2VFX: Symmetric Mad2 Dimer

Structure of the Symmetric Mad2 Dimer. Determined by X-ray diffraction at 1.95 Å resolution. Released 18 Mar 2008.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: HOMO SAPIENS
Chains: 12
Atoms: 21,651
Mol. weight: 288.68 kDa
Ligands: MG, PE4, PE3
Released: 18 Mar 2008

Explore 2VFX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2VFX contains 87 α-helices and 127 β-strands across 12 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 8 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	1-5	5	1
β-strand	11	1	2
α-helix	13-34	22
α-helix	40-42	3
β-strand	43-48	6	3
β-strand	51-56	6	3
α-helix	59-77	19
β-strand	81-90	10	4
β-strand	96-106	11	4
α-helix	115-116	2
β-strand	117	1	2
α-helix	121-139	19
α-helix	143-144	2
β-strand	149-157	9	4
β-strand	178-182	5	4
α-helix	183-185	3
β-strand	186-187	2	4
β-strand	191-200	10	4
α-helix	201-203	3

Chain B: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	11	1	5
α-helix	13-34	22
α-helix	40-42	3
β-strand	43-48	6	6
β-strand	51-56	6	6
α-helix	59-77	19
β-strand	81-90	10	7
β-strand	96-106	11	7
α-helix	115-116	2
β-strand	117	1	5
α-helix	121-139	19
α-helix	143-144	2
β-strand	149-157	9	7
β-strand	178-182	5	7
β-strand	186-187	2	7
β-strand	191-200	10	7
α-helix	201-203	3

Chain C: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	8
β-strand	11	1	9
α-helix	13-34	22
α-helix	40-42	3
β-strand	43-48	6	10
β-strand	51-56	6	10
α-helix	59-77	19
β-strand	81-90	10	11
β-strand	96-106	11	11
β-strand	117	1	9
α-helix	121-139	19
α-helix	143-144	2
β-strand	149-157	9	11
α-helix	162-164	3
α-helix	169-171	3
β-strand	178-182	5	11
β-strand	186-187	2	11
β-strand	191-200	10	11

Chain D: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	11	1	12
α-helix	13-34	22
α-helix	40-42	3
β-strand	43-48	6	13
β-strand	51-56	6	13
α-helix	59-77	19
β-strand	83-90	8	14
β-strand	96-106	11	14
β-strand	117	1	12
α-helix	121-139	19
α-helix	143-144	2
β-strand	149-157	9	14
β-strand	167-169	3	14
β-strand	178-182	5	14
α-helix	183-185	3
β-strand	186-187	2	14
β-strand	191-200	10	14

Chain E: 9 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	11	1	15
α-helix	13-34	22
α-helix	40-42	3
β-strand	43-48	6	16
β-strand	51-56	6	16
α-helix	59-77	19
β-strand	81-90	10	1
β-strand	96-106	11	1
α-helix	110-112	3
β-strand	117	1	15
α-helix	121-139	19
α-helix	143-144	2
β-strand	149-157	9	1
α-helix	163-164	2
β-strand	167-169	3	1
α-helix	170-171	2
β-strand	178-182	5	1
α-helix	183-185	3
β-strand	186-187	2	1
β-strand	191-200	10	1

Chain F: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	1-5	5	17
β-strand	11	1	18
α-helix	13-34	22
α-helix	40-42	3
β-strand	43-48	6	19
β-strand	51-56	6	19
α-helix	59-77	19
β-strand	81-90	10	20
β-strand	96-106	11	20
α-helix	115-116	2
β-strand	117	1	18
α-helix	121-139	19
α-helix	143-144	2
β-strand	149-157	9	20
β-strand	178-187	10	20
β-strand	191-200	10	20
α-helix	201-203	3

Chain G: 8 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	11	1	21
α-helix	13-34	22
α-helix	40-42	3
β-strand	43-48	6	22
β-strand	51-56	6	22
α-helix	59-77	19
β-strand	81-90	10	23
β-strand	96-106	11	23
β-strand	117	1	21
α-helix	121-141	21
α-helix	143-144	2
β-strand	149-157	9	23
α-helix	169-171	3
β-strand	178-182	5	23
α-helix	183-185	3
β-strand	186-187	2	23
β-strand	191-200	10	23
α-helix	201-203	3

Chain H: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	1-5	5	14
β-strand	11	1	24
α-helix	13-34	22
α-helix	40-42	3
β-strand	43-48	6	25
β-strand	51-56	6	25
α-helix	59-77	19
β-strand	81-90	10	26
β-strand	96-106	11	26
α-helix	115-116	2
β-strand	117	1	24
α-helix	121-139	19
α-helix	143-144	2
β-strand	149-157	9	26
α-helix	169-171	3
β-strand	178-182	5	26
β-strand	186-187	2	26
β-strand	191-200	10	26

4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mitotic spindle assembly checkpoint protein MAD2A	A, B, C, D, E, F, G, H, I, J, K, L	protein	206	HOMO SAPIENS	Q13257 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J, K, L), FASTA

>2VFX_1 MITOTIC SPINDLE ASSEMBLY CHECKPOINT PROTEIN MAD2A (chains A, B, C, D, E, F, G, H, I, J, K, L)
GMALQLSREQGITARGSAEIVAEFFSFGINSILYQRGIYPSETFTRVQKYGLTLLVTTDL
ELIKYLNNVVEQLKDWLYKSSVQKLVVVISNIESGEVLERWQFDIESDKTAKDDSAPREK
SQKAIQDEIRSVIRQITATVTFLPLLEVSCSFDLLIYTDKDLVVPEKWEESGPQFITNSE
EVRLRSFTTTIHKVNSMVAYKIPVND

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	8
PE4	2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-etha…	C16 H34 O8	3
PE3	3,6,9,12,15,18,21,24,27,30,33,36,39-tridecaoxahentetracontane-1,41-diol	C28 H58 O15	6

Water and common crystallization additives (CL, PEG) are not listed.

Primary citation

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. et al. PLoS Biol (2008) 6:E50. DOI 10.1371/JOURNAL.PBIO.0060050 · PubMed

Other PDB entries of the same protein (UniProt Q13257 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1GO4 2.05 Å, Crystal structure of Mad1-Mad2 reveals a conserved Mad2 binding motif in Mad1 and Cdc20.
2QYF 2.3 Å, Crystal structure of the Mad2/p31(comet)/Mad2-binding peptide ternary complex
2V64 2.9 Å, Crystallographic structure of the conformational dimer of the Spindle Assembly…
6TLJ 3.8 Å, Cryo-EM structure of the Anaphase-promoting complex/Cyclosome, in complex with the…
3GMH 3.95 Å, Crystal Structure of the Mad2 Dimer
5LCW 4.2 Å, Cryo-EM structure of the Anaphase-promoting complex/Cyclosome, in complex with the…
6F0X 4.6 Å, Cryo-EM structure of TRIP13 in complex with ATP gamma S, p31comet, C-Mad2 and Cdc20
5KHU 4.8 Å, Model of human Anaphase-promoting complex/Cyclosome (APC15 deletion mutant), in complex…
1DUJ Solution structure of the spindle assembly checkpoint protein human MAD2
1KLQ The Mad2 Spindle Checkpoint Protein Undergoes Similar Major Conformational Changes upon…
1S2H The Mad2 spindle checkpoint protein possesses two distinct natively folded states

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