5YPU: Actin monomer

Crystal structure of an actin monomer in complex with the nucleator Cordon-Bleu MET72NLE WH2-motif peptide. Determined by X-ray diffraction at 2.0 Å resolution. Released 26 Sept 2018.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: Oryctolagus cuniculus, Mus musculus
Chains: 4
Atoms: 6,550
Mol. weight: 88.07 kDa
Ligands: CA, ATP
Released: 26 Sept 2018

Explore 5YPU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5YPU contains 51 α-helices and 42 β-strands across 4 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: 23 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	1
β-strand	16-21	6	1
β-strand	24	1	2
β-strand	29-32	4	1
β-strand	35	1	3
β-strand	54	1	3
α-helix	56-60	5
β-strand	68	1	3
β-strand	71-72	2	4
β-strand	75-76	2	4
α-helix	79-88	10
α-helix	89-93	5
α-helix	98-100	3
β-strand	103-107	5	1
α-helix	113-125	13
β-strand	131-136	6	1
α-helix	137-144	8
β-strand	150-155	6	5
β-strand	160-166	7	5
β-strand	169-170	2	5
α-helix	172-174	3
β-strand	176-178	3	5
α-helix	182-192	11
α-helix	193-196	4
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	6
α-helix	246	1
β-strand	247-250	4	6
α-helix	253-259	7
α-helix	264-267	4
α-helix	274-283	10
α-helix	287-294	8
β-strand	297-300	4	5
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	5
α-helix	335-337	3
α-helix	338-348	11
α-helix	350-355	6
β-strand	357-358	2	1
α-helix	359-365	7
α-helix	367-371	5

Chains B and D: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	67-76	10
α-helix	80-83	4
β-strand	85	1	2
α-helix	86	1

Chain C: 22 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	7
β-strand	16-21	6	7
β-strand	24	1	8
β-strand	29-32	4	7
β-strand	35	1	9
β-strand	54	1	9
α-helix	56-60	5
α-helix	66-67	2
β-strand	68	1	9
β-strand	71-72	2	10
β-strand	75-76	2	10
α-helix	79-87	9
α-helix	88-93	6
α-helix	98-100	3
β-strand	103-107	5	7
α-helix	113-125	13
β-strand	131-136	6	7
α-helix	137-144	8
β-strand	150-155	6	11
β-strand	160-166	7	11
β-strand	169-170	2	11
α-helix	172-174	3
β-strand	176-178	3	11
α-helix	182-192	11
α-helix	193-196	4
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	12
β-strand	247-250	4	12
α-helix	253-259	7
α-helix	264-267	4
α-helix	274-283	10
α-helix	287-294	8
β-strand	297-300	4	11
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	11
α-helix	338-348	11
α-helix	350-355	6
β-strand	357-358	2	7
α-helix	359-365	7
α-helix	367-371	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin, alpha skeletal muscle	A, C	protein	368	Oryctolagus cuniculus	P68135 (AlphaFold model)
Cordon-Bleu WH2 motif	B, D	protein	22	Mus musculus	Q5NBX1 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>5YPU_1 Actin, alpha skeletal muscle (chains A, C)
TTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGI
LTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMF
ETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRD
LTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPD
GQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTT
MYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDE
AGPSIVHR

Sequence of entity 2 (B, D), FASTA

>5YPU_2 Cordon-Bleu WH2 motif (chains B, D)
SLHSALLEAIHSSGGREKLRKV

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	7
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	2

Primary citation

Structural evidence for the roles of divalent cations in actin polymerization and activation of ATP hydrolysis. Scipion, C.P.M., Ghoshdastider, U., Ferrer, F.J. et al. Proc Natl Acad Sci U S A (2018) 115:10345-10350. DOI 10.1073/pnas.1806394115 · PubMed

Other PDB entries of the same protein (UniProt P68135 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4B1Y 1.29 Å, Structure of the Phactr1 RPEL-3 bound to G-actin
2FXU 1.35 Å, X-ray Structure of Bistramide A- Actin Complex at 1.35 A resolution.
4K41 1.4 Å, Crystal structure of actin in complex with marine macrolide kabiramide C
1QZ5 1.45 Å, Structure of rabbit actin in complex with kabiramide C
1WUA 1.45 Å, The structure of Aplyronine A-actin complex
2Q0U 1.45 Å, Structure of Pectenotoxin-2 and Latrunculin B Bound to Actin
2V52 1.45 Å, Structure of MAL-RPEL2 complexed to G-actin
3MN5 1.5 Å, Structures of actin-bound WH2 domains of Spire and the implication for filament nucleation
2PBD 1.5 Å, Ternary complex of profilin-actin with the poly-PRO-GAB domain of VASP*
5ZZA 1.53 Å, OdinProfilin/Rabbit Actin Complex
1J6Z 1.54 Å, Uncomplexed actin
1QZ6 1.6 Å, Structure of rabbit actin in complex with jaspisamide A

Browse structure collections

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