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- PDB-1duj: SOLUTION STRUCTURE OF THE SPINDLE ASSEMBLY CHECKPOINT PROTEIN HUM... -

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Basic information

Entry
Database: PDB / ID: 1duj
TitleSOLUTION STRUCTURE OF THE SPINDLE ASSEMBLY CHECKPOINT PROTEIN HUMAN MAD2
ComponentsSPINDLE ASSEMBLY CHECKPOINT PROTEINSpindle checkpoint
KeywordsCELL CYCLE / Mad2 / spindle assembly checkpoint
Function / homology
Function and homology information


mitotic spindle assembly checkpoint MAD1-MAD2 complex / Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components / mitotic checkpoint complex / positive regulation of mitotic cell cycle spindle assembly checkpoint / establishment of centrosome localization / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / nuclear pore nuclear basket / negative regulation of ubiquitin protein ligase activity / mitotic spindle assembly checkpoint signaling ...mitotic spindle assembly checkpoint MAD1-MAD2 complex / Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components / mitotic checkpoint complex / positive regulation of mitotic cell cycle spindle assembly checkpoint / establishment of centrosome localization / Inactivation of APC/C via direct inhibition of the APC/C complex / APC/C:Cdc20 mediated degradation of mitotic proteins / nuclear pore nuclear basket / negative regulation of ubiquitin protein ligase activity / mitotic spindle assembly checkpoint signaling / mitotic sister chromatid segregation / establishment of mitotic spindle orientation / negative regulation of mitotic cell cycle / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / APC-Cdc20 mediated degradation of Nek2A / RHO GTPases Activate Formins / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / negative regulation of protein catabolic process / mitotic spindle / kinetochore / spindle pole / Separation of Sister Chromatids / cell division / negative regulation of apoptotic process / perinuclear region of cytoplasm / protein homodimerization activity / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A / HORMA domain / Mad2-like / HORMA domain / HORMA domain / HORMA domain profile. / HORMA domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Mitotic spindle assembly checkpoint protein MAD2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsLuo, X. / Fang, G. / Coldiron, M. / Lin, Y. / Yu, H.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Structure of the Mad2 spindle assembly checkpoint protein and its interaction with Cdc20.
Authors: Luo, X. / Fang, G. / Coldiron, M. / Lin, Y. / Yu, H. / Kirschner, M.W. / Wagner, G.
History
DepositionJan 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 21, 2022Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SPINDLE ASSEMBLY CHECKPOINT PROTEIN


Theoretical massNumber of molelcules
Total (without water)21,4301
Polymers21,4301
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative

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Components

#1: Protein SPINDLE ASSEMBLY CHECKPOINT PROTEIN / Spindle checkpoint


Mass: 21430.369 Da / Num. of mol.: 1
Fragment: FULL PROTEIN WITHOUT BOTH N- AND C-TERMINAL 10 RESIDUES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PQE-30 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13257

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
3133D 15N-separated NOESY
5253D 13C-separated NOESY
2323D (H)CCH-TOCSY
3433D 15N-separated TOCSY
2523D H(CC)(CO)NH
2623D (H)C(C)(CO)NH
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
11.2mM Mad2 protein U-15N,13C,2H; 50mM sodium phosphate (pH 6.8), 300mM KCl, 5mM DTT, 0.04% NaN3; 90% H2O, 10% D2O90% H2O/10% D2O
21.4mM Mad2 protein U-15N,13C; U-60% 2H; 50mM sodium phosphate (pH 6.8), 300mM KCl, 5mM DTT, 0.04% NaN3; 90% H2O, 10% D2O90% H2O/10% D2O
31.5mM Mad2 protein U-15N; 50mM sodium phosphate (pH 6.8), 300mM KCl, 5mM DTT, 0.04% NaN3; 90% H2O, 10% D2O90% H2O/10% D2O
41.6mM Mad2 protein U-10% 13C; 50mM sodium phosphate (pH 6.8), 300mM KCl, 5mM DTT, 0.04% NaN3; 100% D2O100% D2O
51.7mM Mad2 protein U-15N,13C; 50mM sodium phosphate (pH 6.8), 300mM KCl, 5mM DTT, 0.04% NaN3; 100% D2O100% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1300mM KCl 6.8 ambient 303 K
2300mM KCl 6.8 ambient 303 K
3300mM KCl 6.8 ambient 303 K
4300mM KCl 6.8 ambient 303 K
5300mM KCl 6.8 ambient 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.1Brungerstructure solution
X-PLOR3.1Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 3111 restraints, 2807 are NOE-derived distance constraints, 214 dihedral angle restraints,90 distance restraints from hydrogen bonds.
NMR ensembleConformers submitted total number: 1

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