7E34: SUN1-Speedy A-CDK2

Crystal structure of SUN1-Speedy A-CDK2. Determined by X-ray diffraction at 3.19 Å resolution. Released 14 Apr 2021.

Method: X-ray diffraction
Resolution: 3.19 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,815
Mol. weight: 57.73 kDa
Ligands: ZN
Released: 14 Apr 2021

Explore 7E34 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7E34 contains 29 α-helices and 13 β-strands across 3 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: 17 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	6-12	7	1
β-strand	16-21	6	1
β-strand	30-35	6	1
α-helix	46-55	10
β-strand	63	1	2
α-helix	64-65	2
β-strand	66-71	6	1
β-strand	76-81	6	1
β-strand	85-86	2	2
α-helix	87-93	7
α-helix	101-120	20
β-strand	123-124	2	3
α-helix	130-132	3
β-strand	133-135	3	2
β-strand	141-143	3	2
β-strand	150-151	2	3
α-helix	166-168	3
α-helix	171-174	4
α-helix	183-198	16
α-helix	208-218	11
α-helix	221-223	3
α-helix	240-242	3
α-helix	248-251	4
α-helix	257-266	10
α-helix	275-276	2
α-helix	277-281	5
α-helix	284-287	4
α-helix	292-295	4

Chain B: 12 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	64-67	4	4
α-helix	68-75	8
α-helix	76-79	4
α-helix	81-89	9
α-helix	98-111	14
α-helix	115-117	3
α-helix	120-134	15
α-helix	140-144	5
α-helix	145-148	4
α-helix	150-152	3
α-helix	153-170	18
α-helix	179-186	8
α-helix	193-196	4

Chain C: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	143-146	4	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cyclin-dependent kinase 2	A	protein	298	Homo sapiens	P24941 (AlphaFold model)
Speedy protein A	B	protein	153	Homo sapiens	Q5MJ70 (AlphaFold model)
SUN domain-containing protein 1	C	protein	46	Homo sapiens	O94901 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7E34_1 Cyclin-dependent kinase 2 (chains A)
SENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNH
PNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHS
HRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYY
STAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSF
PKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL

Sequence of entity 2 (B), FASTA

>7E34_2 Speedy protein A (chains B)
GPCLVIQRQDMTAFFKLFDDDLIQDFLWMDCCCKIADKYLLAMTFVYFKRAKFTISEHTR
INFFIALYLANTVEEDEEETKYEIFPWALGKNWRKLFPNFLKLRDQLWDRIDYRAIVSRR
CCEEVMAIAPTHYIWQRERSVHHSGAVRNYNRD

Sequence of entity 3 (C), FASTA

>7E34_3 SUN domain-containing protein 1 (chains C)
DAVTRRPPVLDESWIREQTTVDHFWGLDDDGDLKGGNKAAIQGNGD

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Water and common crystallization additives (GOL) are not listed.

Primary citation

The SUN1-SPDYA interaction plays an essential role in meiosis prophase I. Chen, Y., Wang, Y., Chen, J. et al. Nat Commun (2021) 12:3176-3176. DOI 10.1038/s41467-021-23550-w · PubMed

Other PDB entries of the same protein (UniProt P24941 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6Q4G 0.98 Å, CDK2 in complex with FragLite37
6Q49 1.0 Å, CDK2 in complex with FragLite6
6Q4H 1.0 Å, CDK2 in complex with FragLite36
6Q48 1.03 Å, CDK2 in complex with FragLite7
6Q4J 1.05 Å, CDK2 in complex with FragLite34
6Q4E 1.06 Å, CDK2 in complex with FragLite33
6Q4K 1.06 Å, CDK2 in complex with FragLite38
6Q4D 1.07 Å, CDK2 in complex with FragLite31
6Q3B 1.11 Å, CDK2 in complex with FragLite2
6Q4I 1.11 Å, CDK2 in complex with FragLite35
6Q4B 1.12 Å, CDK2 in complex with FragLite13
6Q4A 1.13 Å, CDK2 in complex with FragLite14

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