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- PDB-5jg6: APC11-Ubv shows role of noncovalent RING-Ubiquitin interactions i... -

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Basic information

Entry
Database: PDB / ID: 5jg6
TitleAPC11-Ubv shows role of noncovalent RING-Ubiquitin interactions in processive multiubiquitination and Ubiquitin chain elongation by APC/C
Components
  • Anaphase-promoting complex subunit 11
  • Polyubiquitin-B
KeywordsCELL CYCLE / RING Ubiquitin Cell Cycle Anaphase-promoting complex-Cyclosome
Function / homology
Function and homology information


Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / anaphase-promoting complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / protein branched polyubiquitination / regulation of meiotic cell cycle / anaphase-promoting complex-dependent catabolic process / Phosphorylation of the APC/C / positive regulation of mitotic metaphase/anaphase transition ...Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / anaphase-promoting complex / Aberrant regulation of mitotic exit in cancer due to RB1 defects / protein branched polyubiquitination / regulation of meiotic cell cycle / anaphase-promoting complex-dependent catabolic process / Phosphorylation of the APC/C / positive regulation of mitotic metaphase/anaphase transition / protein K11-linked ubiquitination / symbiont entry into host cell via disruption of host cell glycocalyx / ubiquitin-ubiquitin ligase activity / symbiont entry into host cell via disruption of host cell envelope / virus tail / Regulation of APC/C activators between G1/S and early anaphase / cullin family protein binding / Transcriptional Regulation by VENTX / APC/C:Cdc20 mediated degradation of Cyclin B / protein K48-linked ubiquitination / APC-Cdc20 mediated degradation of Nek2A / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / regulation of mitotic cell cycle / Assembly of the pre-replicative complex / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / CDK-mediated phosphorylation and removal of Cdc6 / G protein-coupled receptor binding / Separation of Sister Chromatids / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin protein ligase activity / mitotic cell cycle / Senescence-Associated Secretory Phenotype (SASP) / ubiquitin-dependent protein catabolic process / protein ubiquitination / cell division / nucleolus / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Anaphase-promoting complex subunit 11, RING-H2 finger / Anaphase-promoting complex subunit 11 RING-H2 finger / : / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Pectin lyase fold / Pectin lyase fold/virulence factor / Zinc finger RING-type profile. ...Anaphase-promoting complex subunit 11, RING-H2 finger / Anaphase-promoting complex subunit 11 RING-H2 finger / : / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Pectin lyase fold / Pectin lyase fold/virulence factor / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin family / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Tail fiber / Anaphase-promoting complex subunit 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.0013 Å
AuthorsBrown, N.G. / Zhang, W. / Yu, S. / Miller, D.J. / Sidhu, S.S. / Schulman, B.A.
Funding support United States, Canada, 8items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R37GM065930 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P30CA021765 United States
St. Jude Children's Research Hospital (ALSAC) United States
Howard Hughes Medical Institute (HHMI) United States
Canadian Institutes of Health Research (CIHR)MOP#111149 Canada
Canadian Institutes of Health Research (CIHR)136956 Canada
Leukemia & Lymphoma Society United States
Jane Coffin Childs Memorial Fund United States
CitationJournal: Cell / Year: 2016
Title: Dual RING E3 Architectures Regulate Multiubiquitination and Ubiquitin Chain Elongation by APC/C.
Authors: Nicholas G Brown / Ryan VanderLinden / Edmond R Watson / Florian Weissmann / Alban Ordureau / Kuen-Phon Wu / Wei Zhang / Shanshan Yu / Peter Y Mercredi / Joseph S Harrison / Iain F Davidson ...Authors: Nicholas G Brown / Ryan VanderLinden / Edmond R Watson / Florian Weissmann / Alban Ordureau / Kuen-Phon Wu / Wei Zhang / Shanshan Yu / Peter Y Mercredi / Joseph S Harrison / Iain F Davidson / Renping Qiao / Ying Lu / Prakash Dube / Michael R Brunner / Christy R R Grace / Darcie J Miller / David Haselbach / Marc A Jarvis / Masaya Yamaguchi / David Yanishevski / Georg Petzold / Sachdev S Sidhu / Brian Kuhlman / Marc W Kirschner / J Wade Harper / Jan-Michael Peters / Holger Stark / Brenda A Schulman /
Abstract: Protein ubiquitination involves E1, E2, and E3 trienzyme cascades. E2 and RING E3 enzymes often collaborate to first prime a substrate with a single ubiquitin (UB) and then achieve different forms of ...Protein ubiquitination involves E1, E2, and E3 trienzyme cascades. E2 and RING E3 enzymes often collaborate to first prime a substrate with a single ubiquitin (UB) and then achieve different forms of polyubiquitination: multiubiquitination of several sites and elongation of linkage-specific UB chains. Here, cryo-EM and biochemistry show that the human E3 anaphase-promoting complex/cyclosome (APC/C) and its two partner E2s, UBE2C (aka UBCH10) and UBE2S, adopt specialized catalytic architectures for these two distinct forms of polyubiquitination. The APC/C RING constrains UBE2C proximal to a substrate and simultaneously binds a substrate-linked UB to drive processive multiubiquitination. Alternatively, during UB chain elongation, the RING does not bind UBE2S but rather lures an evolving substrate-linked UB to UBE2S positioned through a cullin interaction to generate a Lys11-linked chain. Our findings define mechanisms of APC/C regulation, and establish principles by which specialized E3-E2-substrate-UB architectures control different forms of polyubiquitination.
History
DepositionApr 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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

Downloads & links

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Assembly

Deposited unit
A: Anaphase-promoting complex subunit 11
B: Polyubiquitin-B
C: Polyubiquitin-B
D: Anaphase-promoting complex subunit 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,00510
Polymers34,6124
Non-polymers3926
Water2,090116
1
A: Anaphase-promoting complex subunit 11
B: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5025
Polymers17,3062
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-8 kcal/mol
Surface area7400 Å2
MethodPISA
2
C: Polyubiquitin-B
D: Anaphase-promoting complex subunit 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5025
Polymers17,3062
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-8 kcal/mol
Surface area7390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.066, 35.193, 72.768
Angle α, β, γ (deg.)90.00, 120.42, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Anaphase-promoting complex subunit 11 / APC11 / Cyclosome subunit 11 / Hepatocellular carcinoma-associated RING finger protein


Mass: 8050.358 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC11, HSPC214 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NYG5
#2: Protein Polyubiquitin-B


Mass: 9255.781 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
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.09 Å3/Da / Density % sol: 41.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium acetate, 0.1 M Sodium acetate pH 4.6, 33% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→36.326 Å / Num. obs: 19650 / % possible obs: 99.7 % / Redundancy: 3.3 % / Net I/σ(I): 10.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R2Y and 1UBQ

4r2y

1ubq


Resolution: 2.0013→36.326 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.71
RfactorNum. reflection% reflection
Rfree0.2195 1005 5.18 %
Rwork0.1852 --
obs0.187 19400 98.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.0013→36.326 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2144 0 6 116 2266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072230
X-RAY DIFFRACTIONf_angle_d0.9472989
X-RAY DIFFRACTIONf_dihedral_angle_d13.591819
X-RAY DIFFRACTIONf_chiral_restr0.041329
X-RAY DIFFRACTIONf_plane_restr0.005391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0013-2.10680.27971490.22432402X-RAY DIFFRACTION91
2.1068-2.23880.24721300.20392610X-RAY DIFFRACTION99
2.2388-2.41170.25121400.19912636X-RAY DIFFRACTION100
2.4117-2.65430.23261340.19742653X-RAY DIFFRACTION100
2.6543-3.03820.20151440.1932673X-RAY DIFFRACTION100
3.0382-3.82710.2281410.17372690X-RAY DIFFRACTION100
3.8271-36.33190.19221670.17082731X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -15.0588 Å / Origin y: -0.9797 Å / Origin z: -3.0986 Å
111213212223313233
T0.1214 Å2-0.0272 Å2-0.0336 Å2-0.161 Å20.0084 Å2--0.1655 Å2
L0.6636 °2-0.7571 °2-0.8993 °2-1.1702 °21.0423 °2--1.2695 °2
S0.0191 Å °-0.0223 Å °-0.0154 Å °-0.0091 Å °-0.0151 Å °0.0374 Å °-0.0238 Å °0.012 Å °-0.0066 Å °
Refinement TLS groupSelection details: all

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