360.1611339X-RAY DIFFRACTION100
4.4734-4.81860.18581460.15941345X-RAY DIFFRACTION100
4.8186-5.30330.16021480.16451334X-RAY DIFFRACTION99
5.3033-6.07020.2191300.18061353X-RAY DIFFRACTION100
6.0702-7.64570.22551380.2071339X-RAY DIFFRACTION100
7.6457-63.30180.21331330.17891356X-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