3DAW: Actin-depolymerizing factor homology domain

Structure of the actin-depolymerizing factor homology domain in complex with actin. Determined by X-ray diffraction at 2.55 Å resolution. Released 29 Jul 2008.

Method: X-ray diffraction
Resolution: 2.55 Å
Organisms: Oryctolagus cuniculus, Mus musculus
Chains: 2
Atoms: 4,211
Mol. weight: 62 kDa
Ligands: ATP, CA
Released: 29 Jul 2008

Explore 3DAW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3DAW contains 28 α-helices and 27 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: 20 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	1
β-strand	16-21	6	1
β-strand	22	1	2
β-strand	24	1	2
β-strand	29-32	4	1
β-strand	35-38	4	3
β-strand	53-54	2	3
α-helix	55-60	6
β-strand	65-68	4	3
β-strand	71-72	2	4
β-strand	75-76	2	4
α-helix	79-87	9
α-helix	88-94	7
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	182-195	14
α-helix	203-216	14
α-helix	223-231	9
β-strand	238-241	4	6
β-strand	247-250	4	6
α-helix	253-262	10
α-helix	264-267	4
α-helix	274-283	10
α-helix	290-295	6
β-strand	297-300	4	5
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	5
α-helix	338-347	10
α-helix	350-352	3
β-strand	357-358	2	1
α-helix	359-363	5
α-helix	370-374	5

Chain B: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	180-181	2
β-strand	182	1	7
α-helix	183	1
α-helix	184-194	11
β-strand	200-206	7	7
β-strand	211-216	6	7
α-helix	222-224	3
α-helix	226-228	3
β-strand	235-245	11	7
β-strand	248-258	11	7
α-helix	266-274	9
α-helix	276-287	12
β-strand	291-297	7	7
α-helix	305-312	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin, alpha skeletal muscle	A	protein	377	Oryctolagus cuniculus	P68135 (AlphaFold model)
Twinfilin-1	B	protein	164	Mus musculus	Q91YR1 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3DAW_1 Actin, alpha skeletal muscle (chains A)
MCDEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEA
QSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREK
MTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRL
DLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEK
SYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNV
MSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWIT
KQEYDEAGPSIVHRKCF

Sequence of entity 2 (B), FASTA

>3DAW_2 Twinfilin-1 (chains B)
MSHHHHHHSMDTKHQTLQGVAFPISRDAFQALEKLSKKQLNYVQLEIDIKNETIILANTE
NTELRDLPKRIPKDSARYHFFLYKHSHEGDYLESVVFIYSMPGYTCSIRERMLYSSCKSP
LLEIVERQLQMDVIRKIEIDNGDELTADFLYDEVHPKQHAHKQS

Ligands and cofactors

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

Primary citation

Structure of the actin-depolymerizing factor homology domain in complex with actin. Paavilainen, V.O., Oksanen, E., Goldman, A. et al. J Cell Biol (2008) 182:51-59. DOI 10.1083/jcb.200803100 · 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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