6YP9: Rabbit muscle actin

Rabbit muscle actin in complex with ADF-H and ATP-ATTO-488. Determined by X-ray diffraction at 2.56 Å resolution. Released 9 Dec 2020.

Method: X-ray diffraction
Resolution: 2.56 Å
Organisms: Oryctolagus cuniculus, Mus musculus
Chains: 2
Atoms: 4,271
Mol. weight: 58.86 kDa
Ligands: ATP, CA
Released: 9 Dec 2020

Explore 6YP9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6YP9 contains 31 α-helices and 25 β-strands across 2 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: 24 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	1
β-strand	16-21	6	1
β-strand	29-32	4	1
β-strand	35-38	4	2
β-strand	53-54	2	2
α-helix	56-60	5
α-helix	62-64	3
β-strand	65-68	4	2
β-strand	71-72	2	3
β-strand	75-76	2	3
α-helix	79-88	10
α-helix	89-93	5
α-helix	98-100	3
β-strand	103-107	5	1
α-helix	113-121	9
α-helix	122-126	5
β-strand	131-136	6	1
α-helix	137-145	9
β-strand	150-155	6	4
β-strand	160-166	7	4
β-strand	169-170	2	4
α-helix	172-174	3
β-strand	176-178	3	4
α-helix	182-194	13
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	5
β-strand	247-250	4	5
α-helix	253-259	7
α-helix	264-267	4
α-helix	272-273	2
α-helix	274-283	10
α-helix	287-294	8
β-strand	297-300	4	4
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	4
α-helix	338-348	11
α-helix	351-354	4
β-strand	357-358	2	1
α-helix	359-365	7
α-helix	367-369	3
α-helix	370-373	4

Chain B: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	180-181	2
β-strand	182	1	6
α-helix	183	1
α-helix	184-194	11
β-strand	200-206	7	6
β-strand	211-216	6	6
α-helix	222-228	7
β-strand	235-245	11	6
β-strand	248-258	11	6
α-helix	266-287	22
β-strand	293-297	5	6
α-helix	300-302	3
α-helix	305-312	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin, alpha skeletal muscle	A	protein	375	Oryctolagus cuniculus	P68135 (AlphaFold model)
Twinfilin-1	B	protein	140	Mus musculus	Q91YR1 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6YP9_1 Actin, alpha skeletal muscle (chains A)
DEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQS
KRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMT
QIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDL
AGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSY
ELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMS
GGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQ
EYDEAGPSIVHRKCF

Sequence of entity 2 (B), FASTA

>6YP9_2 Twinfilin-1 (chains B)
QGVAFPISRDAFQALEKLSKKQLNYVQLEIDIKNETIILANTENTELRDLPKRIPKDSAR
YHFFLYKHSHEGDYLESVVFIYSMPGYTCSIRERMLYSSCKSPLLEIVERQLQMDVIRKI
EIDNGDELTADFLYDEVHPK

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1
CA	Calcium ion	Ca	1

Primary citation

A functional family of fluorescent nucleotide analogues to investigate actin dynamics and energetics. Colombo, J., Antkowiak, A., Kogan, K. et al. Nat Commun (2021) 12:548-548. DOI 10.1038/s41467-020-20827-4 · 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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