8RTT: Formin Cdc12

Structure of the formin Cdc12 bound to the barbed end of phalloidin-stabilized F-actin. Determined by electron microscopy at 3.56 Å resolution. Released 10 Apr 2024.

Method: Electron microscopy
Resolution: 3.56 Å
Organisms: Homo sapiens, Schizosaccharomyces pombe, Amanita phalloides
Chains: 9
Atoms: 18,155
Mol. weight: 268.56 kDa
Ligands: PO4, MG, ADP
Released: 10 Apr 2024

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

Secondary structure: helices and β-sheets

8RTT contains 142 α-helices and 93 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: 24 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	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	79-88	10
α-helix	89-94	6
β-strand	103-107	5	1
α-helix	113-126	14
β-strand	132-136	5	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	193-196	4
α-helix	203-215	13
α-helix	223-230	8
β-strand	238-241	4	5
β-strand	247-250	4	5
α-helix	253-256	4
α-helix	258-261	4
α-helix	264-267	4
α-helix	272-273	2
α-helix	274-284	11
α-helix	287-289	3
α-helix	290-294	5
β-strand	297-300	4	4
α-helix	302-305	4
α-helix	309-320	12
β-strand	329-330	2	4
α-helix	335-337	3
α-helix	338-348	11
α-helix	351-355	5
α-helix	359-365	7
α-helix	369-373	5

Chain B: 24 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	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
β-strand	65-68	4	7
β-strand	71-72	2	8
β-strand	75-76	2	8
α-helix	79-88	10
α-helix	89-94	6
β-strand	103-107	5	6
α-helix	113-122	10
α-helix	123-127	5
β-strand	132-136	5	6
α-helix	137-145	9
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	193-195	3
β-strand	198	1	10
α-helix	203-216	14
α-helix	223-230	8
β-strand	238-241	4	11
β-strand	247-250	4	11
α-helix	252-254	3
α-helix	258-261	4
α-helix	264-267	4
α-helix	272-273	2
α-helix	274-284	11
α-helix	290-294	5
β-strand	297-300	4	9
α-helix	303-305	3
α-helix	309-320	12
β-strand	329-330	2	9
α-helix	335-337	3
α-helix	338-348	11
α-helix	351-354	4
α-helix	359-365	7
α-helix	369-373	5

Chain C: 24 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	12
β-strand	16-21	6	12
β-strand	29-32	4	12
β-strand	35-38	4	13
α-helix	41	1
β-strand	42	1	4
β-strand	53-54	2	13
α-helix	56-60	5
α-helix	62-64	3
β-strand	65-68	4	13
β-strand	71-72	2	14
β-strand	75-76	2	14
α-helix	79-88	10
α-helix	89-93	5
β-strand	103-107	5	12
α-helix	113-122	10
α-helix	123-127	5
β-strand	131-136	6	12
α-helix	137-143	7
β-strand	150-154	5	15
β-strand	160-165	6	15
β-strand	176-178	3	15
α-helix	182-193	12
α-helix	194-196	3
α-helix	203-216	14
α-helix	223-231	9
β-strand	238-241	4	16
β-strand	247-250	4	16
α-helix	253-262	10
α-helix	264-267	4
α-helix	276-283	8
α-helix	287-295	9
β-strand	297-300	4	15
α-helix	303-305	3
α-helix	309-320	12
β-strand	329-330	2	15
α-helix	335-337	3
α-helix	338-348	11
α-helix	351-354	4
β-strand	357-358	2	12
α-helix	359-365	7
α-helix	366-368	3
α-helix	369-373	5

Chain D: 22 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	8-9	2	17
β-strand	11	1	18
β-strand	16-19	4	18
β-strand	21	1	17
β-strand	29-32	4	18
β-strand	35-38	4	19
β-strand	42	1	9
β-strand	53-54	2	19
α-helix	56-60	5
α-helix	62-64	3
β-strand	65-68	4	19
β-strand	71-72	2	20
β-strand	75-76	2	20
α-helix	79-87	9
α-helix	88-94	7
α-helix	98-100	3
β-strand	103-107	5	17
α-helix	113-122	10
α-helix	123-127	5
β-strand	132-136	5	17
α-helix	137-145	9
β-strand	150-154	5	21
β-strand	160-165	6	21
β-strand	166	1	22
β-strand	169	1	22
β-strand	176-178	3	21
α-helix	182-193	12
β-strand	198	1	23
α-helix	203-215	13
α-helix	223-232	10
β-strand	238-241	4	24
β-strand	247-250	4	24
α-helix	258-261	4
α-helix	264-266	3
α-helix	274-284	11
α-helix	290-294	5
β-strand	297-300	4	21
α-helix	303-305	3
α-helix	309-320	12
β-strand	329-330	2	21
α-helix	335-337	3
α-helix	338-348	11
α-helix	350-355	6
α-helix	359-365	7
α-helix	369-373	5

Chain E: 23 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	990	1	25
α-helix	991-993	3
α-helix	1012-1024	13
α-helix	1026-1033	8
β-strand	1035	1	25
α-helix	1055-1064	10
α-helix	1073-1081	9
α-helix	1085-1087	3
α-helix	1088-1094	7
α-helix	1097-1100	4
α-helix	1103-1109	7
β-strand	1114-1115	2	26
β-strand	1121-1122	2	26
α-helix	1134-1139	6
α-helix	1140-1144	5
α-helix	1150-1185	36
α-helix	1188-1204	17
α-helix	1207-1209	3
α-helix	1216-1221	6
β-strand	1226	1	27
β-strand	1233	1	27
α-helix	1234-1245	12
α-helix	1247-1249	3
α-helix	1258-1262	5
α-helix	1267-1290	24
α-helix	1292-1294	3
α-helix	1305-1341	37
α-helix	1348-1352	5
α-helix	1355-1384	30

Chain F: 25 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	990	1	28
α-helix	1006-1008	3
α-helix	1012-1023	12
α-helix	1027-1033	7
β-strand	1035	1	28
α-helix	1055-1064	10
α-helix	1066-1068	3
α-helix	1073-1079	7
α-helix	1080-1082	3
α-helix	1085-1087	3
α-helix	1090-1094	5
α-helix	1097-1100	4
α-helix	1103-1109	7
β-strand	1114-1115	2	29
β-strand	1121-1122	2	29
α-helix	1134-1139	6
α-helix	1140-1144	5
α-helix	1150-1185	36
α-helix	1188-1204	17
α-helix	1207-1209	3
α-helix	1216-1221	6
β-strand	1226	1	30
β-strand	1233	1	30
α-helix	1234-1245	12
α-helix	1247-1249	3
α-helix	1258-1262	5
α-helix	1267-1290	24
α-helix	1292-1294	3
α-helix	1305-1339	35
α-helix	1348-1352	5
α-helix	1355-1376	22

Chains H and J: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3	1	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin, cytoplasmic 1, N-terminally processed	A, B, C, D	protein	375	Homo sapiens	P60709 (AlphaFold model)
Cell division control protein 12	E, F	protein	419	Schizosaccharomyces pombe	Q10059 (AlphaFold model)
Phalloidin	H, I, J	protein	7	Amanita phalloides

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

>8RTT_1 Actin, cytoplasmic 1, N-terminally processed (chains A, B, C, D)
MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQS
KRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMT
QIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDL
AGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSY
ELPDGQVITIGNERFRCPEALFQPSFLGMESAGIHETTFNSIMKCDVDIRKDLYANTVLS
GGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQ
EYDESGPSIVHRKCF

Sequence of entity 2 (E, F), FASTA

>8RTT_2 Cell division control protein 12 (chains E, F)
SKDDLHKTTGLTRRPTRRLKQMHWEKLNSGLEFTFWTGPSDEANKILETLHTSGVLDELD
ESFAMKEAKTLVKKTCARTDYMSSELQKLFGIHFHKLSHKNPNEIIRMILHCDDSMNECV
EFLSSDKVLNQPKLKADLEPYRIDWANGGDLVNSEKDASELSRWDYLYVRLIVDLGGYWN
QRMNALKVKNIIETNYENLVRQTKLIGRAALELRDSKVFKGLLYLILYLGNYMNDYVRQA
KGFAIGSLQRLPLIKNANNTKSLLHILDITIRKHFPQFDNFSPELSTVTEAAKLNIEAIE
QECSELIRGCQNLQIDCDSGALSDPTVFHPDDKILSVILPWLMEGTKKMDFLKEHLRTMN
TTLNNAMRYFGEQPNDPNSKNLFFKRVDSFIIDYSKARSDNLKSEEEEASQHRRLNLVN

Sequence of entity 3 (H, I, J), FASTA

>8RTT_3 Phalloidin (chains H, I, J)
WXATCPA

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	3
MG	Magnesium ion	Mg	4
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	4

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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