2VFX | pdb_00002vfx

Structure of the Symmetric Mad2 Dimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 
    0.247 (Depositor), 0.244 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2VFX

This is version 1.4 of the entry. See complete history

Literature

Insights Into MAD2 Regulation in the Spindle Checkpoint Revealed by the Crystal Structure of the Symmetric MAD2 Dimer.

Yang, M.Li, B.Liu, C.-J.Tomchick, D.R.Machius, M.Rizo, J.Yu, H.Luo, X.

(2008) PLoS Biol 6: E50

  • DOI: https://doi.org/10.1371/journal.pbio.0060050
  • Primary Citation Related Structures: 
    2VFX

  • PubMed Abstract: 

    In response to misaligned sister chromatids during mitosis, the spindle checkpoint protein Mad2 inhibits the anaphase-promoting complex or cyclosome (APC/C) through binding to its mitotic activator Cdc20, thus delaying anaphase onset. Mad1, an upstream regulator of Mad2, forms a tight core complex with Mad2 and facilitates Mad2 binding to Cdc20. In the absence of its binding proteins, free Mad2 has two natively folded conformers, termed N1-Mad2/open-Mad2 (O-Mad2) and N2-Mad2/closed Mad2 (C-Mad2), with C-Mad2 being more active in APC/C(Cdc20) inhibition. Here, we show that whereas O-Mad2 is monomeric, C-Mad2 forms either symmetric C-Mad2-C-Mad2 (C-C) or asymmetric O-Mad2-C-Mad2 (O-C) dimers. We also report the crystal structure of the symmetric C-C Mad2 dimer, revealing the basis for the ability of unliganded C-Mad2, but not O-Mad2 or liganded C-Mad2, to form symmetric dimers. A Mad2 mutant that predominantly forms the C-C dimer is functional in vitro and in living cells. Finally, the Mad1-Mad2 core complex facilitates the conversion of O-Mad2 to C-Mad2 in vitro. Collectively, our results establish the existence of a symmetric Mad2 dimer and provide insights into Mad1-assisted conformational activation of Mad2 in the spindle checkpoint.


  • Organizational Affiliation
    • Department of Pharmacology, The University of Texas Southwestern Medical Center, Dallas, Texas, United States of America.

Macromolecule Content 

  • Total Structure Weight: 288.68 kDa 
  • Atom Count: 21,651 
  • Modeled Residue Count: 2,438 
  • Deposited Residue Count: 2,472 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MITOTIC SPINDLE ASSEMBLY CHECKPOINT PROTEIN MAD2A
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
206Homo sapiensMutation(s): 3 
UniProt & NIH Common Fund Data Resources
Find proteins for Q13257 (Homo sapiens)
Explore Q13257 
Go to UniProtKB:  Q13257
PHAROS:  Q13257
GTEx:  ENSG00000164109 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13257
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PE3

Query on PE3



Download:Ideal Coordinates CCD File
BA [auth C]
JB [auth K]
QA [auth F]
UA [auth G]
V [auth B]
BA [auth C],
JB [auth K],
QA [auth F],
UA [auth G],
V [auth B],
VA [auth H]
3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL
C28 H58 O15
ILLKMACMBHTSHP-UHFFFAOYSA-N
PE4

Query on PE4



Download:Ideal Coordinates CCD File
LA [auth E],
NB [auth L],
Q [auth A]
2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
ZA [auth I]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
AA [auth C]
AB [auth I]
BB [auth J]
CA [auth D]
CB [auth J]
AA [auth C],
AB [auth I],
BB [auth J],
CA [auth D],
CB [auth J],
DA [auth D],
DB [auth J],
EA [auth D],
EB [auth J],
FA [auth D],
FB [auth J],
GA [auth D],
HB [auth K],
IA [auth E],
IB [auth K],
JA [auth E],
KA [auth E],
LB [auth L],
MA [auth E],
MB [auth L],
N [auth A],
NA [auth E],
O [auth A],
OB [auth L],
P [auth A],
PA [auth F],
RA [auth F],
S [auth B],
T [auth B],
TA [auth G],
U [auth B],
W [auth B],
WA [auth I],
XA [auth I],
Y [auth C],
YA [auth I],
Z [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
GB [auth K]
HA [auth E]
KB [auth L]
M [auth A]
OA [auth F]
GB [auth K],
HA [auth E],
KB [auth L],
M [auth A],
OA [auth F],
R [auth B],
SA [auth G],
X [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free:  0.247 (Depositor), 0.244 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.337α = 90
b = 191.407β = 90.02
c = 154.307γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-03-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2019-01-30
    Changes: Data collection, Derived calculations, Experimental preparation, Other
  • Version 1.3: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description