6JJO: DegP dodecamer with a modulator

Crystal structure of the DegP dodecamer with a modulator. Determined by X-ray diffraction at 4.16 Å resolution. Released 2 Sept 2020.

Method: X-ray diffraction
Resolution: 4.16 Å
Organisms: Escherichia coli K-12, Escherichia coli
Chains: 18
Atoms: 16,906
Mol. weight: 303.14 kDa
Released: 2 Sept 2020

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

Secondary structure: helices and β-sheets

6JJO contains 81 α-helices and 192 β-strands across 16 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: 13 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	1
α-helix	16-22	7
α-helix	23-25	3
β-strand	26-31	6	2
β-strand	86-94	9	2
β-strand	99-102	4	2
α-helix	104-107	4
β-strand	113-116	4	2
β-strand	122-131	10	2
β-strand	136-142	7	2
α-helix	149-151	3
β-strand	152	1	3
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	221-228	8	3
β-strand	239-243	5	3
α-helix	244-257	14
β-strand	262	1	5
β-strand	264	1	6
β-strand	267-271	5	7
α-helix	274-279	6
β-strand	288-293	6	7
α-helix	298-302	5
β-strand	309-310	2	7
β-strand	312-313	2	8
β-strand	316-317	2	8
α-helix	318	1
α-helix	321-328	8
β-strand	332	1	5
β-strand	336-343	8	8
β-strand	346-353	8	8
β-strand	355	1	6
β-strand	374-378	5	9
β-strand	385-390	6	9
α-helix	397-399	3
β-strand	406-410	5	9
β-strand	413-414	2	9
α-helix	418-426	9
β-strand	432-438	7	9
β-strand	441-442	2	9
β-strand	445-447	3	9

Chain B: 13 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	16-22	7
α-helix	23-25	3
β-strand	26-34	9	10
β-strand	83-94	12	10
β-strand	99-103	5	10
α-helix	104-107	4
β-strand	110-116	7	10
β-strand	122-131	10	10
β-strand	136-142	7	10
β-strand	152	1	11
α-helix	155-157	3
β-strand	162	1	1
β-strand	163-168	6	11
α-helix	170-172	3
β-strand	176-187	12	11
β-strand	198-201	4	11
β-strand	213-215	3	11
β-strand	221-228	8	11
β-strand	239-243	5	11
α-helix	244-256	13
β-strand	264	1	12
β-strand	267-271	5	13
α-helix	274-279	6
β-strand	288-293	6	13
α-helix	298-302	5
β-strand	309-313	5	13
β-strand	316-317	2	13
α-helix	318	1
α-helix	321-328	8
α-helix	332	1
β-strand	336-343	8	13
β-strand	346-353	8	13
β-strand	355	1	12
β-strand	362-363	2	14
α-helix	365-368	4
β-strand	374-378	5	14
β-strand	385-390	6	14
β-strand	405-410	6	14
β-strand	413-414	2	14
α-helix	418-425	8
β-strand	432-438	7	14
β-strand	445-447	3	14

Chain C: 14 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	4
α-helix	16-22	7
α-helix	23-25	3
β-strand	26-34	9	15
β-strand	83-94	12	15
β-strand	99-102	4	15
α-helix	104-107	4
β-strand	110-116	7	15
β-strand	122-131	10	15
β-strand	136-142	7	15
α-helix	149-151	3
β-strand	152	1	16
α-helix	155-157	3
β-strand	163-168	6	16
α-helix	170-172	3
β-strand	176-187	12	16
β-strand	198-201	4	16
β-strand	213-215	3	16
β-strand	221-228	8	16
β-strand	239-243	5	16
α-helix	244-256	13
β-strand	264	1	17
β-strand	267-271	5	18
α-helix	274-279	6
β-strand	288-293	6	18
α-helix	298-302	5
β-strand	309-310	2	18
β-strand	312-313	2	19
β-strand	316-317	2	19
α-helix	318	1
α-helix	321-328	8
α-helix	332	1
β-strand	337-343	7	19
β-strand	346-352	7	19
β-strand	355	1	17
β-strand	369-370	2	20
β-strand	375-376	2	20
β-strand	385-386	2	21
β-strand	387	1	20
α-helix	397-399	3
β-strand	406-410	5	21
β-strand	413-414	2	21
α-helix	418-425	8
β-strand	432-437	6	21
β-strand	445-447	3	21

Chain D: 14 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	22
α-helix	16-22	7
α-helix	23-25	3
β-strand	26-34	9	23
β-strand	83-94	12	23
β-strand	99-102	4	23
α-helix	104-107	4
β-strand	110-116	7	23
β-strand	122-131	10	23
β-strand	136-141	6	23
α-helix	151	1
β-strand	152	1	24
α-helix	153	1
α-helix	155-157	3
β-strand	162	1	25
β-strand	163-168	6	24
α-helix	170-172	3
β-strand	176-187	12	24
β-strand	198-201	4	24
β-strand	213-215	3	24
β-strand	221-228	8	24
β-strand	239-243	5	24
α-helix	244-256	13
β-strand	264	1	26
β-strand	267-271	5	27
α-helix	274-279	6
β-strand	288-293	6	27
α-helix	298-302	5
β-strand	309-310	2	27
β-strand	312-313	2	28
β-strand	316-317	2	28
α-helix	321-328	8
α-helix	332	1
β-strand	338-343	6	28
β-strand	346-351	6	28
β-strand	355	1	26
β-strand	363	1	29
β-strand	374-378	5	29
β-strand	385-390	6	29
α-helix	397-399	3
β-strand	406-410	5	29
β-strand	413-414	2	29
α-helix	418-425	8
β-strand	432-437	6	29
β-strand	443-447	5	29

Chain E: 13 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	16-22	7
α-helix	23-25	3
β-strand	26-34	9	30
β-strand	83-94	12	30
β-strand	99-102	4	30
α-helix	104-107	4
β-strand	110-116	7	30
β-strand	122-131	10	30
β-strand	136-142	7	30
β-strand	151-152	2	31
α-helix	155-157	3
β-strand	162	1	22
β-strand	163-168	6	31
α-helix	170-172	3
β-strand	176-187	12	31
β-strand	198-201	4	31
β-strand	213-215	3	31
β-strand	220-229	10	31
β-strand	239-243	5	31
α-helix	244-257	14
β-strand	263-264	2	32
β-strand	267-271	5	33
α-helix	274-279	6
β-strand	288-293	6	33
α-helix	298-302	5
β-strand	309-313	5	33
β-strand	316-317	2	33
α-helix	318	1
α-helix	321-328	8
α-helix	332	1
β-strand	336-343	8	33
β-strand	346-353	8	33
β-strand	355-356	2	32
α-helix	365-368	4
β-strand	374-378	5	34
β-strand	385-390	6	34
β-strand	406-410	5	34
β-strand	413-414	2	34
α-helix	418-425	8
β-strand	432-438	7	34
β-strand	441-442	2	34
β-strand	445-447	3	34

Chain F: 13 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	25
α-helix	16-22	7
α-helix	23-25	3
β-strand	26-31	6	35
β-strand	86-94	9	35
β-strand	99-102	4	35
α-helix	104-107	4
β-strand	113-116	4	35
β-strand	122-131	10	35
β-strand	136-142	7	35
α-helix	151	1
β-strand	152	1	36
α-helix	153	1
α-helix	155-157	3
β-strand	163-168	6	36
α-helix	170-172	3
β-strand	176-187	12	36
β-strand	198-201	4	36
β-strand	212-215	4	36
β-strand	221-228	8	36
β-strand	239-243	5	36
α-helix	244-257	14
β-strand	264	1	37
β-strand	267-271	5	38
α-helix	274-279	6
β-strand	288-293	6	38
α-helix	298-302	5
β-strand	309-313	5	38
β-strand	316-317	2	38
α-helix	321-328	8
α-helix	332	1
β-strand	336-343	8	38
β-strand	346-353	8	38
β-strand	355	1	37
β-strand	374-378	5	39
β-strand	385-390	6	39
β-strand	406-410	5	39
β-strand	413-414	2	39
α-helix	418-425	8
β-strand	432-438	7	39
β-strand	441-442	2	39
β-strand	445-447	3	39

Chains G, I and J: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	462-463	2	3

Chain H: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	462	1	11

3 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
Periplasmic serine endoprotease DegP	A, B, C, D, E, F	protein	469	Escherichia coli K-12	P0C0V0 (AlphaFold model)
TMB-CYRKL modulator	G, H, I, J, K, L, M, N, O, P, Q, R	protein	5	Escherichia coli

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

>6JJO_1 Periplasmic serine endoprotease DegP (chains A, B, C, D, E, F)
MGSSHHHHHHSSGLVPRGSHMAETSSATTAQQMPSLAPMLEKVMPSVVSINVEGSTTVNT
PRMPRNFQQFFGDDSPFCQEGSPFQSSPFCQGGQGGNGGGQQQKFMALGSGVIIDADKGY
VVTNNHVVDNATVIKVQLSDGRKFDAKMVGKDPRSDIALIQIQNPKNLTAIKMADSDALR
VGDYTVAIGNPFGLGETVTSGIVSALGRSGLNAENYENFIQTDAAINRGNAGGALVNLNG
ELIGINTAILAPDGGNIGIGFAIPSNMVKNLTSQMVEYGQVKRGELGIMGTELNSELAKA
MKVDAQRGAFVSQVLPNSSAAKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKLTL
GLLRDGKQVNVNLELQQSSQNQVDSSSIFNGIEGAEMSNKGKDQGVVVNNVKTGTPAAQI
GLKKGDVIIGANQQAVKNIAELRKVLDSKPSVLALNIQRGDSTIYLLMQ

Sequence of entity 2 (G, H, I, J, K, L, M, N, O, P, Q, R), FASTA

>6JJO_2 TMB-CYRKL modulator (chains G, H, I, J, K, L, M, N, O, P, Q, R)
CYRKL

Primary citation

Over-activation of a nonessential bacterial protease DegP as an antibiotic strategy. Cho, H., Choi, Y., Min, K. et al. Commun Biol (2020) 3:547-547. DOI 10.1038/s42003-020-01266-9 · PubMed

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

8F0A 2.6 Å, Client-bound structure of a DegP trimer within a 12mer cage
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
6JJL 4.2 Å, Crystal structure of the DegP dodecamer with a modulator

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