9DVA: Actin, alpha skeletal muscle

F-actin binding interface of alpha-E-catenin ABD (cadherin-catenin complex) and afadin. Determined by electron microscopy at 3.1 Å resolution. Released 30 Oct 2024.

Method: Electron microscopy
Resolution: 3.1 Å
Organisms: Gallus gallus, Mus musculus
Chains: 8
Atoms: 18,529
Mol. weight: 438.01 kDa
Ligands: MG, ADP
Released: 30 Oct 2024

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

Secondary structure: helices and β-sheets

9DVA contains 158 α-helices and 103 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: 23 helices, 20 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	41-42	2	3
β-strand	53-54	2	2
α-helix	56-59	4
α-helix	62-64	3
β-strand	65-68	4	2
β-strand	71-72	2	4
β-strand	75-76	2	4
α-helix	79-91	13
α-helix	98-100	3
β-strand	103-107	5	1
α-helix	113-125	13
β-strand	131-136	6	1
α-helix	137-145	9
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	182-192	11
α-helix	193-196	4
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	6
β-strand	247-250	4	6
α-helix	252-254	3
α-helix	258-261	4
α-helix	264-266	3
α-helix	272-273	2
α-helix	274-283	10
α-helix	290-293	4
β-strand	297-300	4	5
α-helix	302-305	4
α-helix	309-320	12
β-strand	329-330	2	5
α-helix	335-337	3
α-helix	338-347	10
β-strand	357-358	2	1
α-helix	359-365	7
α-helix	369-373	5

Chain B: 26 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	8-12	5	7
β-strand	16-21	6	7
β-strand	29-32	4	7
β-strand	35-38	4	8
β-strand	42	1	9
β-strand	53-54	2	8
α-helix	56-60	5
α-helix	62-64	3
β-strand	65-68	4	8
β-strand	71-72	2	10
β-strand	75-76	2	10
α-helix	79-87	9
α-helix	88-93	6
α-helix	98-100	3
β-strand	103-107	5	7
α-helix	113-122	10
α-helix	123-127	5
β-strand	131-136	6	7
α-helix	137-144	8
β-strand	150-155	6	3
β-strand	160-166	7	3
β-strand	169-170	2	3
α-helix	172-174	3
β-strand	176-178	3	3
α-helix	182-193	12
α-helix	194-196	3
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	11
β-strand	247-250	4	11
α-helix	253-259	7
α-helix	264-266	3
α-helix	272-273	2
α-helix	274-283	10
α-helix	290-294	5
β-strand	297-300	4	3
α-helix	302-305	4
α-helix	309-320	12
β-strand	329-330	2	3
α-helix	335-337	3
α-helix	338-348	11
β-strand	357-358	2	7
α-helix	359-365	7
α-helix	366-368	3
α-helix	369-373	5

Chain C: 25 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	8-12	5	12
β-strand	16-21	6	12
β-strand	29-32	4	12
β-strand	35-38	4	13
β-strand	53-54	2	13
α-helix	56-59	4
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
α-helix	98-100	3
β-strand	103-107	5	12
α-helix	113-122	10
α-helix	123-127	5
β-strand	131-136	6	12
α-helix	137-144	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	182-196	15
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	15
β-strand	247-250	4	15
α-helix	253-259	7
α-helix	264-267	4
α-helix	272-273	2
α-helix	274-283	10
α-helix	290-294	5
β-strand	297-300	4	9
α-helix	302-305	4
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
β-strand	357-358	2	12
α-helix	359-365	7
α-helix	369-373	5

Chain D: 26 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	42	1	18
β-strand	53-54	2	17
α-helix	56-59	4
α-helix	62-64	3
β-strand	65-68	4	17
β-strand	71-72	2	19
β-strand	75-76	2	19
α-helix	79-87	9
α-helix	88-93	6
α-helix	98-100	3
β-strand	103-107	5	16
α-helix	113-122	10
α-helix	123-127	5
β-strand	131-136	6	16
α-helix	137-145	9
β-strand	150-155	6	20
β-strand	160-166	7	20
β-strand	169-170	2	20
α-helix	172-174	3
β-strand	176-178	3	20
α-helix	182-192	11
α-helix	193-196	4
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	21
β-strand	247-250	4	21
α-helix	253-259	7
α-helix	264-267	4
α-helix	272-273	2
α-helix	274-283	10
α-helix	287-289	3
α-helix	290-294	5
β-strand	297-300	4	20
α-helix	302-305	4
α-helix	309-320	12
β-strand	329-330	2	20
α-helix	335-337	3
α-helix	338-347	10
α-helix	353-355	3
β-strand	357-358	2	16
α-helix	359-365	7
α-helix	369-373	5

Chain E: 27 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	22
β-strand	16-21	6	22
β-strand	29-32	4	22
β-strand	35-38	4	23
β-strand	53-54	2	23
α-helix	56-60	5
α-helix	62-64	3
β-strand	65-68	4	23
β-strand	71-72	2	24
β-strand	75-76	2	24
α-helix	79-88	10
α-helix	89-93	5
α-helix	98-100	3
β-strand	103-107	5	22
α-helix	113-122	10
α-helix	123-127	5
β-strand	132-136	5	22
α-helix	137-144	8
β-strand	150-155	6	18
β-strand	160-166	7	18
β-strand	169-170	2	18
α-helix	172-174	3
β-strand	176-178	3	18
α-helix	182-193	12
α-helix	194-196	3
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	18
α-helix	302-305	4
α-helix	309-320	12
β-strand	329-330	2	18
α-helix	335-337	3
α-helix	338-347	10
α-helix	351-355	5
α-helix	359-365	7
α-helix	366-368	3
α-helix	369	1
α-helix	370-374	5

Chain F: 15 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	693-695	3
α-helix	696-702	7
α-helix	703-706	4
α-helix	712-729	18
α-helix	739-764	26
α-helix	768	1
α-helix	771-804	34
α-helix	812-814	3
α-helix	816-842	27
α-helix	855-858	4
β-strand	859-861	3	26
α-helix	862-868	7
α-helix	871-873	3
α-helix	876-879	4
β-strand	882-884	3	11
α-helix	885-892	8
α-helix	893-898	6
β-strand	900-902	3	26

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	1513-1542	30
α-helix	1549-1551	3
α-helix	1552-1574	23

Chain H: 13 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	691-702	12
α-helix	712-727	16
α-helix	739-766	28
α-helix	768	1
α-helix	771-804	34
α-helix	812-814	3
α-helix	816-842	27
α-helix	855-857	3
β-strand	859-861	3	27
α-helix	862-868	7
α-helix	876-879	4
β-strand	882-884	3	6
α-helix	885-888	4
α-helix	890-892	3
α-helix	893-898	6
β-strand	900-902	3	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin, alpha skeletal muscle	A, B, C, D, E	protein	375	Gallus gallus	P68139 (AlphaFold model)
Catenin alpha-1	F, H	protein	906	Mus musculus	P26231 (AlphaFold model)
Afadin	G	protein	219	Mus musculus	Q9QZQ1 (AlphaFold model)

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

>9DVA_1 Actin, alpha skeletal muscle (chains A, B, C, D, E)
DEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQS
KRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMT
QIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDL
AGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSY
ELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMS
GGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQ
EYDEAGPSIVHRKCF

Sequence of entity 2 (F, H), FASTA

>9DVA_2 Catenin alpha-1 (chains F, H)
MTAVHAGNINFKWDPKSLEIRTLAVERLLEPLVTQVTTLVNTNSKGPSNKKRGRSKKAHV
LAASVEQATENFLEKGDKIAKESQFLKEELVVAVEDVRKQGDLMKSAAGEFADDPCSSVK
RGNMVRAARALLSAVTRLLILADMADVYKLLVQLKVVEDGILKLRNAGNEQDLGIQYKAL
KPEVDKLNIMAAKRQQELKDVGNRDQMAAARGILQKNVPILYTASQACLQHPDVAAYKAN
RDLIYKQLQQAVTGISNAAQATASDDAAQHQGGSGGELAYALNNFDKQIIVDPLSFSEER
FRPSLEERLESIISGAALGADSSCTEDDRRERIVAECNAVRQALQDLLSEYMGNAGRKER
SDALNSAIDKMTKKTRDLRRQLRKAVMDHVSDSFLETNVPLLVLIEAAKNGNEKEVKEYA
QVFREHANKLIEVANLACSISNNEEGVKLVRMSASQLEALCPQVINAALALAAKPQSKLA
QENMDLFKEQWEKQVRVLTDAVDDITSIDDFLAVSENHILEDVNKCVIALQEKDVDGLDR
TAGAIRGRAAEVIHVVTSEMDNYEPGVYTEKVLEATKLLSNTVMPRFTEQVEAAVEALSS
DPAQPMDENEFIDASRLVYDGIRDIRKAVLMIRTPEELDDSDFETEDFDVRSRTSVQTED
DQLIAGQSARAIMAQLPQEQKAKIAEQVASFQEEKSKLDAEVSKWDDSGNDIIVLAKQMC
MIMMEMTDFTRGKGPLKNTSDVISAAKKIAEAGSRMDKLGRTIADHCPDSACKQDLLAYL
QRIALYCHQLNICSKVKAEVQNLGGELVVSGVDSAMSLIQAAKNLMNAVVQTVKASYVAS
TKYQKSQGMASLNLPAVSWKMKAPEKKPLVKREKQDETQTKIKRASQKKHVNPVQALSEF
KAMDSI

Sequence of entity 3 (G), FASTA

>9DVA_3 Afadin (chains G)
SGTRELRGSANQAGPQSAQVAAAEWKKREEHQRWYEKEKARLEEERERKRREQERKLGQM
RSQTLNPASFSPLATQAKPEKPSTLQRPQETVIRELQPQQQPRTIERKDLQYITISKEEL
SSGDSLSPDPWKRDAREKLEKQQQMHIVDMLSKEIHELQNKVDRTAEESDRLRKLMLEWQ
FQKRLQESKQKDEDDDEEEDDDVDTMLIMQRLEAERRAR

Ligands and cofactors

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

Primary citation

Afadin mediates cadherin-catenin complex clustering on F-actin linked to cooperative binding and filament curvature. Gong, R., Reynolds, M.J., Sun, X. et al. bioRxiv (2024). DOI 10.1101/2024.10.08.617332 · PubMed

Other PDB entries of the same protein (UniProt P68139 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7W4Z 1.15 Å, Crystal structure of fragmin domain-1 in complex with actin (AMPPNP-form)
7W50 1.15 Å, Crystal structure of fragmin domain-1 in complex with actin (ADP-Pi-form)
7W51 1.2 Å, Crystal structure of fragmin domain-1 in complex with actin (ADP-form)
9L2N 1.7 Å, Crystal structure of Cytochalasin D bound to a filamentous conformation actin
7W52 2.0 Å, Crystal structure of fragmin domain-1 (15-160) in complex with actin
1MDU 2.2 Å, Crystal structure of the chicken actin trimer complexed with human gelsolin segment 1…
8D13 2.43 Å, Helical ADP-F-actin
8D14 2.51 Å, Helical ADP-Pi-F-actin
7R94 2.6 Å, T-Plastin-F-actin complex
8C4E 2.6 Å, F-actin decorated by SipA426-685
9JW0 2.69 Å, Structure of the N-terminal 3 domains (V1-V3) villin bound to actin
7YNE 2.7 Å, Crystal structure of fragmin domain-1 (1-160) in complex with G-form actin

Browse structure collections

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