3MN6: Actin-5C

Structures of actin-bound WH2 domains of Spire and the implication for filament nucleation. Determined by X-ray diffraction at 2.0 Å resolution. Released 2 Jun 2010.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Drosophila melanogaster
Chains: 6
Atoms: 9,612
Mol. weight: 131.72 kDa
Ligands: ATP, CA
Released: 2 Jun 2010

Explore 3MN6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3MN6 contains 68 α-helices and 64 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: 22 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	1
β-strand	16-21	6	1
β-strand	24	1	2
β-strand	29-32	4	1
β-strand	35-38	4	3
β-strand	53-54	2	3
α-helix	56-60	5
β-strand	65-68	4	3
β-strand	71-72	2	4
β-strand	75-76	2	4
α-helix	79-88	10
α-helix	89-94	6
α-helix	98-100	3
β-strand	103-107	5	1
α-helix	113-125	13
β-strand	131-136	6	1
α-helix	137-144	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	182-194	13
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	6
β-strand	247-250	4	6
α-helix	253-259	7
α-helix	264-267	4
α-helix	274-283	10
α-helix	287-289	3
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	338-346	9
α-helix	350-352	3
β-strand	357-358	2	1
α-helix	359-365	7
α-helix	367-369	3
α-helix	370-373	4

Chain F: 21 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	7
β-strand	16-21	6	7
β-strand	24	1	8
β-strand	29-32	4	7
β-strand	35-38	4	9
β-strand	53-54	2	9
α-helix	56-60	5
β-strand	65-68	4	9
β-strand	71-72	2	10
β-strand	75-76	2	10
α-helix	79-88	10
α-helix	89-94	6
α-helix	98-100	3
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	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	182-194	13
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	12
β-strand	247-250	4	12
α-helix	253-259	7
α-helix	264-267	4
α-helix	274-283	10
α-helix	290-294	5
β-strand	297-300	4	11
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	11
α-helix	338-346	9
α-helix	350-352	3
β-strand	357-358	2	7
α-helix	359-365	7
α-helix	367-369	3
α-helix	370-373	4

Chain K: 22 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	13
β-strand	16-21	6	13
β-strand	22	1	14
β-strand	24	1	14
β-strand	29-32	4	13
β-strand	35-38	4	15
β-strand	53-54	2	15
α-helix	56-60	5
β-strand	65-68	4	15
β-strand	71-72	2	16
β-strand	75-76	2	16
α-helix	79-88	10
α-helix	89-94	6
α-helix	98-100	3
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	17
β-strand	160-166	7	17
β-strand	169-170	2	17
α-helix	172-174	3
β-strand	176-178	3	17
α-helix	182-194	13
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	18
β-strand	247-250	4	18
α-helix	253-259	7
α-helix	264-267	4
α-helix	274-283	10
α-helix	287-289	3
α-helix	290-294	5
β-strand	297-300	4	17
α-helix	302-304	3
α-helix	309-320	12
β-strand	329-330	2	17
α-helix	338-348	11
α-helix	350-352	3
β-strand	357-358	2	13
α-helix	359-365	7
α-helix	367-369	3
α-helix	370-373	4

Chains X and Y: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	4-12	9
β-strand	17	1	2

Chain Z: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	3-12	10
β-strand	17	1	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin-5C	A, F, K	protein	374	Drosophila melanogaster	P10987 (AlphaFold model)
Protein spire	X, Y, Z	protein	19	Drosophila melanogaster	Q9U1K1 (AlphaFold model)

Sequence of entity 1 (A, F, K), FASTA

>3MN6_1 Actin-5C (chains A, F, K)
DEEVAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSK
RGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQ
IMFETFNTPAMYVAIQAVLSLYASGRTTGIVLDSGDGVSHTVPIYEGYALPHAILRLDLA
GRDLTDYLMKILTERGYSFTTTEEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYE
LKDGQVITIGNERFRCPEALFQPSFLGMEACGIHETTYNSIMKCDVDIRKDLYANTVLSG
GTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQE
YDESGPSIVHRKCF

Sequence of entity 2 (X, Y, Z), FASTA

>3MN6_2 Protein spire (chains X, Y, Z)
XXXXXXXXXXXXXXXXXXX

Ligands and cofactors

ID	Name	Formula	Copies
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	3
CA	Calcium ion	Ca	3

Primary citation

Structures of actin-bound Wiskott-Aldrich syndrome protein homology 2 (WH2) domains of Spire and the implication for filament nucleation. Ducka, A.M., Joel, P., Popowicz, G.M. et al. Proc Natl Acad Sci U S A (2010) 107:11757-11762. DOI 10.1073/pnas.1005347107 · PubMed

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
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
5WFN 3.0 Å, Revised model of leiomodin 2-mediated actin regulation (alternate refinement of PDB 4RWT)

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