8RU2: F-actin barbed end bound by formin mDia1

Structure of the F-actin barbed end bound by formin mDia1. Determined by electron microscopy at 3.49 Å resolution. Released 10 Apr 2024.

Method: Electron microscopy
Resolution: 3.49 Å
Organisms: Homo sapiens, Mus musculus
Chains: 5
Atoms: 14,773
Mol. weight: 299.19 kDa
Ligands: MG, ADP
Released: 10 Apr 2024

Explore 8RU2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8RU2 contains 104 α-helices and 72 β-strands across 5 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 B: 24 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	1
β-strand	16-21	6	1
β-strand	30-32	3	1
β-strand	35-38	4	2
α-helix	41-42	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	80-87	8
α-helix	88-93	6
β-strand	103-107	5	1
α-helix	113-122	10
α-helix	123-127	5
β-strand	132-136	5	1
α-helix	137-145	9
α-helix	151	1
β-strand	152-155	4	4
β-strand	160-163	4	4
β-strand	165-166	2	5
β-strand	169-170	2	5
α-helix	172-174	3
β-strand	176-178	3	4
α-helix	182-196	15
α-helix	205-215	11
α-helix	224-232	9
β-strand	239-241	3	6
β-strand	247-249	3	6
α-helix	253-259	7
α-helix	264-266	3
α-helix	272-273	2
α-helix	274-283	10
α-helix	288-290	3
α-helix	291-294	4
β-strand	297	1	7
β-strand	298-300	3	4
α-helix	303-305	3
α-helix	309-318	10
β-strand	329	1	7
α-helix	338-348	11
α-helix	350-354	5
α-helix	359-363	5
α-helix	367-371	5

Chain C: 24 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	8
β-strand	17-21	5	8
β-strand	29-31	3	8
β-strand	35-36	2	9
β-strand	53-54	2	9
α-helix	56-60	5
β-strand	68	1	9
β-strand	71-72	2	10
β-strand	75-76	2	10
α-helix	80-88	9
α-helix	89-93	5
β-strand	103-107	5	8
α-helix	113-121	9
α-helix	122-126	5
β-strand	131-136	6	8
α-helix	137-142	6
β-strand	152-155	4	11
β-strand	160-163	4	11
β-strand	165	1	12
β-strand	170	1	12
α-helix	172-174	3
β-strand	178	1	11
α-helix	182-192	11
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	13
β-strand	247-250	4	13
α-helix	253-256	4
α-helix	258-261	4
α-helix	264-267	4
α-helix	272-273	2
α-helix	274-283	10
α-helix	290-294	5
β-strand	298-300	3	11
α-helix	302-305	4
α-helix	309-320	12
α-helix	335-337	3
α-helix	338-348	11
α-helix	351-355	5
β-strand	357-358	2	8
α-helix	359-365	7
α-helix	366-368	3
α-helix	369-373	5

Chain D: 22 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	8-9	2	14
β-strand	10-11	2	15
β-strand	16-19	4	15
β-strand	29-32	4	15
β-strand	35-38	4	16
β-strand	53-54	2	16
α-helix	56-60	5
α-helix	62-64	3
β-strand	65-68	4	16
β-strand	71-72	2	17
β-strand	75-76	2	17
α-helix	81-88	8
α-helix	89-93	5
β-strand	103-107	5	14
α-helix	113-121	9
α-helix	122-126	5
β-strand	131-136	6	14
α-helix	139-144	6
β-strand	151-154	4	18
β-strand	160-163	4	18
β-strand	166	1	19
β-strand	169	1	19
β-strand	176-178	3	18
α-helix	182-193	12
α-helix	206-216	11
α-helix	226-232	7
β-strand	239-241	3	20
β-strand	247-249	3	20
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	297-299	3	18
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	18
α-helix	338-348	11
α-helix	350-353	4
β-strand	357-358	2	14
α-helix	359-365	7
α-helix	366-368	3
α-helix	369-372	4

Chain E: 18 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	762	1	21
α-helix	764-766	3
β-strand	769	1	22
α-helix	792-801	10
β-strand	803	1	21
α-helix	837-847	11
α-helix	854-863	10
α-helix	871-878	8
α-helix	884-887	4
α-helix	889-892	4
α-helix	902-911	10
α-helix	916-923	8
α-helix	926-951	26
α-helix	954-970	17
β-strand	982	1	23
α-helix	987-989	3
β-strand	994	1	24
β-strand	1001	1	24
α-helix	1002-1013	12
α-helix	1020-1023	4
α-helix	1027-1032	6
α-helix	1035-1058	24
α-helix	1070-1105	36
α-helix	1114-1147	34

Chain F: 16 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	762	1	25
β-strand	769	1	23
α-helix	792-801	10
β-strand	803	1	25
α-helix	837-850	14
α-helix	854-863	10
α-helix	871-880	10
α-helix	886-892	7
α-helix	902-912	11
α-helix	916-923	8
α-helix	926-951	26
α-helix	954-970	17
β-strand	982	1	22
α-helix	987-990	4
β-strand	994	1	26
β-strand	1001	1	26
α-helix	1002-1013	12
α-helix	1020-1023	4
α-helix	1027-1031	5
α-helix	1035-1058	24
α-helix	1070-1104	35
α-helix	1114-1147	34

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin, cytoplasmic 1, N-terminally processed	B, C, D	protein	374	Homo sapiens	P60709 (AlphaFold model)
Methylated-DNA--protein-cysteine methyltransferase,Protein diaphanous homolog 1	E, F	protein	783	Homo sapiens, Mus musculus	O08808 (AlphaFold model), P16455 (AlphaFold model)

Sequence of entity 1 (B, C, D), FASTA

>8RU2_1 Actin, cytoplasmic 1, N-terminally processed (chains B, C, D)
DDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSK
RGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQ
IMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLA
GRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYE
LPDGQVITIGNERFRCPEALFQPSFLGMESAGIHETTFNSIMKCDVDIRKDLYANTVLSG
GTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQE
YDESGPSIVHRKCF

Sequence of entity 2 (E, F), FASTA

>8RU2_2 Methylated-DNA--protein-cysteine methyltransferase,Protein diaphanous homolog 1 (chains E, F)
MASTMDIKLTGEFAMDKDCEMKRTTLDSPLGKLELSGCEQGLHEIKLLGKGTSAADAVEV
PAPAAVLGGPEPLMQATAWLNAYFHQPEAIEEFPVPALHHPVFQQESFTRQVLWKLLKVV
KFGEVISYQQLAALAGNPAATAAVKTALSGNPVPILIPCHRVVSSSGAVGGYEGGLAVKE
WLLAHEGHRLGKPGLGPAGGSPGGGSGGSEMASLSAVVVAPSVSSSAAVPPAPPLPGDSG
TVIPPPPPGMGVPPPPPFGFGVPAAPVLPFGLTPKKVYKPEVQLRRPNWSKFVAEDLSQD
CFWTKVKEDRFENNELFAKLTLAFSAQTKTSKAKKDQEGGEEKKSVQKKKVKELKVLDSK
TAQNLSIFLGSFRMPYQEIKNVILEVNEAVLTESMIQNLIKQMPEPEQLKMLSELKEEYD
DLAESEQFGVVMGTVPRLRPRLNAILFKLQFSEQVENIKPEIVSVTAACEELRKSENFSS
LLELTLLVGNYMNAGSRNAGAFGFNISFLCKLRDTKSADQKMTLLHFLAELCENDHPEVL
KFPDELAHVEKASRVSAENLQKSLDQMKKQIADVERDVQNFPAATDEKDKFVEKMTSFVK
DAQEQYNKLRMMHSNMETLYKELGDYFVFDPKKLSVEEFFMDLHNFRNMFLQAVKENQKR
RETEEKMRRAKLAKEKAEKERLEKQQKREQLIDMNAEGDETGVMDSLLEALQSGAAFRRK
RGPRQVNRKAGCAVTSLLASELTKDDAMAPGPVKVPKKSEGVPTILEEAKELVGRASHHH
HHH

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	3
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	3

Primary citation

Molecular mechanism of actin filament elongation by formins. Oosterheert, W., Boiero Sanders, M., Funk, J. et al. Science (2024) 384:eadn9560-eadn9560. DOI 10.1126/science.adn9560 · PubMed

Other PDB entries of the same protein (UniProt P60709 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6MBK 1.69 Å, SETD3, a Histidine Methyltransferase, in Complex with an Actin Peptide and SAH, First…
6OX0 1.75 Å, SETD3 in Complex with an Actin Peptide with Sinefungin Replacing SAH as Cofactor
6MBJ 1.78 Å, SETD3, a Histidine Methyltransferase, in Complex with an Actin Peptide and SAH, P21…
6OX3 1.78 Å, SETD3 in Complex with an Actin Peptide with His73 Replaced with Lysine
7W28 1.79 Å, Crystal Structure of SETD3-SAH in complex with betaA-4PyrAla73 peptide
6OX1 1.95 Å, SETD3 in Complex with an Actin Peptide with Target Histidine Partially Methylated
6ICT 1.95 Å, Structure of SETD3 bound to SAH and methylated actin
6OX2 2.09 Å, SETD3in Complex with an Actin Peptide with the Target Histidine Fully Methylated
6OX5 2.1 Å, A SETD3 Mutant (N255A) in Complex with an Actin Peptide with His73 Replaced with Lysine
6ICV 2.15 Å, Structure of SETD3 bound to SAH and unmodified actin
9QEW 2.18 Å, Cryo-EM structure of the undecorated actin filament in the ADP-Pi state.
6MBL 2.2 Å, SETD3, a Histidine Methyltransferase, in Complex with an Actin Peptide and SAH, Second…

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