3OTP: DegP dodecamer with a model substrate

Crystal structure of the DegP dodecamer with a model substrate. Determined by X-ray diffraction at 3.76 Å resolution. Released 19 Jan 2011.

Method: X-ray diffraction
Resolution: 3.76 Å
Organisms: Escherichia coli, Gallus gallus
Chains: 12
Atoms: 17,037
Mol. weight: 317.67 kDa
Released: 19 Jan 2011

Explore 3OTP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3OTP contains 77 α-helices and 211 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: 10 helices, 34 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	99-103	5	2
α-helix	104-107	4
β-strand	113-116	4	2
β-strand	122-131	10	2
β-strand	136-141	6	2
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	221-229	9	3
β-strand	239-243	5	3
α-helix	244-256	13
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	309-313	5	7
β-strand	316-317	2	7
α-helix	321-329	9
β-strand	332	1	5
β-strand	336-343	8	7
β-strand	346-353	8	7
β-strand	355	1	6
β-strand	369-371	3	8
β-strand	374-376	3	8
β-strand	385-386	2	9
β-strand	387-389	3	8
β-strand	406-407	2	9
β-strand	409-410	2	10
β-strand	413-414	2	10
α-helix	418-425	8
β-strand	432-436	5	10
β-strand	443-447	5	10

Chain B: 15 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	11
α-helix	16-22	7
α-helix	23-25	3
β-strand	26-34	9	12
β-strand	83-94	12	12
β-strand	99-103	5	12
α-helix	104-107	4
β-strand	110-116	7	12
β-strand	122-131	10	12
β-strand	136-141	6	12
α-helix	149-151	3
β-strand	152	1	13
α-helix	155-157	3
β-strand	162	1	1
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	221-229	9	13
β-strand	239-243	5	13
α-helix	244-257	14
β-strand	263-264	2	14
β-strand	267-271	5	15
α-helix	274-279	6
β-strand	288-293	6	15
α-helix	298-302	5
β-strand	309-313	5	15
β-strand	316-317	2	15
α-helix	318	1
α-helix	321-330	10
α-helix	332	1
β-strand	336-342	7	15
β-strand	347-353	7	15
β-strand	355-356	2	14
β-strand	362-363	2	16
α-helix	365-368	4
β-strand	374-378	5	16
β-strand	385-390	6	16
α-helix	397-399	3
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	441-442	2	16
β-strand	445-447	3	16

Chain C: 13 helices, 33 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	17
β-strand	83-94	12	17
β-strand	99-103	5	17
α-helix	104-107	4
β-strand	110-116	7	17
β-strand	122-131	10	17
β-strand	136-141	6	17
α-helix	151	1
β-strand	152	1	18
α-helix	153	1
α-helix	155-157	3
β-strand	162	1	11
β-strand	163-168	6	18
α-helix	170-172	3
β-strand	176-187	12	18
β-strand	198-201	4	18
β-strand	213-215	3	18
β-strand	221-229	9	18
β-strand	239-243	5	18
α-helix	244-257	14
β-strand	262	1	19
β-strand	264	1	20
β-strand	267-271	5	21
α-helix	274-279	6
β-strand	288-293	6	21
α-helix	298-302	5
β-strand	309-313	5	21
β-strand	316-317	2	21
α-helix	321-330	10
β-strand	332	1	19
β-strand	336-343	8	21
β-strand	346-353	8	21
β-strand	355	1	20
β-strand	369-371	3	22
β-strand	374-378	5	22
β-strand	385-389	5	22
α-helix	395-398	4
β-strand	406-407	2	22
β-strand	409-410	2	23
β-strand	413-414	2	23
α-helix	418-425	8
β-strand	432-435	4	23
β-strand	445-447	3	23

Chain D: 14 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	24
α-helix	16-22	7
α-helix	23-25	3
β-strand	26-34	9	25
β-strand	83-94	12	25
β-strand	99-103	5	25
α-helix	104-107	4
β-strand	110-116	7	25
β-strand	122-131	10	25
β-strand	136-141	6	25
α-helix	149-151	3
β-strand	152	1	26
α-helix	153	1
α-helix	155-157	3
β-strand	162	1	27
β-strand	163-168	6	26
α-helix	170-172	3
β-strand	176-187	12	26
β-strand	198-201	4	26
β-strand	213-215	3	26
β-strand	221-229	9	26
β-strand	239-243	5	26
α-helix	244-257	14
β-strand	262	1	28
β-strand	264	1	29
β-strand	267-271	5	30
α-helix	274-279	6
β-strand	288-293	6	30
α-helix	298-302	5
β-strand	309-313	5	30
β-strand	316-317	2	30
α-helix	321-328	8
β-strand	332	1	28
β-strand	336-343	8	30
β-strand	346-353	8	30
β-strand	355	1	29
β-strand	363	1	31
α-helix	365-368	4
β-strand	374-378	5	31
β-strand	385-390	6	31
α-helix	397-399	3
β-strand	406-407	2	31
β-strand	409-410	2	32
β-strand	413-414	2	32
α-helix	418-425	8
β-strand	432-435	4	32
β-strand	437-438	2	33
β-strand	441-442	2	33
β-strand	445-447	3	32

Chain E: 14 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	34
α-helix	16-22	7
α-helix	23-25	3
β-strand	26-34	9	35
β-strand	83-94	12	35
β-strand	99-103	5	35
α-helix	104-107	4
β-strand	110-116	7	35
β-strand	122-131	10	35
β-strand	136-141	6	35
α-helix	149-151	3
β-strand	152	1	36
α-helix	153	1
α-helix	155-157	3
β-strand	162	1	24
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	213-215	3	36
β-strand	221-229	9	36
β-strand	239-243	5	36
α-helix	244-257	14
β-strand	263-264	2	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	355-356	2	37
α-helix	365-368	4
β-strand	374-378	5	39
β-strand	385-390	6	39
β-strand	406-407	2	39
β-strand	409-410	2	40
β-strand	413-414	2	40
α-helix	418-425	8
β-strand	432-435	4	40
β-strand	437-438	2	41
β-strand	441-442	2	41
β-strand	445-447	3	40

Chain F: 11 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	27
α-helix	16-22	7
α-helix	23-25	3
β-strand	26-31	6	42
β-strand	86-94	9	42
β-strand	99-103	5	42
α-helix	104-107	4
β-strand	113-116	4	42
β-strand	122-131	10	42
β-strand	136-141	6	42
α-helix	149-151	3
β-strand	152	1	43
α-helix	155-157	3
β-strand	162	1	34
β-strand	163-168	6	43
α-helix	170-172	3
β-strand	176-187	12	43
β-strand	198-201	4	43
β-strand	213-215	3	43
β-strand	221-229	9	43
β-strand	239-243	5	43
α-helix	244-256	13
β-strand	262	1	44
β-strand	263-264	2	45
β-strand	267-271	5	46
α-helix	274-279	6
β-strand	288-293	6	46
α-helix	298-302	5
β-strand	309-313	5	46
β-strand	316-317	2	46
α-helix	321-329	9
β-strand	332	1	44
β-strand	336-343	8	46
β-strand	346-353	8	46
β-strand	355-356	2	45
β-strand	369-371	3	47
β-strand	374-376	3	47
β-strand	385-386	2	48
β-strand	387-389	3	47
β-strand	406-407	2	48
β-strand	409-410	2	49
β-strand	413-414	2	49
α-helix	418-425	8
β-strand	432-435	4	49
β-strand	445-447	3	49

Chains G, H, I, J, K and L: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	29-31	3	3
β-strand	56-57	2	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protease do	A, B, C, D, E, F	protein	459	Escherichia coli	P0C0V0 (AlphaFold model)
Lysozyme C	G, H, I, J, K, L	protein	44	Gallus gallus	P00698 (AlphaFold model)

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

>3OTP_1 Protease do (chains A, B, C, D, E, F)
AETSSATTAQQMPSLAPMLEKVMPSVVSINVEGSTTVNTPRMPRNFQQFFGDDSPFCQEG
SPFQSSPFCQGGQGGNGGGQQQKFMALGSGVIIDADKGYVVTNNHVVDNATVIKVQLSDG
RKFDAKMVGKDPRSDIALIQIQNPKNLTAIKMADSDALRVGDYTVAIGNPFGLGETVTSG
IVSALGRSGLNAENYENFIQTDAAINRGNAGGALVNLNGELIGINTAILAPDGGNIGIGF
AIPSNMVKNLTSQMVEYGQVKRGELGIMGTELNSELAKAMKVDAQRGAFVSQVLPNSSAA
KAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKLTLGLLRDGKQVNVNLELQQSSQN
QVDSSSIFNGIEGAEMSNKGKDQGVVVNNVKTGTPAAQIGLKKGDVIIGANQQAVKNIAE
LRKVLDSKPSVLALNIQRGDSTIYLLMQAAALEHHHHHH

Sequence of entity 2 (G, H, I, J, K, L), FASTA

>3OTP_2 Lysozyme C (chains G, H, I, J, K, L)
GTGDNYRGYSLGNWVSAAKFESNFNTQATNRNTDGSTDYGILQI

Primary citation

Covalent Linkage of Distinct Substrate Degrons Controls Assembly and Disassembly of DegP Proteolytic Cages. Kim, S., Grant, R.A., Sauer, R.T. Cell (2011) 145:67-78. DOI 10.1016/j.cell.2011.02.024 · 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
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

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