8ZSF: CryoEM Helical Structure of KomC

CryoEM Helical Structure of KomC. Determined by electron microscopy at 3.24 Å resolution. Released 10 Dec 2025.

Method: Electron microscopy
Resolution: 3.24 Å
Organism: Escherichia coli
Chains: 12
Atoms: 25,992
Mol. weight: 367.87 kDa
Released: 10 Dec 2025

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

Secondary structure: helices and β-sheets

8ZSF contains 177 α-helices and 119 β-strands across 12 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: 16 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	2-9	8
β-strand	13-17	5	5
α-helix	20-22	3
α-helix	32-41	10
α-helix	49-51	3
α-helix	55-58	4
α-helix	60-63	4
α-helix	69-78	10
α-helix	90-96	7
β-strand	102-105	4	5
α-helix	111-117	7
β-strand	123-126	4	5
α-helix	129-132	4
β-strand	140-144	5	5
α-helix	159-165	7
α-helix	171-179	9
β-strand	184-188	5	5
α-helix	196-210	15
α-helix	218-219	2
β-strand	220-223	4	5
α-helix	229-236	8
β-strand	240-243	4	5
α-helix	250-262	13

Chain B: 16 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	2-8	7
β-strand	13-17	5	9
α-helix	20-22	3
α-helix	30-41	12
α-helix	45-48	4
α-helix	56-64	9
α-helix	69-78	10
α-helix	90-97	8
β-strand	102-105	4	9
α-helix	111-118	8
β-strand	123-126	4	9
α-helix	132-134	3
β-strand	140-144	5	9
α-helix	160-165	6
α-helix	171-179	9
β-strand	184-188	5	9
α-helix	196-210	15
β-strand	220-223	4	9
α-helix	229-235	7
α-helix	236-238	3
β-strand	240-243	4	9
α-helix	250-258	9
α-helix	259-261	3

Chain C: 15 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	4-10	7
β-strand	13-17	5	6
α-helix	20-22	3
α-helix	30-41	12
α-helix	45-48	4
α-helix	54-59	6
β-strand	60	1	7
β-strand	63	1	7
α-helix	69-78	10
α-helix	86-88	3
α-helix	90-96	7
β-strand	102-105	4	6
α-helix	111-118	8
β-strand	123	1	8
β-strand	126	1	6
α-helix	132-134	3
β-strand	140	1	8
β-strand	141-144	4	6
α-helix	160-164	5
α-helix	171-179	9
β-strand	184-188	5	6
α-helix	199-210	12
β-strand	220-224	5	6
α-helix	229-237	9
β-strand	240-244	5	6
α-helix	250-259	10

Chain D: 11 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	2-8	7
β-strand	13-17	5	1
α-helix	30-41	12
α-helix	56-65	10
α-helix	69-79	11
α-helix	90-97	8
β-strand	102	1	2
β-strand	103-105	3	1
α-helix	111-118	8
β-strand	123	1	3
β-strand	126	1	4
β-strand	140	1	3
β-strand	141	1	2
β-strand	143	1	4
β-strand	144	1	1
α-helix	160-165	6
α-helix	171-179	9
β-strand	184-188	5	1
α-helix	195-210	16
β-strand	221-223	3	1
α-helix	229-237	9
β-strand	241-243	3	1
α-helix	250-259	10

Chain E: 15 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	2-10	9
β-strand	13-17	5	14
α-helix	19-22	4
α-helix	30-41	12
α-helix	48-51	4
α-helix	54-63	10
α-helix	69-78	10
α-helix	86-88	3
α-helix	90-96	7
β-strand	102-105	4	14
α-helix	111-118	8
β-strand	123-126	4	14
β-strand	140-144	5	14
α-helix	159-165	7
α-helix	171-179	9
β-strand	184-188	5	14
α-helix	195-211	17
α-helix	218-219	2
β-strand	220-223	4	14
α-helix	229-237	9
β-strand	240-243	4	14
α-helix	250-261	12

Chain F: 13 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	2-10	9
β-strand	13-17	5	24
α-helix	19-22	4
α-helix	30-41	12
α-helix	47-49	3
α-helix	54-63	10
α-helix	69-78	10
α-helix	90-96	7
β-strand	102-105	4	24
α-helix	111-117	7
β-strand	123-126	4	24
β-strand	140-144	5	24
β-strand	148	1	25
β-strand	151	1	25
α-helix	159-166	8
α-helix	171-179	9
β-strand	184-188	5	24
α-helix	197-210	14
β-strand	220-224	5	24
α-helix	229-237	9
β-strand	240-244	5	24
α-helix	250-262	13

Chain G: 19 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	4-9	6
β-strand	13-14	2	18
β-strand	15-17	3	19
α-helix	21-23	3
α-helix	30-41	12
α-helix	45-49	5
α-helix	55-62	8
α-helix	69-78	10
α-helix	86-88	3
α-helix	90-97	8
β-strand	102-105	4	19
α-helix	111-118	8
β-strand	123-126	4	19
α-helix	132-134	3
β-strand	140-144	5	19
α-helix	159-164	6
α-helix	165-167	3
α-helix	171-179	9
β-strand	184-185	2	18
β-strand	188	1	19
α-helix	196-210	15
α-helix	218-219	2
β-strand	220	1	20
β-strand	223	1	19
α-helix	229-235	7
α-helix	236-238	3
β-strand	240	1	20
β-strand	243	1	19
α-helix	250-258	9
α-helix	259-261	3

Chain H: 17 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	2-9	8
β-strand	13-17	5	29
α-helix	20-22	3
α-helix	30-40	11
α-helix	45-48	4
α-helix	54-62	9
α-helix	69-78	10
α-helix	90-96	7
β-strand	102-105	4	29
α-helix	111-118	8
β-strand	123-126	4	29
α-helix	129-131	3
β-strand	140-144	5	29
α-helix	160-164	5
α-helix	165-167	3
α-helix	171-179	9
β-strand	184-187	4	29
α-helix	195-210	16
β-strand	220	1	30
β-strand	221-222	2	29
β-strand	223-224	2	31
α-helix	229-235	7
α-helix	236-238	3
β-strand	240	1	30
β-strand	243-244	2	31
α-helix	250-258	9
α-helix	259-261	3

4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Sir2 family NAD-dependent protein deacetylase	A, B, C, D, E, F, G, H, I, J, K, L	protein	264	Escherichia coli	P75960 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J, K, L), FASTA

>8ZSF_1 Sir2 family NAD-dependent protein deacetylase (chains A, B, C, D, E, F, G, H, I, J, K, L)
MEQLLADYKKGNVILFVGAGVSMNLGLPSWSQLVDHIATELGYDPDIYRTFGSALELAEY
YKLKKGKIGPLRSWMDRMWHSSDIDINKSKVHEYIAKANFPIIYTTNYDRWIETALSNYG
KEYIKISSVSDIAKIDNNKTQIIKFHGDFDDDSSIVLDETSYFQRLEFETPLDIKFRSDV
LGKSVLFIGYSLSDINIRLLFYKLSKLWKEQKLEEAQPKSYIFLPRPNPIQEEILEQWRI
GMISSENDNPGESLEEFLKNFVLV

Primary citation

Filament-mediated repurposing of toxic dITP for immunity in the Kongming system. Feng, H., Shao, K., Zeng, Z. et al. Mol Cell (2026) 86:1148-1163.e5. DOI 10.1016/j.molcel.2026.01.027 · PubMed

Other PDB entries of the same protein (UniProt P75960 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6RXK 1.35 Å, Crystal structure of CobB wt in complex with H4K16-Butyryl peptide
6RXS 1.6 Å, Crystal structure of CobB Ac3(A76G,Y92A, I131L, V187Y) in complex with H4K16-Acetyl…
6RXJ 1.6 Å, Crystal structure of CobB wt in complex with H4K16-Acetyl peptide
6RXQ 1.7 Å, Crystal structure of CobB Ac2 (A76G,I131C,V162A) in complex with H4K16Cr-2'OH-ADPr…
6RXR 1.7 Å, Crystal structure of CobB Ac2 (A76G, I131C, V162G) in complex with H4K16Cr-2'OH-ADPr…
6RXP 1.8 Å, Crystal structure of CobB Ac2 (A76G,I131C,V162A) in complex with H4K16-Crotonyl peptide
6RXM 1.92 Å, Crystal structure of CobB Ac2 (A76G, I131C, V162G) in complex with H4K16-Acetyl peptide
6RXO 1.95 Å, Crystal structure of CobB Ac2 (A76G, I131C, V162A) in complex with H4K16-Buturyl peptide
1S5P 1.96 Å, Structure and substrate binding properties of cobB, a Sir2 homolog protein deacetylase…
6RXL 2.3 Å, Crystal structure of CobB wt in complex with H4K16-Crotonyl peptide

Browse structure collections

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