6NBW: Actin, cytoplasmic 1

Ternary Complex of Beta/Gamma-Actin with Profilin and AnCoA-NAA80. Determined by X-ray diffraction at 2.5 Å resolution. Released 29 Jan 2020.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 3
Atoms: 5,593
Mol. weight: 84.8 kDa
Ligands: SOP, LAB, ATP, CA
Released: 29 Jan 2020

Explore 6NBW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6NBW contains 41 α-helices and 34 β-strands across 3 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: 26 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	8-12	5	1
β-strand	16-21	6	1
β-strand	29-32	4	1
β-strand	35-38	4	2
β-strand	53-54	2	2
α-helix	55-60	6
α-helix	62-64	3
β-strand	65-68	4	2
β-strand	71-72	2	3
β-strand	75-76	2	3
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	4
β-strand	160-166	7	4
β-strand	169-170	2	4
α-helix	172-174	3
β-strand	176-178	3	4
α-helix	182-194	13
α-helix	203-216	14
α-helix	223-232	10
β-strand	238-241	4	5
β-strand	247-250	4	5
α-helix	253-259	7
α-helix	264-267	4
α-helix	274-283	10
α-helix	287-289	3
α-helix	290-295	6
β-strand	297-300	4	4
α-helix	302-305	4
α-helix	309-320	12
β-strand	329-330	2	4
α-helix	335-337	3
α-helix	338-346	9
α-helix	352-355	4
α-helix	356	1
β-strand	357-358	2	1
α-helix	359-365	7
α-helix	369-373	5

Chain N: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	83-86	4	6
α-helix	87-89	3
α-helix	91-93	3
α-helix	94-104	11
α-helix	109-117	9
β-strand	125-131	7	6
β-strand	141-151	11	6
β-strand	154-165	12	6
α-helix	167-169	3
α-helix	174-188	15
β-strand	193-198	6	6
α-helix	202-207	6
β-strand	211-212	2	6
β-strand	218	1	6
α-helix	219-221	3
α-helix	264-270	7
β-strand	302-307	6	6

Chain P: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	4-11	8
β-strand	16-23	8	7
β-strand	29-33	5	7
α-helix	39-41	3
α-helix	44-50	7
α-helix	57-61	5
β-strand	63-65	3	7
β-strand	68-76	9	7
β-strand	84-89	6	7
β-strand	99-104	6	7
β-strand	108-114	7	7
α-helix	115	1
α-helix	120-136	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin, cytoplasmic 1	A	protein	374	Homo sapiens	P60709 (AlphaFold model)
N-alpha-acetyltransferase 80	N	protein	235	Homo sapiens	Q93015 (AlphaFold model)
Profilin-1	P	protein	140	Homo sapiens	P07737 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6NBW_1 Actin, cytoplasmic 1 (chains A)
DDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSK
RGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQ
IMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLA
GRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYE
LPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLSG
GTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQE
YDESGPSIVHRKCF

Sequence of entity 2 (N), FASTA

>6NBW_2 N-alpha-acetyltransferase 80 (chains N)
AGHMSLAELTLEPVHRRPELLDACADLINDQWPRSRTSRLHSLGQSSDAFPLCLMLLSPH
PTLEAAPVVVGHARLSRVLNQPQSLLVETVVVARALRGRGFGRRLMEGLEVFARARGFRK
LHLTTHDQVHFYTHLGYQLGEPVQGLVFTSRRLPATLLNAFPTAPSPRPPRKAPNLTAQA
APRGPKGPPLPPPPPLPECLTISPPVPSGPPSKSLLETQYQNVRGRPIFWMEKDI

Sequence of entity 3 (P), FASTA

>6NBW_3 Profilin-1 (chains P)
MAGWNAYIDNLMADGTCQDAAIVGYKDSPSVWAAVPGKTFVNITPAEVGVLVGKDRSSFY
VNGLTLGGQKCSVIRDSLLQDGEFSMDLRTKSTGGAPTFNVTVTKTDKTLVLLMGKEGVH
GGLINKKCYEMASHLRRSQY

Ligands and cofactors

ID	Name	Formula	Copies
SOP	[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofu…	C24 H40 N7 O17 P3 S	1
LAB	Latrunculin B	C20 H29 N O5 S	1
ATP	Adenosine-5'-triphosphate	C10 H16 N5 O13 P3	1
CA	Calcium ion	Ca	1

Water and common crystallization additives (MES, GOL) are not listed.

Primary citation

Mechanism of actin N-terminal acetylation. Rebowski, G., Boczkowska, M., Drazic, A. et al. Sci Adv (2020) 6:eaay8793-eaay8793. DOI 10.1126/sciadv.aay8793 · PubMed

Other PDB entries of the same protein (UniProt P60709 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6MBK 1.69 Å, SETD3, a Histidine Methyltransferase, in Complex with an Actin Peptide and SAH, First…
6OX0 1.75 Å, SETD3 in Complex with an Actin Peptide with Sinefungin Replacing SAH as Cofactor
6MBJ 1.78 Å, SETD3, a Histidine Methyltransferase, in Complex with an Actin Peptide and SAH, P21…
6OX3 1.78 Å, SETD3 in Complex with an Actin Peptide with His73 Replaced with Lysine
7W28 1.79 Å, Crystal Structure of SETD3-SAH in complex with betaA-4PyrAla73 peptide
6OX1 1.95 Å, SETD3 in Complex with an Actin Peptide with Target Histidine Partially Methylated
6ICT 1.95 Å, Structure of SETD3 bound to SAH and methylated actin
6OX2 2.09 Å, SETD3in Complex with an Actin Peptide with the Target Histidine Fully Methylated
6OX5 2.1 Å, A SETD3 Mutant (N255A) in Complex with an Actin Peptide with His73 Replaced with Lysine
6ICV 2.15 Å, Structure of SETD3 bound to SAH and unmodified actin
9QEW 2.18 Å, Cryo-EM structure of the undecorated actin filament in the ADP-Pi state.
6MBL 2.2 Å, SETD3, a Histidine Methyltransferase, in Complex with an Actin Peptide and SAH, Second…

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