8DNF: Nonmuscle gamma-actin

Cryo-EM structure of nonmuscle gamma-actin. Determined by electron microscopy at 3.38 Å resolution. Released 12 Apr 2023.

Method: Electron microscopy
Resolution: 3.38 Å
Organism: Homo sapiens
Chains: 4
Atoms: 11,812
Mol. weight: 168.79 kDa
Ligands: ADP, MG
Released: 12 Apr 2023

Explore 8DNF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8DNF contains 88 α-helices and 76 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, B and C: 22 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	7-10	4	1
β-strand	15-20	6	1
β-strand	28-31	4	1
β-strand	34-37	4	2
β-strand	52-53	2	2
α-helix	55-59	5
β-strand	64-67	4	2
β-strand	70-71	2	3
β-strand	74-75	2	3
α-helix	79-87	9
α-helix	88-92	5
β-strand	102-106	5	1
α-helix	114-121	8
α-helix	122-126	5
β-strand	130-135	6	1
α-helix	136-144	9
β-strand	149-154	6	4
β-strand	159-164	6	4
β-strand	169	1	4
α-helix	171-173	3
β-strand	175-177	3	4
α-helix	181-192	12
α-helix	193-195	3
α-helix	202-215	14
α-helix	222-231	10
β-strand	237-240	4	5
β-strand	246-249	4	5
α-helix	252-255	4
α-helix	257-260	4
α-helix	263-266	4
α-helix	273-282	10
α-helix	289-293	5
β-strand	296-299	4	4
α-helix	301-304	4
α-helix	308-319	12
β-strand	328-329	2	4
α-helix	334-336	3
α-helix	337-346	10
α-helix	349-351	3
β-strand	356-357	2	1
α-helix	358-372	15

Chain D: 22 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	7-9	3	16
β-strand	15-20	6	16
β-strand	28-31	4	16
β-strand	34-37	4	17
β-strand	52-53	2	17
α-helix	55-59	5
β-strand	64-67	4	17
β-strand	70-71	2	18
β-strand	74-75	2	18
α-helix	79-87	9
α-helix	88-92	5
β-strand	102-106	5	16
α-helix	114-121	8
α-helix	122-126	5
β-strand	130-135	6	16
α-helix	136-144	9
β-strand	149-154	6	19
β-strand	159-164	6	19
β-strand	169	1	19
α-helix	171-173	3
β-strand	175-177	3	19
α-helix	181-192	12
α-helix	193-195	3
α-helix	202-215	14
α-helix	222-231	10
β-strand	237-240	4	20
β-strand	246-249	4	20
α-helix	252-255	4
α-helix	257-260	4
α-helix	263-266	4
α-helix	273-282	10
α-helix	289-293	5
β-strand	296-299	4	19
α-helix	301-304	4
α-helix	308-319	12
β-strand	328-329	2	19
α-helix	334-336	3
α-helix	337-346	10
α-helix	349-351	3
β-strand	356-357	2	16
α-helix	358-372	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin, cytoplasmic 2, N-terminally processed	A, B, C, D	protein	375	Homo sapiens	P63261 (AlphaFold model)

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

>8DNF_1 Actin, cytoplasmic 2, N-terminally processed (chains A, B, C, D)
XEEEIAALVIDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQS
KRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMT
QIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDL
AGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSY
ELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLS
GGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQ
EYDESGPSIVHRKCF

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	4
MG	Magnesium ion	Mg	4

Primary citation

Structural insights into actin isoforms. Arora, A.S., Huang, H.L., Singh, R. et al. Elife (2023) 12. DOI 10.7554/eLife.82015 · PubMed

Other PDB entries of the same protein (UniProt P63261 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6WK2 1.76 Å, SETD3 mutant (N255V) in Complex with an Actin Peptide with His73 Replaced with Methionine
6WK1 1.89 Å, SETD3 in Complex with an Actin Peptide with His73 Replaced with Methionine
6V63 2.02 Å, SETD3 WT in Complex with an Actin Peptide with His73 Replaced with Glutamine
6V62 2.36 Å, SETD3 double mutant (N255F/W273A) in Complex with an Actin Peptide with His73 Replaced…
7NVM 3.1 Å, Human TRiC complex in closed state with nanobody Nb18, actin and PhLP2A bound
9SMX 3.67 Å, CM1-activated gTuRC in complex with nascent alpha-E254D mutant microtubules
5JLH 3.9 Å, Cryo-EM structure of a human cytoplasmic actomyosin complex at near-atomic resolution
6G2T 9.0 Å, human cardiac myosin binding protein C C1 Ig-domain bound to native cardiac thin filament
6CXI 11.0 Å, Cardiac thin filament decorated with C0C1 fragment of cardiac myosin binding protein C…
6CXJ 11.0 Å, Cardiac thin filament decorated with C0C1 fragment of cardiac myosin binding protein C…

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