6JJL: DegP dodecamer with a modulator

Crystal structure of the DegP dodecamer with a modulator. Determined by X-ray diffraction at 4.2 Å resolution. Released 2 Sept 2020.

Method: X-ray diffraction
Resolution: 4.2 Å
Organism: Escherichia coli K-12
Chains: 18
Atoms: 17,212
Mol. weight: 284.83 kDa
Released: 2 Sept 2020

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

Secondary structure: helices and β-sheets

6JJL contains 77 α-helices and 198 β-strands across 14 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: 12 helices, 35 β-strands

Element	Residues	Length	Sheet
α-helix	16-22	7
α-helix	23-25	3
β-strand	26-31	6	1
β-strand	86-94	9	1
β-strand	99-103	5	1
α-helix	104-107	4
β-strand	113-116	4	1
β-strand	122	1	1
β-strand	124-129	6	1
β-strand	136-142	7	1
β-strand	152	1	2
α-helix	155-157	3
β-strand	162	1	3
β-strand	163-168	6	2
α-helix	170-172	3
β-strand	176-187	12	2
β-strand	198-201	4	2
β-strand	213-216	4	2
β-strand	221-228	8	2
β-strand	239-243	5	2
α-helix	244-257	14
β-strand	262	1	4
β-strand	264	1	5
β-strand	267-271	5	6
α-helix	274-279	6
β-strand	288-293	6	6
α-helix	294	1
α-helix	298-301	4
β-strand	309-310	2	6
β-strand	312-313	2	7
β-strand	316-317	2	7
α-helix	321-328	8
β-strand	332	1	4
β-strand	337-343	7	7
β-strand	346-352	7	7
β-strand	355	1	5
β-strand	386	1	8
α-helix	395-398	4
β-strand	406	1	8
β-strand	409-410	2	9
β-strand	413-414	2	9
α-helix	418-426	9
β-strand	432-435	4	9
β-strand	437-438	2	10
β-strand	441-442	2	10
β-strand	443	1	11
β-strand	445-447	3	9

Chain B: 14 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	16-22	7
α-helix	23-25	3
β-strand	26-33	8	12
β-strand	85-94	10	12
β-strand	99-102	4	12
β-strand	110-116	7	12
β-strand	124-131	8	12
β-strand	136-142	7	12
α-helix	149-151	3
β-strand	152	1	13
α-helix	155-157	3
β-strand	163-168	6	13
α-helix	170-172	3
β-strand	176-187	12	13
β-strand	198-201	4	13
β-strand	213-215	3	13
β-strand	221-228	8	13
β-strand	239-243	5	13
α-helix	244-257	14
β-strand	264	1	14
β-strand	267-272	6	15
α-helix	274-279	6
β-strand	287-293	7	15
α-helix	298-302	5
β-strand	309-313	5	15
β-strand	316-317	2	15
α-helix	318	1
α-helix	321-329	9
α-helix	332	1
β-strand	336-342	7	15
β-strand	349-353	5	15
β-strand	355	1	14
β-strand	362-363	2	16
α-helix	364-368	5
β-strand	375-378	4	16
β-strand	385-389	5	16
α-helix	395-398	4
β-strand	406-407	2	16
β-strand	409-410	2	17
β-strand	413-414	2	17
α-helix	418-425	8
β-strand	433-434	2	18
β-strand	445-446	2	18

Chain C: 12 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	3
α-helix	16-22	7
β-strand	26-28	3	19
β-strand	31-33	3	19
β-strand	84	1	19
β-strand	89-94	6	19
β-strand	99-102	4	19
α-helix	104-107	4
β-strand	110-113	4	19
β-strand	116	1	19
β-strand	122	1	19
β-strand	124-131	8	19
β-strand	136-142	7	19
α-helix	149-151	3
β-strand	152	1	20
α-helix	155-157	3
β-strand	163-168	6	20
α-helix	170-172	3
β-strand	176-187	12	20
β-strand	198-201	4	20
β-strand	213-215	3	20
β-strand	221-228	8	20
β-strand	239-243	5	20
α-helix	244-256	13
β-strand	262	1	21
β-strand	264	1	22
β-strand	267	1	23
β-strand	270-272	3	24
α-helix	276-279	4
β-strand	287-289	3	24
β-strand	293	1	23
α-helix	294	1
α-helix	298-302	5
β-strand	309-313	5	24
α-helix	321-329	9
β-strand	332	1	21
β-strand	336-342	7	24
β-strand	347-353	7	24
β-strand	355	1	22
β-strand	377	1	25
α-helix	380-382	3
β-strand	386	1	25
β-strand	387	1	26
β-strand	405	1	26
β-strand	409-410	2	27
β-strand	413-414	2	27
α-helix	418-425	8
β-strand	437-438	2	26
β-strand	441-442	2	26

Chain D: 12 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	28
α-helix	16-22	7
α-helix	23-25	3
β-strand	26-32	7	29
β-strand	85-92	8	29
β-strand	99-102	4	29
α-helix	104-107	4
β-strand	112-116	5	29
β-strand	122-131	10	29
β-strand	136-141	6	29
α-helix	149-150	2
β-strand	151-152	2	30
α-helix	155-157	3
β-strand	163-168	6	30
α-helix	170-172	3
β-strand	176-187	12	30
β-strand	198-201	4	30
β-strand	213-215	3	30
β-strand	220-228	9	30
β-strand	239-243	5	30
α-helix	244-256	13
β-strand	267	1	31
β-strand	268-269	2	32
β-strand	271-272	2	33
α-helix	276-279	4
β-strand	287-289	3	33
β-strand	293	1	31
α-helix	298-301	4
α-helix	304-305	2
β-strand	309-310	2	33
β-strand	312-313	2	34
β-strand	316-317	2	34
α-helix	321-328	8
β-strand	336-340	5	34
β-strand	350-353	4	34
β-strand	378-379	2	35
β-strand	384-385	2	35
α-helix	418-425	8
β-strand	432-434	3	36
β-strand	437-438	2	37
β-strand	441-442	2	37
β-strand	445-447	3	36

Chain E: 13 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	16-22	7
α-helix	23-25	3
β-strand	26-33	8	38
β-strand	84-87	4	38
β-strand	90-94	5	38
β-strand	99-102	4	38
α-helix	104-107	4
β-strand	112-116	5	38
β-strand	122	1	38
β-strand	124-129	6	38
β-strand	137-142	6	38
α-helix	149-151	3
β-strand	152	1	39
α-helix	155-157	3
β-strand	162	1	28
β-strand	163-168	6	39
α-helix	170-172	3
β-strand	176-187	12	39
β-strand	198-201	4	39
β-strand	212-215	4	39
β-strand	221-229	9	39
β-strand	239-243	5	39
α-helix	244-256	13
β-strand	263-264	2	40
β-strand	267-271	5	41
α-helix	274-279	6
β-strand	288-293	6	41
α-helix	298-302	5
β-strand	309-313	5	41
β-strand	316-317	2	41
α-helix	321-328	8
α-helix	332	1
β-strand	337-342	6	41
β-strand	348-352	5	41
β-strand	355-356	2	40
β-strand	376	1	42
β-strand	387	1	42
β-strand	402	1	43
β-strand	405	1	43
α-helix	410-412	3
α-helix	418-425	8
β-strand	432-434	3	44
β-strand	445-447	3	44

Chain F: 14 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	16-22	7
α-helix	23-25	3
β-strand	26	1	45
β-strand	28-31	4	45
β-strand	86	1	45
β-strand	91-94	4	45
β-strand	99-102	4	45
α-helix	104-107	4
β-strand	113-116	4	45
β-strand	122	1	45
β-strand	124-131	8	45
β-strand	136-142	7	45
α-helix	149-151	3
β-strand	152	1	46
α-helix	155-157	3
β-strand	163-168	6	46
α-helix	170-172	3
β-strand	176-187	12	46
β-strand	198-201	4	46
β-strand	213-216	4	46
β-strand	221-228	8	46
β-strand	239-243	5	46
α-helix	244-256	13
β-strand	267-272	6	47
α-helix	274-279	6
β-strand	287-293	7	47
α-helix	294	1
α-helix	298-301	4
β-strand	309-313	5	47
β-strand	316-317	2	47
α-helix	321-327	7
α-helix	332	1
β-strand	336-343	8	47
β-strand	346-353	8	47
β-strand	374-377	4	48
β-strand	385-390	6	48
α-helix	395-398	4
β-strand	406-407	2	48
β-strand	409-410	2	49
β-strand	414	1	49
α-helix	418-426	9
β-strand	432-435	4	49
β-strand	445-447	3	49

Chains G and I: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	462	1	2

Chain K: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	461-463	3	39

1 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	440	Escherichia coli K-12	P0C0V0 (AlphaFold model)
Cys-tyr-arg-lys-leu	G, H, I, J, K, L, M, N, O, P, Q, R	protein	5	Escherichia coli K-12

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

>6JJL_1 Periplasmic serine endoprotease DegP (chains A, B, C, D, E, F)
AQQMPSLAPMLEKVMPSVVSINVEGSTTVNTPRMPRNFQQFFGDDSPFCQEGSPFQSSPF
CQGGQGGNGGGQQQKFMALGSGVIIDADKGYVVTNNHVVDNATVIKVQLSDGRKFDAKMV
GKDPRSDIALIQIQNPKNLTAIKMADSDALRVGDYTVAIGNPFGLGETVTSGIVSALGRS
GLNAENYENFIQTDAAINRGNAGGALVNLNGELIGINTAILAPDGGNIGIGFAIPSNMVK
NLTSQMVEYGQVKRGELGIMGTELNSELAKAMKVDAQRGAFVSQVLPNSSAAKAGIKAGD
VITSLNGKPISSFAALRAQVGTMPVGSKLTLGLLRDGKQVNVNLELQQSSQNQVDSSSIF
NGIEGAEMSNKGKDQGVVVNNVKTGTPAAQIGLKKGDVIIGANQQAVKNIAELRKVLDSK
PSVLALNIQRGDSTIYLLMQ

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

>6JJL_2 CYS-TYR-ARG-LYS-LEU (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
6JJO 4.16 Å, Crystal structure of the DegP dodecamer with a modulator

Browse structure collections

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