4JHD: Actin Dimer

Crystal Structure of an Actin Dimer in Complex with the Actin Nucleator Cordon-Bleu. Determined by X-ray diffraction at 2.91 Å resolution. Released 19 Jun 2013.

Method: X-ray diffraction
Resolution: 2.91 Å
Organisms: Drosophila melanogaster, Mus musculus
Chains: 6
Atoms: 13,002
Mol. weight: 210.24 kDa
Ligands: MG, ANP
Released: 19 Jun 2013

Explore 4JHD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4JHD contains 101 α-helices and 86 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, 21 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	1
β-strand	16-21	6	1
β-strand	22	1	2
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	113-121	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
α-helix	172-174	3
β-strand	176-178	3	5
α-helix	182-196	15
α-helix	203-216	14
α-helix	223-231	9
β-strand	238-240	3	6
β-strand	248-250	3	6
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	5
α-helix	302-304	3
α-helix	309-318	10
β-strand	329-330	2	5
α-helix	335-337	3
α-helix	338-347	10
α-helix	350-352	3
β-strand	357-358	2	1
α-helix	359-365	7
α-helix	369-372	4

Chain B: 24 helices, 21 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	22	1	8
β-strand	24	1	8
β-strand	29-32	4	7
β-strand	35-38	4	9
α-helix	39-40	2
β-strand	53-54	2	9
α-helix	56-60	5
α-helix	62-64	3
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	89-93	5
α-helix	98-100	3
β-strand	103-107	5	7
α-helix	113-124	12
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	182-196	15
α-helix	203-216	14
α-helix	223-231	9
β-strand	238-240	3	12
β-strand	248-250	3	12
α-helix	253-259	7
α-helix	264-267	4
α-helix	274-284	11
α-helix	287-294	8
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	338-347	10
α-helix	350-352	3
β-strand	357-358	2	7
α-helix	359-365	7
α-helix	367-372	6

Chain C: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	67-76	10
α-helix	104-117	14
β-strand	125	1	8
α-helix	133-136	4

Chain D: 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
α-helix	47-48	2
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	79-87	9
α-helix	88-93	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
β-strand	176-178	3	17
α-helix	182-196	15
α-helix	203-216	14
α-helix	223-231	9
β-strand	238-240	3	18
β-strand	248-250	3	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
α-helix	322	1
β-strand	329-330	2	17
α-helix	338-347	10
α-helix	350-352	3
β-strand	357-358	2	13
α-helix	359-365	7
α-helix	369-372	4

Chain E: 26 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	8-12	5	19
β-strand	16-21	6	19
β-strand	22	1	20
β-strand	24	1	20
β-strand	29-32	4	19
β-strand	35-38	4	21
α-helix	39-40	2
β-strand	53-54	2	21
α-helix	56-60	5
α-helix	62-64	3
β-strand	65-68	4	21
β-strand	71-72	2	22
β-strand	75-76	2	22
α-helix	79-88	10
α-helix	89-93	5
α-helix	98-100	3
β-strand	103-107	5	19
α-helix	113-121	9
α-helix	122-126	5
β-strand	131-136	6	19
α-helix	137-143	7
β-strand	150-155	6	23
β-strand	160-166	7	23
β-strand	169-170	2	23
α-helix	172-174	3
β-strand	176-178	3	23
α-helix	182-196	15
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-240	3	24
β-strand	248-250	3	24
α-helix	253-256	4
α-helix	258-261	4
α-helix	264-267	4
α-helix	274-283	10
α-helix	287-295	9
β-strand	297-300	4	23
α-helix	302-305	4
α-helix	309-320	12
β-strand	329-330	2	23
α-helix	335-337	3
α-helix	338-347	10
α-helix	350-352	3
β-strand	357-358	2	19
α-helix	359-365	7
α-helix	367-373	7

Chain F: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	67-76	10
α-helix	104-117	14
β-strand	125	1	20
α-helix	126	1
α-helix	130-139	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin-5C	A, D	protein	384	Drosophila melanogaster	P10987 (AlphaFold model)
Actin-5C	B, E	protein	384	Drosophila melanogaster	P10987 (AlphaFold model)
Protein cordon-bleu	C, F	protein	171	Mus musculus	Q5NBX1 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>4JHD_1 Actin-5C (chains A, D)
MAHHHHHHMCDEEVAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKD
SYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLN
PKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVLDSGDGVSHTVPIYEGYAL
PHAILRLDLAGRDLTDYLMKILTERGYSFTTTEEREIVRDIKEKLCYVALDFEQEMATAA
SSSSLEKSYELKDGQVITIGNERFRCPEALFQPSFLGMEACGIHETTYNSIMKCDVDIRK
DLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLST
FQQMWISKQEYDESGPSIVHRKCF

Sequence of entity 2 (B, E), FASTA

>4JHD_2 Actin-5C (chains B, E)
MAHHHHHHMCDEEVAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKD
SYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLN
PKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVLDSGDGVSHTVPIYEGYAL
PHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAA
SSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMEACGIHETTYNSIMKCDVDIRE
DLYANTVLSGGTTMYPGIADRMQKEITALAKSTMKIKIIAPPERKYSVWIGGSILASLST
FQQMWISKQEYDESGPSIVHRKCF

Sequence of entity 3 (C, F), FASTA

>4JHD_3 Protein cordon-bleu (chains C, F)
MAHHHHHHVQRPLPKDVSLHSALMEAIHSSGGREKLRKVAEQTSEGRPKKPSYVEAESER
SALLAAIRGHSGTLSLRKVSSLASEELQSFRNAALGAPGLDKPQQEDLGLPPPPALPPTP
APAPQAPSASVTVSRFSTGTPSNSVNARQALMDAIRSGTGAARLRKVPLLV

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	4
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	4

Primary citation

Structural basis of actin filament nucleation by tandem w domains. Chen, X., Ni, F., Tian, X. et al. Cell Rep (2013) 3:1910-1920. DOI 10.1016/j.celrep.2013.04.028 · 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
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
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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