9B3D: MDia1 in the middle of F-actin

mDia1 in the middle of F-actin. Determined by electron microscopy at 3.41 Å resolution. Released 29 May 2024.

Method: Electron microscopy
Resolution: 3.41 Å
Organisms: Oryctolagus cuniculus, Mus musculus
Chains: 8
Atoms: 23,621
Mol. weight: 343.66 kDa
Ligands: MG, ADP
Released: 29 May 2024

Explore 9B3D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9B3D contains 178 α-helices and 124 β-strands across 8 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: 21 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
β-strand	65-68	4	2
β-strand	71-72	2	3
β-strand	75-76	2	3
α-helix	79-87	9
α-helix	88-94	7
β-strand	103-107	5	1
α-helix	113-125	13
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	182-192	11
α-helix	193-195	3
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	5
β-strand	247-250	4	5
α-helix	253-256	4
α-helix	259-262	4
α-helix	264-266	3
α-helix	274-283	10
α-helix	287-289	3
α-helix	290-294	5
β-strand	297-300	4	4
α-helix	309-320	12
β-strand	329-330	2	4
α-helix	338-347	10
α-helix	350-354	5
β-strand	357-358	2	1
α-helix	359-365	7
α-helix	370-373	4

Chain B: 22 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	6
β-strand	16-21	6	6
β-strand	29-32	4	6
β-strand	35-38	4	7
β-strand	53-54	2	7
α-helix	56-60	5
α-helix	62-64	3
β-strand	65-68	4	7
β-strand	71-72	2	8
β-strand	75-76	2	8
α-helix	79-87	9
α-helix	88-94	7
β-strand	103-107	5	6
α-helix	113-125	13
β-strand	131-136	6	6
α-helix	137-144	8
β-strand	150-155	6	9
β-strand	160-166	7	9
β-strand	169-170	2	9
α-helix	172-174	3
β-strand	176-178	3	9
α-helix	182-192	11
α-helix	203-215	13
α-helix	223-232	10
β-strand	238-241	4	10
β-strand	247-250	4	10
α-helix	253-256	4
α-helix	258-260	3
α-helix	264-266	3
α-helix	274-283	10
α-helix	290-293	4
β-strand	297-300	4	9
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	9
α-helix	338-346	9
α-helix	350-354	5
β-strand	357-358	2	6
α-helix	359-365	7
α-helix	366-368	3
α-helix	369-373	5

Chain C: 25 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	11
β-strand	16-21	6	11
β-strand	29-32	4	11
β-strand	35-38	4	12
β-strand	41-42	2	4
β-strand	53-54	2	12
α-helix	56-60	5
α-helix	62-64	3
β-strand	65-68	4	12
β-strand	71-72	2	13
β-strand	75-76	2	13
α-helix	79-88	10
α-helix	89-94	6
α-helix	98-100	3
β-strand	103-107	5	11
α-helix	113-125	13
β-strand	131-136	6	11
α-helix	137-144	8
β-strand	150-155	6	14
β-strand	160-166	7	14
β-strand	169-170	2	14
α-helix	172-174	3
β-strand	176-178	3	14
α-helix	182-192	11
α-helix	193-195	3
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	15
β-strand	247-250	4	15
α-helix	253-256	4
α-helix	258-261	4
α-helix	264-267	4
α-helix	274-283	10
α-helix	287-289	3
α-helix	290-294	5
β-strand	297-300	4	14
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	14
α-helix	338-346	9
α-helix	351-354	4
β-strand	357-358	2	11
α-helix	359-365	7
α-helix	366-368	3
α-helix	369-373	5

Chain D: 23 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	16
β-strand	16-21	6	16
β-strand	29-32	4	16
β-strand	35-38	4	17
β-strand	41-42	2	9
β-strand	53-54	2	17
α-helix	56-60	5
α-helix	62-64	3
β-strand	65-68	4	17
β-strand	71-72	2	18
β-strand	75-76	2	18
α-helix	79-88	10
α-helix	89-93	5
α-helix	98-100	3
β-strand	103-107	5	16
α-helix	113-125	13
β-strand	131-136	6	16
α-helix	137-144	8
β-strand	150-155	6	19
β-strand	160-166	7	19
β-strand	169-170	2	19
α-helix	172-174	3
β-strand	176-178	3	19
α-helix	182-192	11
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	20
β-strand	247-250	4	20
α-helix	253-256	4
α-helix	258-260	3
α-helix	264-266	3
α-helix	274-283	10
α-helix	290-294	5
β-strand	297-300	4	19
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	19
α-helix	338-346	9
α-helix	350-354	5
β-strand	357-358	2	16
α-helix	359-365	7
α-helix	366-368	3
α-helix	369-373	5

Chain E: 24 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	21
β-strand	16-21	6	21
β-strand	29-32	4	21
β-strand	35-38	4	22
β-strand	41-42	2	14
β-strand	53-54	2	22
α-helix	56-60	5
α-helix	62-64	3
β-strand	65-68	4	22
β-strand	71-72	2	23
β-strand	75-76	2	23
α-helix	79-88	10
α-helix	89-93	5
α-helix	98-100	3
β-strand	103-107	5	21
α-helix	113-125	13
β-strand	131-136	6	21
α-helix	137-144	8
β-strand	150-155	6	24
β-strand	160-166	7	24
β-strand	169-170	2	24
α-helix	172-174	3
β-strand	176-178	3	24
α-helix	182-192	11
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	25
β-strand	247-250	4	25
α-helix	253-256	4
α-helix	258-261	4
α-helix	264-266	3
α-helix	274-283	10
α-helix	290-294	5
β-strand	297-300	4	24
α-helix	303-305	3
α-helix	309-320	12
β-strand	329-330	2	24
α-helix	335-337	3
α-helix	338-347	10
α-helix	351-355	5
β-strand	357-358	2	21
α-helix	359-365	7
α-helix	366-368	3
α-helix	369-373	5

Chain F: 24 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	26
β-strand	16-21	6	26
β-strand	29-32	4	26
β-strand	35-38	4	27
β-strand	41-42	2	19
β-strand	53-54	2	27
α-helix	56-60	5
α-helix	62-64	3
β-strand	65-68	4	27
β-strand	71-72	2	28
β-strand	75-76	2	28
α-helix	79-87	9
α-helix	88-94	7
α-helix	98-100	3
β-strand	103-107	5	26
α-helix	113-125	13
β-strand	131-136	6	26
α-helix	137-144	8
β-strand	150-155	6	29
β-strand	160-166	7	29
β-strand	169-170	2	29
β-strand	176-178	3	29
α-helix	182-192	11
α-helix	193-195	3
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	30
β-strand	247-250	4	30
α-helix	253-256	4
α-helix	259-262	4
α-helix	264-266	3
α-helix	274-283	10
α-helix	290-295	6
β-strand	297-300	4	29
α-helix	303-305	3
α-helix	309-320	12
α-helix	326-327	2
β-strand	329-330	2	29
α-helix	338-348	11
α-helix	350-354	5
β-strand	357-358	2	26
α-helix	359-365	7
α-helix	366-368	3
α-helix	369-373	5

Chain G: 18 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	781-783	3
α-helix	786-789	4
α-helix	792-801	10
α-helix	837-850	14
α-helix	854-863	10
α-helix	871-879	9
α-helix	884-891	8
α-helix	894-896	3
α-helix	902-910	9
α-helix	916-947	32
α-helix	954-970	17
α-helix	984-990	7
β-strand	994	1	31
β-strand	1001	1	31
α-helix	1002-1012	11
α-helix	1017-1019	3
α-helix	1020-1023	4
α-helix	1036-1057	22
α-helix	1069-1104	36
α-helix	1114-1142	29

Chain H: 21 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	747-749	3
α-helix	750-754	5
β-strand	762	1	32
α-helix	769-771	3
α-helix	781-783	3
α-helix	786-789	4
α-helix	792-801	10
β-strand	803	1	32
α-helix	837-850	14
α-helix	854-863	10
α-helix	871-879	9
α-helix	884-891	8
α-helix	894-896	3
α-helix	902-912	11
α-helix	921-927	7
α-helix	929-949	21
α-helix	958-970	13
α-helix	984-990	7
β-strand	994	1	33
β-strand	1001	1	33
α-helix	1002-1012	11
α-helix	1017-1019	3
α-helix	1037-1057	21
α-helix	1069-1104	36
α-helix	1115-1142	28

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin, alpha skeletal muscle	A, B, C, D, E, F	protein	371	Oryctolagus cuniculus	P68135 (AlphaFold model)
Protein diaphanous homolog 1	G, H	protein	399	Mus musculus	O08808 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>9B3D_1 Actin, alpha skeletal muscle (chains A, B, C, D, E, F)
TTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGI
LTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMF
ETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRD
LTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPD
GQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTT
MYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDE
AGPSIVHRKCF

Sequence of entity 2 (G, H), FASTA

>9B3D_2 Protein diaphanous homolog 1 (chains G, H)
VLPFGLTPKKVYKPEVQLRRPNWSKFVAEDLSQDCFWTKVKEDRFENNELFAKLTLAFSA
QTKTSKAKKDQEGGEEKKSVQKKKVKELKVLDSKTAQNLSIFLGSFRMPYQEIKNVILEV
NEAVLTESMIQNLIKQMPEPEQLKMLSELKEEYDDLAESEQFGVVMGTVPRLRPRLNAIL
FKLQFSEQVENIKPEIVSVTAACEELRKSENFSSLLELTLLVGNYMNAGSRNAGAFGFNI
SFLCKLRDTKSADQKMTLLHFLAELCENDHPEVLKFPDELAHVEKASRVSAENLQKSLDQ
MKKQIADVERDVQNFPAATDEKDKFVEKMTSFVKDAQEQYNKLRMMHSNMETLYKELGDY
FVFDPKKLSVEEFFMDLHNFRNMFLQAVKENQKRRETEE

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	6
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	6

Primary citation

Mechanisms of actin filament severing and elongation by formins. Palmer, N.J., Barrie, K.R., Dominguez, R. Nature (2024) 632:437-442. DOI 10.1038/s41586-024-07637-0 · 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

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