2QYF: PDB entry 2QYF

Crystal structure of the Mad2/p31(comet)/Mad2-binding peptide ternary complex. Determined by X-ray diffraction at 2.3 Å resolution. Released 29 Jan 2008.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 6
Atoms: 6,944
Mol. weight: 105.47 kDa
Released: 29 Jan 2008

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

Secondary structure: helices and β-sheets

2QYF contains 34 α-helices and 38 β-strands across 6 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: 10 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	11	1	1
α-helix	13-34	22
α-helix	40-42	3
β-strand	43-48	6	2
β-strand	51-56	6	2
α-helix	59-77	19
β-strand	83-90	8	3
β-strand	96-106	11	3
α-helix	108-111	4
β-strand	117	1	1
α-helix	121-137	17
α-helix	138-140	3
α-helix	143-144	2
β-strand	149-156	8	3
α-helix	160-162	3
β-strand	168-170	3	3
β-strand	177-182	6	3
α-helix	183-184	2
β-strand	186-187	2	3
β-strand	191-200	10	3
α-helix	201-202	2

Chain B: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	55-59	5	4
α-helix	67-83	17
α-helix	91-94	4
α-helix	126-144	19
β-strand	149-154	6	4
β-strand	163-168	6	4
α-helix	183-196	14
α-helix	205-208	4
β-strand	210-218	9	4
β-strand	227-229	3	4
β-strand	239-246	8	4
β-strand	260-264	5	4
α-helix	268	1
β-strand	269-270	2	4
α-helix	271	1

Chain C: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	13-34	22
α-helix	40-42	3
β-strand	43-48	6	5
β-strand	51-56	6	5
α-helix	59-77	19
β-strand	83-90	8	3
β-strand	96-106	11	3
α-helix	121-137	17
α-helix	138-140	3
α-helix	143-144	2
β-strand	149-156	8	3
α-helix	162-164	3
β-strand	168-170	3	3
β-strand	178-182	5	3
β-strand	186-187	2	3
β-strand	191-200	10	3
α-helix	201-202	2

Chain D: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	55-59	5	6
α-helix	66-83	18
α-helix	91-94	4
α-helix	120-144	25
β-strand	149-154	6	6
β-strand	163-168	6	6
α-helix	182-196	15
α-helix	205-208	4
β-strand	210-218	9	6
α-helix	219-221	3
β-strand	227-229	3	6
β-strand	239-246	8	6
β-strand	260-264	5	6
β-strand	269-270	2	6
α-helix	271	1

Chains E and F: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2-5	4	3
α-helix	6-9	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Mitotic spindle assembly checkpoint protein MAD2A	A, C	protein	206	Homo sapiens	Q13257 (AlphaFold model)
MAD2L1-binding protein	B, D	protein	240	Homo sapiens	Q15013 (AlphaFold model)
peptide	E, F	protein	12

Sequence of entity 1 (A, C), FASTA

>2QYF_1 Mitotic spindle assembly checkpoint protein MAD2A (chains A, C)
GMALQLSREQGITARGSAEIVAEFFSFGINSILYQRGIYPSETFTRVQKYGLTLLVTTDL
ELIKYLNNVVEQLKDWLYKCSVQKLVVVISNIESGEVLERWQFDIECDKTAKDDSAPREK
SQKAIQDEIRSVIRQITATVTFLPLLEVSCSFDLLIYTDKDLVVPEKWEESGPQFITNSE
EVRLRSFTTTIHKVNSMVAYKIPVND

Sequence of entity 2 (B, D), FASTA

>2QYF_2 MAD2L1-binding protein (chains B, D)
MTSSTQEPLNASEAFCPRDCMVPVVFPGPVSQEGCCQFTCELLKHIMYQRQQLPLPYEQL
KHFYRKPSPQAEEMLKKKPRATTEVSSRKCQQALAELESVLSHLEDFFARTLVPRVLILL
GGNALSPKEFYELDLSLLAPYSVDQSLSTAACLRRLFRAIFMADAFSELQAPPLMGTVVM
AQGHRNCGEDWFRPKLNYRVPSRGHKLTVTLSCGRPSIRTTAWEDYIWFQAPVTFKGFRE

Sequence of entity 3 (E, F), FASTA

>2QYF_3 peptide (chains E, F)
SWYSYPPPQRAV

Primary citation

p31comet blocks Mad2 activation through structural mimicry. Yang, M., Li, B., Tomchick, D.R. et al. Cell (2007) 131:744-755. DOI 10.1016/j.cell.2007.08.048 · PubMed

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

2VFX 1.95 Å, Structure of the Symmetric Mad2 Dimer
1GO4 2.05 Å, Crystal structure of Mad1-Mad2 reveals a conserved Mad2 binding motif in Mad1 and Cdc20.
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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