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- PDB-5lgg: The N-terminal WD40 domain of Apc1 (Anaphase promoting complex su... -

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Basic information

Entry
Database: PDB / ID: 5lgg
TitleThe N-terminal WD40 domain of Apc1 (Anaphase promoting complex subunit 1)
ComponentsAnaphase-promoting complex subunit 1,Anaphase-promoting complex subunit 1,Anaphase-promoting complex subunit 1,Anaphase-promoting complex subunit 1
KeywordsCELL CYCLE / APC/C / WD40
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 / regulation of meiotic cell cycle / metaphase/anaphase transition of mitotic cell cycle / anaphase-promoting complex-dependent catabolic process / Phosphorylation of the APC/C / protein K11-linked ubiquitination ...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 / regulation of meiotic cell cycle / metaphase/anaphase transition of mitotic cell cycle / anaphase-promoting complex-dependent catabolic process / Phosphorylation of the APC/C / protein K11-linked ubiquitination / Regulation of APC/C activators between G1/S and early anaphase / Transcriptional Regulation by VENTX / regulation of mitotic cell cycle / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / 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 / Separation of Sister Chromatids / Antigen processing: Ubiquitination & Proteasome degradation / Senescence-Associated Secretory Phenotype (SASP) / molecular adaptor activity / cell division / nucleoplasm / cytosol
Similarity search - Function
: / Anaphase-promoting complex subunit 1, C-terminal / Anaphase-promoting complex subunit 1, middle domain / : / : / Anaphase-promoting complex subunit 1 WD40 beta-propeller domain / Anaphase-promoting complex sub unit 1 C-terminal domain / Anaphase-promoting complex subunit 1 middle domain / APC1 beta sandwich domain / Anaphase-promoting complex subunit 1 / Armadillo-like helical
Similarity search - Domain/homology
Anaphase-promoting complex subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsLi, Q. / Aibara, S. / Barford, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UK United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2016
Title: WD40 domain of Apc1 is critical for the coactivator-induced allosteric transition that stimulates APC/C catalytic activity.
Authors: Qiuhong Li / Leifu Chang / Shintaro Aibara / Jing Yang / Ziguo Zhang / David Barford /
Abstract: The anaphase-promoting complex/cyclosome (APC/C) is a large multimeric cullin-RING E3 ubiquitin ligase that orchestrates cell-cycle progression by targeting cell-cycle regulatory proteins for ...The anaphase-promoting complex/cyclosome (APC/C) is a large multimeric cullin-RING E3 ubiquitin ligase that orchestrates cell-cycle progression by targeting cell-cycle regulatory proteins for destruction via the ubiquitin proteasome system. The APC/C assembly comprises two scaffolding subcomplexes: the platform and the TPR lobe that together coordinate the juxtaposition of the catalytic and substrate-recognition modules. The platform comprises APC/C subunits Apc1, Apc4, Apc5, and Apc15. Although the role of Apc1 as an APC/C scaffolding subunit has been characterized, its specific functions in contributing toward APC/C catalytic activity are not fully understood. Here, we report the crystal structure of the N-terminal domain of human Apc1 (Apc1N) determined at 2.2-Å resolution and provide an atomic-resolution description of the architecture of its WD40 (WD40 repeat) domain (Apc1(WD40)). To understand how Apc1(WD40) contributes to APC/C activity, a mutant form of the APC/C with Apc1(WD40) deleted was generated and evaluated biochemically and structurally. We found that the deletion of Apc1(WD40) abolished the UbcH10-dependent ubiquitination of APC/C substrates without impairing the Ube2S-dependent ubiquitin chain elongation activity. A cryo-EM structure of an APC/C-Cdh1 complex with Apc1(WD40) deleted showed that the mutant APC/C is locked into an inactive conformation in which the UbcH10-binding site of the catalytic module is inaccessible. Additionally, an EM density for Apc15 is not visible. Our data show that Apc1(WD40) is required to mediate the coactivator-induced conformational change of the APC/C that is responsible for stimulating APC/C catalytic activity by promoting UbcH10 binding. In contrast, Ube2S activity toward APC/C substrates is not dependent on the initiation-competent conformation of the APC/C.
History
DepositionJul 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references / Source and taxonomy / Structure summary
Revision 1.2Aug 30, 2017Group: Advisory / Author supporting evidence / Category: pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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 1,Anaphase-promoting complex subunit 1,Anaphase-promoting complex subunit 1,Anaphase-promoting complex subunit 1


Theoretical massNumber of molelcules
Total (without water)47,9091
Polymers47,9091
Non-polymers00
Water3,009167
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.633, 113.262, 100.436
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Anaphase-promoting complex subunit 1,Anaphase-promoting complex subunit 1,Anaphase-promoting complex subunit 1,Anaphase-promoting complex subunit 1 / APC1 / Cyclosome subunit 1 / Mitotic checkpoint regulator / Testis-specific gene 24 protein


Mass: 47909.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANAPC1, TSG24 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9H1A4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.45 Å3/Da / Density % sol: 49.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M citric acid, pH5.0, 2M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.15→40.131 Å / Num. obs: 25408 / % possible obs: 97.8 % / Redundancy: 4.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05931 / Rsym value: 0.06606 / Net I/σ(I): 16.76
Reflection shellResolution: 2.15→2.223 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 2.01 / CC1/2: 0.891 / % possible all: 84.7

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Processing

Software
NameVersionClassification
PHENIXdev_1810refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4UI9

4ui9


Resolution: 2.15→40.131 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.87
RfactorNum. reflection% reflectionSelection details
Rfree0.2265 1246 4.91 %RANDOM
Rwork0.1786 ---
obs0.181 25388 97.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.15→40.131 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2989 0 0 167 3156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093049
X-RAY DIFFRACTIONf_angle_d1.1984129
X-RAY DIFFRACTIONf_dihedral_angle_d15.041124
X-RAY DIFFRACTIONf_chiral_restr0.048475
X-RAY DIFFRACTIONf_plane_restr0.005522
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.23610.30091190.26932304X-RAY DIFFRACTION85
2.2361-2.33790.35821210.25692610X-RAY DIFFRACTION96
2.3379-2.46110.29521380.23652690X-RAY DIFFRACTION100
2.4611-2.61530.27231500.2132719X-RAY DIFFRACTION100
2.6153-2.81710.2771390.20632715X-RAY DIFFRACTION100
2.8171-3.10050.21811350.19782734X-RAY DIFFRACTION100
3.1005-3.5490.24691500.17032741X-RAY DIFFRACTION100
3.549-4.47040.18441330.14692770X-RAY DIFFRACTION100
4.4704-40.13760.19151610.15682859X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.18030.1737-0.16752.3207-0.96755.16370.4478-0.57840.10750.7419-0.42250.1120.1536-0.1168-0.08670.374-0.0781-0.00510.37630.05730.2897-10.9525-27.00916.5
25.5498-0.02620.57413.3976-0.33073.31160.2478-0.6774-0.8695-0.0379-0.11320.3070.46410.1980.01190.46640.1439-0.05540.46-0.00530.4677-19.7445-37.1466-8.2891
33.6754-0.7932-0.27942.49460.38864.43710.20130.1516-0.10190.1007-0.08470.16880.38670.3208-0.11630.3202-0.007-0.01910.3066-0.0270.2853-26.006-31.0187-15.4675
42.60430.16731.38891.38471.20094.0108-0.1660.58910.3336-0.37170.0183-0.1955-0.70290.64730.07420.4363-0.1008-0.00750.42870.10460.3462-20.8931-15.3523-24.5126
51.7915-0.33890.58491.0245-0.29192.2726-0.4050.26920.4072-0.18350.0563-0.0237-1.23080.3950.12510.6397-0.1262-0.09710.25260.08550.4463-19.248-7.4507-13.8021
61.5776-1.61061.28613.7453-0.72475.069-0.21290.03850.09070.09370.04370.0097-0.74110.16290.15690.2986-0.0357-0.02240.25130.02150.3315-14.2753-14.15661.8658
72.3199-0.2562.57691.3664-0.78013.02180.47220.3091-0.2682-0.1834-0.1723-0.05480.50620.3566-0.2610.26540.0593-0.01990.3078-0.06620.2955-7.6163-30.62723.9368
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 22 )
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 89 )
3X-RAY DIFFRACTION3chain 'A' and (resid 90 through 154 )
4X-RAY DIFFRACTION4chain 'A' and (resid 155 through 260 )
5X-RAY DIFFRACTION5chain 'A' and (resid 261 through 439 )
6X-RAY DIFFRACTION6chain 'A' and (resid 440 through 511 )
7X-RAY DIFFRACTION7chain 'A' and (resid 512 through 613 )

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