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- PDB-2m6n: 3D solution structure of EMI1 (Early Mitotic Inhibitor 1) -

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Basic information

Entry
Database: PDB / ID: 2m6n
Title3D solution structure of EMI1 (Early Mitotic Inhibitor 1)
ComponentsF-box only protein 5
KeywordsCELL CYCLE / EMI1 / APC / E3 ligase / ZBR
Function / homology
Function and homology information


negative regulation of DNA endoreduplication / negative regulation of mitotic metaphase/anaphase transition / negative regulation of meiotic nuclear division / positive regulation of biomineral tissue development / positive regulation of mesenchymal stem cell migration / Mitotic Metaphase/Anaphase Transition / vesicle organization / Phosphorylation of Emi1 / anaphase-promoting complex binding / negative regulation of ubiquitin-protein transferase activity ...negative regulation of DNA endoreduplication / negative regulation of mitotic metaphase/anaphase transition / negative regulation of meiotic nuclear division / positive regulation of biomineral tissue development / positive regulation of mesenchymal stem cell migration / Mitotic Metaphase/Anaphase Transition / vesicle organization / Phosphorylation of Emi1 / anaphase-promoting complex binding / negative regulation of ubiquitin-protein transferase activity / oocyte maturation / spindle assembly involved in female meiosis I / meiotic spindle / ubiquitin ligase inhibitor activity / negative regulation of ubiquitin protein ligase activity / regulation of mitotic nuclear division / G1/S-Specific Transcription / molecular function inhibitor activity / microtubule polymerization / regulation of DNA replication / negative regulation of cellular senescence / Regulation of APC/C activators between G1/S and early anaphase / positive regulation of osteoblast differentiation / positive regulation of G2/M transition of mitotic cell cycle / regulation of mitotic cell cycle / SCF-beta-TrCP mediated degradation of Emi1 / spindle / protein ubiquitination / cell division / DNA damage response / positive regulation of cell population proliferation / protein kinase binding / nucleoplasm / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
N-terminal domain of TfIIb - #20 / Zinc finger ZBR-type domain / : / Zinc finger ZBR-type profile. / F-box domain / F-box domain / N-terminal domain of TfIIb / Single Sheet / Mainly Beta
Similarity search - Domain/homology
F-box only protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsFrye, J.J. / Brown, N.G. / Petzold, G. / Watson, E.R. / Royappa, G.R. / Nourse, A. / Jarvis, M. / Kriwacki, R.W. / Peters, J. / Stark, H. / Schulman, B.A.
CitationJournal: Nat Struct Mol Biol / Year: 2013
Title: Electron microscopy structure of human APC/C(CDH1)-EMI1 reveals multimodal mechanism of E3 ligase shutdown.
Authors: Jeremiah J Frye / Nicholas G Brown / Georg Petzold / Edmond R Watson / Christy R R Grace / Amanda Nourse / Marc A Jarvis / Richard W Kriwacki / Jan-Michael Peters / Holger Stark / Brenda A Schulman /
Abstract: The anaphase-promoting complex/cyclosome (APC/C) is a ~1.5-MDa multiprotein E3 ligase enzyme that regulates cell division by promoting timely ubiquitin-mediated proteolysis of key cell-cycle ...The anaphase-promoting complex/cyclosome (APC/C) is a ~1.5-MDa multiprotein E3 ligase enzyme that regulates cell division by promoting timely ubiquitin-mediated proteolysis of key cell-cycle regulatory proteins. Inhibition of human APC/C(CDH1) during interphase by early mitotic inhibitor 1 (EMI1) is essential for accurate coordination of DNA synthesis and mitosis. Here, we report a hybrid structural approach involving NMR, electron microscopy and enzymology, which reveal that EMI1's 143-residue C-terminal domain inhibits multiple APC/C(CDH1) functions. The intrinsically disordered D-box, linker and tail elements, together with a structured zinc-binding domain, bind distinct regions of APC/C(CDH1) to synergistically both block the substrate-binding site and inhibit ubiquitin-chain elongation. The functional importance of intrinsic structural disorder is explained by enabling a small inhibitory domain to bind multiple sites to shut down various functions of a 'molecular machine' nearly 100 times its size.
History
DepositionApr 6, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Jul 17, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: F-box only protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7363
Polymers9,6051
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein F-box only protein 5 / EMI1 / Early mitotic inhibitor 1


Mass: 9605.360 Da / Num. of mol.: 1 / Fragment: zinc binding domain (UNP residues 364-447)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FBXO5, EMI1, FBX5 / Plasmid: pGEX4T1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UKT4
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-15N HSQC
1312D 1H-13C HSQC
1413D HN(CA)CB
1513D HNCA
1613D CBCA(CO)NH
1713D (H)CCH-TOCSY
1813D H(CCO)NH
1913D 1H-15N NOESY
11013D 1H-13C NOESY aliphatic
11113D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 0.8 mM [U-100% 13C; U-100% 15N] F-box only protein 5, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 0.8 mM / Component: F-box only protein 5 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 50 / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance8001
Bruker AvanceBrukerAvance6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 931 / NOE intraresidue total count: 211 / NOE long range total count: 256 / NOE medium range total count: 0 / NOE sequential total count: 83 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 19 / Protein psi angle constraints total count: 19
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0.1997 ° / Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0.0093 Å / Maximum torsion angle constraint violation: 0.86 ° / Maximum upper distance constraint violation: 0.21 Å / Torsion angle constraint violation method: Talos program
NMR ensemble rmsDistance rms dev: 0.046 Å / Distance rms dev error: 0.004 Å

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