2YJF: Oligomeric assembly of actin

Oligomeric assembly of actin bound to MRTF-A. Determined by X-ray diffraction at 3.5 Å resolution. Released 6 Jul 2011.

Method: X-ray diffraction
Resolution: 3.5 Å
Organisms: ORYCTOLAGUS CUNICULUS, MUS MUSCULUS
Chains: 6
Atoms: 13,272
Mol. weight: 229.83 kDa
Ligands: MG, ATP, LAB
Released: 6 Jul 2011

Explore 2YJF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2YJF contains 119 α-helices and 70 β-strands across 6 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, 14 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	1
β-strand	16-21	6	1
β-strand	29-32	4	1
α-helix	55-60	6
α-helix	72-74	3
α-helix	79-88	10
α-helix	89-93	5
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	2
β-strand	160-166	7	2
β-strand	169-170	2	2
α-helix	172-174	3
β-strand	176-178	3	2
α-helix	182-193	12
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	3
α-helix	246	1
β-strand	247-250	4	3
α-helix	253-259	7
α-helix	264-267	4
α-helix	272-273	2
α-helix	274-283	10
α-helix	287-294	8
β-strand	297-300	4	2
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	2
α-helix	335-337	3
α-helix	338-348	11
α-helix	351-355	5
β-strand	357-358	2	1
α-helix	359-365	7
α-helix	369-373	5

Chain B: 22 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	4
β-strand	17-21	5	4
β-strand	29-31	3	4
α-helix	72-74	3
α-helix	79-88	10
α-helix	89-93	5
β-strand	103-107	5	4
α-helix	113-125	13
β-strand	131-136	6	4
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	182-193	12
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	6
α-helix	246	1
β-strand	247-250	4	6
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	5
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	5
α-helix	333-337	5
α-helix	338-348	11
α-helix	351-355	5
β-strand	357-358	2	4
α-helix	359-365	7
α-helix	369-373	5

Chain C: 23 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	7
β-strand	17-21	5	7
β-strand	29-31	3	7
α-helix	55-59	5
α-helix	72-74	3
α-helix	79-88	10
α-helix	89-93	5
β-strand	103-107	5	7
α-helix	113-125	13
β-strand	131-136	6	7
α-helix	137-144	8
β-strand	150-155	6	8
β-strand	160-166	7	8
β-strand	169-170	2	8
α-helix	172-174	3
β-strand	176-178	3	8
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	9
α-helix	246	1
β-strand	247-250	4	9
α-helix	253-259	7
α-helix	264-267	4
α-helix	272-273	2
α-helix	274-283	10
α-helix	290-295	6
β-strand	297-300	4	8
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	8
α-helix	335-337	3
α-helix	338-348	11
β-strand	357-358	2	7
α-helix	359-365	7
α-helix	369-373	5

Chain D: 22 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	10
β-strand	16-21	6	10
β-strand	29-32	4	10
α-helix	72-74	3
α-helix	79-88	10
α-helix	89-93	5
β-strand	103-107	5	10
α-helix	113-125	13
β-strand	131-136	6	10
α-helix	137-144	8
β-strand	150-155	6	11
β-strand	160-166	7	11
β-strand	169-170	2	11
α-helix	172-174	3
β-strand	176-178	3	11
α-helix	182-193	12
α-helix	203-216	14
α-helix	223-229	7
β-strand	238-241	4	12
α-helix	246	1
β-strand	247-250	4	12
α-helix	253-259	7
α-helix	264-267	4
α-helix	272-273	2
α-helix	274-283	10
α-helix	287-295	9
β-strand	297-300	4	11
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	11
α-helix	335-337	3
α-helix	338-348	11
α-helix	351-355	5
β-strand	357-358	2	10
α-helix	359-365	7
α-helix	366-371	6

Chain E: 21 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	13
β-strand	17-21	5	13
β-strand	29-30	2	13
α-helix	72-74	3
α-helix	79-88	10
α-helix	89-93	5
β-strand	103-107	5	13
α-helix	113-125	13
β-strand	131-136	6	13
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	182-193	12
α-helix	203-216	14
α-helix	223-232	10
α-helix	253-259	7
α-helix	264-267	4
α-helix	272-273	2
α-helix	274-283	10
α-helix	290-295	6
β-strand	297-300	4	14
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	14
α-helix	335-337	3
α-helix	338-348	11
α-helix	351-355	5
β-strand	357-358	2	13
α-helix	359-365	7
α-helix	367-370	4

Chain M: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	69-77	9
α-helix	84-88	5
α-helix	94-95	2
β-strand	96	1	15
β-strand	98	1	15
α-helix	104-123	20
α-helix	128-134	7
α-helix	138	1
α-helix	144-167	24
α-helix	172-177	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin, alpha skeletal muscle	A, B, C, D, E	protein	377	ORYCTOLAGUS CUNICULUS	P68135 (AlphaFold model)
Mkl/myocardin-like protein 1	M	protein	137	MUS MUSCULUS	Q8K4J6 (AlphaFold model)

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

>2YJF_1 ACTIN, ALPHA SKELETAL MUSCLE (chains A, B, C, D, E)
MCDEDETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEA
QSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREK
MTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRL
DLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEK
SYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNV
MSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWIT
KQEYDEAGPSIVHRKCF

Sequence of entity 2 (M), FASTA

>2YJF_2 MKL/MYOCARDIN-LIKE PROTEIN 1 (chains M)
APGSLSERKNVLQLKLQQRRTREELVSQGIMPPLKSPAAFHEQRESLERARTEDYLKRKI
RSRPERAELVRMHILEETSAEPSLQAKQLKLKRARLADDLNEKIAQRPERMELVEKNILP
VESSLKEAIIVGQVNYP

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	5
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	5
LAB	Latrunculin B	C20 H29 N O5 S	2

Primary citation

Structure of a pentavalent G-actin*MRTF-A complex reveals how G-actin controls nucleocytoplasmic shuttling of a transcriptional coactivator. Mouilleron, S., Langer, C.A., Guettler, S. et al. Sci Signal (2011) 4:ra40-ra40. DOI 10.1126/scisignal.2001750 · 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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