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- PDB-6c16: Ubiquitin variant (UbV.Fbl10.1) bound to a human Skp1-Fbl11 fragm... -

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Basic information

Entry
Database: PDB / ID: 6c16
TitleUbiquitin variant (UbV.Fbl10.1) bound to a human Skp1-Fbl11 fragment complex.
Components
  • Lysine-specific demethylase 2A
  • Polyubiquitin-B
  • S-phase kinase-associated protein 1
KeywordsPROTEIN BINDING / Ubiquitination
Function / homology
Function and homology information


[histone H3]-dimethyl-L-lysine36 demethylase / histone H3K36me/H3K36me2 demethylase activity / F-box domain binding / unmethylated CpG binding / PcG protein complex / histone H3K36 demethylase activity / negative regulation of transcription by competitive promoter binding / positive regulation of ubiquitin protein ligase activity / Cul7-RING ubiquitin ligase complex / maintenance of protein location in nucleus ...[histone H3]-dimethyl-L-lysine36 demethylase / histone H3K36me/H3K36me2 demethylase activity / F-box domain binding / unmethylated CpG binding / PcG protein complex / histone H3K36 demethylase activity / negative regulation of transcription by competitive promoter binding / 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 / symbiont entry into host cell via disruption of host cell glycocalyx / histone demethylase activity / SCF ubiquitin ligase complex / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / symbiont entry into host cell via disruption of host cell envelope / ubiquitin ligase complex scaffold activity / virus tail / Prolactin receptor signaling / cullin family protein binding / protein monoubiquitination / ubiquitin-like ligase-substrate adaptor activity / protein K48-linked ubiquitination / Nuclear events stimulated by ALK signaling in cancer / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / NIK-->noncanonical NF-kB signaling / SCF-beta-TrCP mediated degradation of Emi1 / Vpu mediated degradation of CD4 / molecular function activator activity / Dectin-1 mediated noncanonical NF-kB signaling / Activation of NF-kappaB in B cells / Iron uptake and transport / Degradation of GLI1 by the proteasome / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / HDMs demethylate histones / 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 / transcription coregulator activity / Degradation of beta-catenin by the destruction complex / NOTCH1 Intracellular Domain Regulates Transcription / circadian regulation of gene expression / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / regulation of circadian rhythm / FCERI mediated NF-kB activation / beta-catenin binding / Interleukin-1 signaling / Orc1 removal from chromatin / double-strand break repair via nonhomologous end joining / Cyclin D associated events in G1 / Regulation of RUNX2 expression and activity / : / protein polyubiquitination / Regulation of PLK1 Activity at G2/M Transition / Downstream TCR signaling / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / chromosome / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / chromatin remodeling / protein domain specific binding / centrosome / regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
PHD-finger / F-box domain / Jumonji, helical domain / Jumonji helical domain / : / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / F-box-like / SKP1 component, dimerisation / S-phase kinase-associated protein 1 ...PHD-finger / F-box domain / Jumonji, helical domain / Jumonji helical domain / : / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / 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 / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / 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. / Pectin lyase fold / Pectin lyase fold/virulence factor / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / SKP1/BTB/POZ domain superfamily / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Leucine-rich repeat domain superfamily / Zinc finger, FYVE/PHD-type / Ubiquitin family / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tail fiber / S-phase kinase-associated protein 1 / Lysine-specific demethylase 2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.27 Å
AuthorsManczyk, N. / Sicheri, F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)FDN 143277 Canada
CitationJournal: Structure / Year: 2018
Title: A Structure-Based Strategy for Engineering Selective Ubiquitin Variant Inhibitors of Skp1-Cul1-F-Box Ubiquitin Ligases.
Authors: Gorelik, M. / Manczyk, N. / Pavlenco, A. / Kurinov, I. / Sidhu, S.S. / Sicheri, F.
History
DepositionJan 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 19, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S-phase kinase-associated protein 1
B: S-phase kinase-associated protein 1
C: Lysine-specific demethylase 2A
D: Polyubiquitin-B
F: Lysine-specific demethylase 2A
H: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)69,4656
Polymers69,4656
Non-polymers00
Water00
1
A: S-phase kinase-associated protein 1
C: Lysine-specific demethylase 2A
H: Polyubiquitin-B


Theoretical massNumber of molelcules
Total (without water)34,7333
Polymers34,7333
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-30 kcal/mol
Surface area13250 Å2
MethodPISA
2
B: S-phase kinase-associated protein 1
D: Polyubiquitin-B
F: Lysine-specific demethylase 2A


Theoretical massNumber of molelcules
Total (without water)34,7333
Polymers34,7333
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-33 kcal/mol
Surface area13340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.241, 119.582, 63.707
Angle α, β, γ (deg.)90.00, 98.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: 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: 18808.096 Da / Num. of mol.: 2
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
#2: Protein/peptide Lysine-specific demethylase 2A / CXXC-type zinc finger protein 8 / F-box and leucine-rich repeat protein 11 / F-box protein FBL7 / F- ...CXXC-type zinc finger protein 8 / F-box and leucine-rich repeat protein 11 / F-box protein FBL7 / F-box protein Lilina / F-box/LRR-repeat protein 11 / JmjC domain-containing histone demethylation protein 1A / [Histone-H3]-lysine-36 demethylase 1A


Mass: 5952.017 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KDM2A, CXXC8, FBL7, FBXL11, JHDM1A, KIAA1004 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9Y2K7, [histone H3]-dimethyl-L-lysine36 demethylase
#3: Protein Polyubiquitin-B


Mass: 9972.468 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47

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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: 2.07 Å3/Da / Density % sol: 40.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M malic acid pH 4.5, 0.15 M sodium chloride, 27% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 93.15 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 31, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.27→19.82 Å / Num. obs: 8718 / % possible obs: 98.9 % / Redundancy: 3.6 % / CC1/2: 0.986 / Rsym value: 0.179 / Net I/σ(I): 5.2
Reflection shellResolution: 3.27→3.53 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1811 / CC1/2: 0.547 / Rsym value: 1.068 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UBQ

1ubq


Resolution: 3.27→19.818 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 36.47
RfactorNum. reflection% reflection
Rfree0.3172 464 5.36 %
Rwork0.26 --
obs0.2632 8658 98.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.27→19.818 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3529 0 0 0 3529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033587
X-RAY DIFFRACTIONf_angle_d0.6154932
X-RAY DIFFRACTIONf_dihedral_angle_d21.9261134
X-RAY DIFFRACTIONf_chiral_restr0.043621
X-RAY DIFFRACTIONf_plane_restr0.006639
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2703-3.74070.38241590.33932708X-RAY DIFFRACTION98
3.7407-4.70250.33291600.2772716X-RAY DIFFRACTION99
4.7025-19.8180.28691450.22962770X-RAY DIFFRACTION99

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