8F0A: Periplasmic serine endoprotease DegP

Client-bound structure of a DegP trimer within a 12mer cage. Determined by electron microscopy at 2.6 Å resolution. Released 23 Nov 2022.

Method: Electron microscopy
Resolution: 2.6 Å
Organisms: Escherichia coli (strain K12), Homo sapiens
Chains: 9
Atoms: 8,871
Mol. weight: 143.29 kDa
Released: 23 Nov 2022

Explore 8F0A in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8F0A contains 45 α-helices and 96 β-strands across 9 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: 1 helix, 3 β-strands

Element	Residues	Length	Sheet
β-strand	29-31	3	3
β-strand	34-36	3	2
α-helix	38-48	11
β-strand	52-53	2	11

Chains A, B and C: 12 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	1
α-helix	16-19	4
α-helix	23-25	3
β-strand	26-34	9	2
β-strand	83-94	12	2
β-strand	99-103	5	2
α-helix	104-107	4
β-strand	110-116	7	2
β-strand	122-131	10	2
β-strand	136-141	6	2
α-helix	149-151	3
β-strand	152	1	3
α-helix	153	1
α-helix	155-157	3
β-strand	162	1	4
β-strand	163-168	6	3
α-helix	170-172	3
β-strand	176-187	12	3
β-strand	198-201	4	3
β-strand	213-215	3	3
β-strand	221-229	9	3
β-strand	239-243	5	3
α-helix	244-257	14
β-strand	263-264	2	5
β-strand	267-271	5	6
α-helix	274-279	6
β-strand	288-293	6	6
α-helix	298-302	5
β-strand	309-313	5	6
β-strand	316-317	2	6
α-helix	321-328	8
α-helix	332	1
β-strand	336-343	8	6
β-strand	346-353	8	6
β-strand	355-356	2	5

Chains D, E and F: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	375-378	4	16
β-strand	385-389	5	16
α-helix	395-398	4
β-strand	406-410	5	16
β-strand	413-414	2	16
α-helix	418-425	8
β-strand	432-438	7	16
β-strand	441-447	7	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Periplasmic serine endoprotease DegP	A, B, C	protein	348	Escherichia coli (strain K12)	P0C0V0 (AlphaFold model)
Periplasmic serine endoprotease DegP	D, E, F	protein	75	Escherichia coli (strain K12)	P0C0V0 (AlphaFold model)
Telomeric repeat-binding factor 1	a, b, c	protein	27	Homo sapiens	P54274 (AlphaFold model)

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

>8F0A_1 Periplasmic serine endoprotease DegP (chains A, B, C)
MPSLAPMLEKVMPSVVSINVEGSTTVNTPRMPRNFQQFFGDDSPFCQEGSPFQSSPFCQG
GQGGNGGGQQQKFMALGSGVIIDADKGYVVTNNHVVDNATVIKVQLSDGRKFDAKMVGKD
PRSDIALIQIQNPKNLTAIKMADSDALRVGDYTVAIGNPFGLGETVTSGIVSALGRSGLN
AENYENFIQTDAAINRGNAGGALVNLNGELIGINTAILAPDGGNIGIGFAIPSNMVKNLT
SQMVEYGQVKRGELGIMGTELNSELAKAMKVDAQRGAFVSQVLPNSSAAKAGIKAGDVIT
SLNGKPISSFAALRAQVGTMPVGSKLTLGLLRDGKQVNVNLELQQSSQ

Sequence of entity 2 (D, E, F), FASTA

>8F0A_2 Periplasmic serine endoprotease DegP (chains D, E, F)
AEMSNKGKDQGVVVNNVKTGTPAAQIGLKKGDVIIGANQQAVKNIAELRKVLDSKPSVLA
LNIQRGDSTIYLLMQ

Sequence of entity 3 (a, b, c), FASTA

>8F0A_3 Telomeric repeat-binding factor 1 (chains a, b, c)
SKILLHYKFNNRTSVMLKDRWRTMKKL

Primary citation

Flexible Client-Dependent Cages in the Assembly Landscape of the Periplasmic Protease-Chaperone DegP. Harkness, R.W., Ripstein, Z.A., Di Trani, J.M. et al. J Am Chem Soc (2023) 145:13015-13026. DOI 10.1021/jacs.2c11849 · PubMed

Other PDB entries of the same protein (UniProt P0C0V0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1KY9 2.8 Å, Crystal Structure of DegP (HtrA)
3MH7 2.96 Å, HtrA proteases are activated by a conserved mechanism that can be triggered by distinct…
3CS0 3.0 Å, Crystal structure of DegP24
3MH5 3.0 Å, HtrA proteases are activated by a conserved mechanism that can be triggered by distinct…
3OU0 3.0 Å, re-refined 3CS0
3MH4 3.1 Å, HtrA proteases are activated by a conserved mechanism that can be triggered by distinct…
8F0U 3.1 Å, Structure of a 12mer DegP cage bound to the client protein hTRF1
3MH6 3.6 Å, HtrA proteases are activated by a conserved mechanism that can be triggered by distinct…
6JJK 3.6 Å, Crystal structure of the DegP dodecamer with a modulator
3OTP 3.76 Å, Crystal structure of the DegP dodecamer with a model substrate
6JJO 4.16 Å, Crystal structure of the DegP dodecamer with a modulator
6JJL 4.2 Å, Crystal structure of the DegP dodecamer with a modulator

Browse structure collections

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