5WFN: Actin-5C

Revised model of leiomodin 2-mediated actin regulation (alternate refinement of PDB 4RWT). Determined by X-ray diffraction at 3.0 Å resolution. Released 30 Aug 2017.

Method: X-ray diffraction
Resolution: 3.0 Å
Organisms: Drosophila melanogaster, Homo sapiens
Chains: 4
Atoms: 8,906
Mol. weight: 200.34 kDa
Ligands: MG, ANP
Released: 30 Aug 2017

Explore 5WFN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5WFN contains 60 α-helices and 52 β-strands across 4 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.

Chains A and B: 21 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	1
β-strand	17-21	5	1
β-strand	24	1	2
β-strand	29-31	3	1
β-strand	35-38	4	3
β-strand	53-54	2	3
α-helix	56-59	4
α-helix	62-64	3
β-strand	65-68	4	3
β-strand	71-72	2	4
β-strand	75-76	2	4
α-helix	79-87	9
α-helix	88-94	7
α-helix	98-100	3
β-strand	103-107	5	1
α-helix	113-121	9
α-helix	122-126	5
β-strand	131-136	6	1
α-helix	137-144	8
β-strand	150-155	6	5
β-strand	160-166	7	5
β-strand	169-170	2	5
β-strand	176-178	3	5
α-helix	182-196	15
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	6
β-strand	247-250	4	6
α-helix	252-262	11
α-helix	264-267	4
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	338-348	11
α-helix	350-352	3
β-strand	357-358	2	1
α-helix	359-365	7
α-helix	367-370	4

Chains C and D: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	199-208	10
β-strand	215-217	3	7
α-helix	226-237	12
β-strand	244-246	3	7
α-helix	254-266	13
β-strand	272-274	3	7
α-helix	282-291	10
α-helix	292-294	3
β-strand	300-302	3	7
α-helix	312-322	11
β-strand	330-332	3	7
α-helix	338-363	26
α-helix	520-530	11
α-helix	534-536	3
β-strand	538	1	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin-5C	A, B	protein	384	Drosophila melanogaster	P10987 (AlphaFold model)
Leiomodin-2	C, D	protein	506	Homo sapiens	Q6P5Q4 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5WFN_1 Actin-5C (chains A, B)
MCDEEVAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQ
SKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKM
TQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVLDSGDGVSHTVPIYEGYALPHAILRLD
LAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKS
YELPDGQVITIGNERFRCPEALFQPSFLGMEACGIHETTYNSIMKCDVDIREDLYANTVL
SGGTTMYPGIADRMQKEITALAKSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISK
QEYDESGPSIVHRKCFASHHHHHH

Sequence of entity 2 (C, D), FASTA

>5WFN_2 Leiomodin-2 (chains C, D)
MAHHHHHHVGTMSTFGYRRGLSKYESIDEDELLASLSAEELKELERELEDIEPDRNLPVG
LRQKSLTEKTPTGTFSREALMAYWEKESQKLLEKERLGECGKVAEDKEEEEDSDEEERTI
ETAKGINGTVNYDSVNSDNSKPKIFKSQIENINLTNGSNGRNTESPAAIHPCGNPTVIED
ALDKIKSNDPDTTEVNLNNIENITTQTLTRFAEALKDNTVVKTFSLANTHADDSAAMAIA
EMLKVNEHITNVNVESNFITGKGILAIMRALQHNTVLTELRFHNQRHIMGSQVEMEIVKL
LKENTTLLRLGYHFELPGPRMSMTSILTRNMDKQRQKRLQEQKQQEGYDGGPNLRTKVWQ
RGTPSSSPYVSPRHSPWSSPKLPKKVQTVRSRPLSPVATPPPPPPPPLPEKKLITRNIAE
VIKQQESAQRALQNGQGSGSGGSVGSQPNSILKEIKNSLRSVQEKKMEDSSRPSTPQRSA
HENLMEAIRGSSIKQLKRVEVPEALR

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	2

Primary citation

Crystal structure of leiomodin 2 in complex with actin: a structural and functional reexamination. Boczkowska, M., Yurtsever, Z., Rebowski, G. et al. Biophys J (2017) 113:889-899. DOI 10.1016/j.bpj.2017.07.007

Other PDB entries of the same protein (UniProt P10987 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2HF3 1.8 Å, Crystal structure of monomeric Actin in the ADP bound state
2HF4 1.8 Å, Crystal structure of Monomeric Actin in its ATP-bound state
3EKS 1.8 Å, Crystal Structure of Monomeric Actin bound to Cytochalasin D
3MN6 2.0 Å, Structures of actin-bound WH2 domains of Spire and the implication for filament nucleation
3MN7 2.0 Å, Structures of actin-bound WH2 domains of Spire and the implication for filament nucleation
3MN9 2.0 Å, Structures of actin-bound WH2 domains of Spire and the implication for filament nucleation
3EKU 2.5 Å, Crystal Structure of Monomeric Actin bound to Cytochalasin D
3EL2 2.5 Å, Crystal Structure of Monomeric Actin Bound to Ca-ATP
4M63 2.75 Å, Crystal Structure of a Filament-Like Actin Trimer Bound to the Bacterial Effector VopL
3MMV 2.8 Å, Structures of actin-bound WH2 domains of Spire and the implication for filament nucleation
4JHD 2.91 Å, Crystal Structure of an Actin Dimer in Complex with the Actin Nucleator Cordon-Bleu
4RWT 2.98 Å, Structure of actin-Lmod complex

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