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- PDB-5jh5: Structural Basis for the Hierarchical Assembly of the Core of PRC1.1 -

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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


initiation of neural tube closure / fourth ventricle development / midbrain-hindbrain boundary morphogenesis / third ventricle development / histone H3K36me/H3K36me2 demethylase activity / [histone H3]-dimethyl-L-lysine36 demethylase / embryonic camera-type eye morphogenesis / PRC1 complex / lateral ventricle development / negative regulation of neural precursor cell proliferation ...initiation of neural tube closure / fourth ventricle development / midbrain-hindbrain boundary morphogenesis / third ventricle development / histone H3K36me/H3K36me2 demethylase activity / [histone H3]-dimethyl-L-lysine36 demethylase / embryonic camera-type eye morphogenesis / PRC1 complex / lateral ventricle development / negative regulation of neural precursor cell proliferation / F-box domain binding / hindbrain development / PcG protein complex / unmethylated CpG binding / histone H3K36 demethylase activity / Cul7-RING ubiquitin ligase complex / positive regulation of ubiquitin protein ligase activity / maintenance of protein location in nucleus / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / SCF ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / midbrain development / positive regulation of stem cell population maintenance / Prolactin receptor signaling / protein monoubiquitination / cullin family protein binding / ubiquitin-like ligase-substrate adaptor activity / histone demethylase activity / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / forebrain development / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / molecular function activator activity / Vpu mediated degradation of CD4 / promoter-specific chromatin binding / Dectin-1 mediated noncanonical NF-kB signaling / transcription coregulator activity / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Negative regulation of NOTCH4 signaling / Iron uptake and transport / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / 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 / Degradation of beta-catenin by the destruction complex / HDMs demethylate histones / NOTCH1 Intracellular Domain Regulates Transcription / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / beta-catenin binding / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / FCERI mediated NF-kB activation / Interleukin-1 signaling / protein polyubiquitination / Orc1 removal from chromatin / transcription corepressor activity / Regulation of RUNX2 expression and activity / Cyclin D associated events in G1 / Regulation of PLK1 Activity at G2/M Transition / Antigen processing: Ubiquitination & Proteasome degradation / Circadian Clock / Downstream TCR signaling / Neddylation / chromosome / chromatin organization / positive regulation of cell growth / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / negative regulation of neuron apoptotic process / rRNA binding / protein ubiquitination / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / centrosome / nucleolus / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / 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 / Leucine-rich repeat, cysteine-containing subtype ...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 / Leucine-rich repeat - CC (cysteine-containing) subfamily / Zinc finger, C3HC4 type (RING finger) / Cupin-like domain 8 / Cupin-like domain / 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 / Ankyrin repeats (3 copies) / Leucine-rich repeat domain superfamily / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / Zinc finger, PHD-type / PHD zinc finger / ankyrin repeats / Ankyrin repeat / Zinc finger RING-type profile. / Zinc finger, RING-type / Ankyrin repeat-containing domain superfamily / Zinc finger, FYVE/PHD-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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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 / Water


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

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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: 2.22 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

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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

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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

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