2ZLE: DegP12/OMP

Cryo-EM structure of DegP12/OMP. Determined by electron microscopy at 28.0 Å resolution. Released 3 Jun 2008.

Method: Electron microscopy
Resolution: 28.0 Å
Organism: Escherichia coli
Chains: 13
Atoms: 37,730
Mol. weight: 600.76 kDa
Released: 3 Jun 2008

Explore 2ZLE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2ZLE contains 185 α-helices and 451 β-strands across 13 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: 15 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	1
α-helix	6-12	7
α-helix	13-15	3
β-strand	16-27	12	2
α-helix	28-31	4
β-strand	43-57	15	2
β-strand	62-66	5	2
α-helix	67-70	4
β-strand	73-79	7	2
β-strand	85-94	10	2
β-strand	99-105	7	2
α-helix	113-114	2
β-strand	115	1	3
α-helix	116	1
α-helix	118-120	3
β-strand	125	1	4
β-strand	126-131	6	3
β-strand	139-148	10	3
β-strand	154-156	3	3
β-strand	168-170	3	3
β-strand	176-181	6	3
β-strand	194-198	5	3
α-helix	199-212	14
β-strand	218-219	2	5
β-strand	222-225	4	6
α-helix	230-233	4
β-strand	243-248	6	6
α-helix	249	1
α-helix	253-257	5
β-strand	264-265	2	6
β-strand	267-268	2	7
β-strand	271-272	2	7
α-helix	276-282	7
α-helix	283-285	3
β-strand	291	1	8
β-strand	294-295	2	7
β-strand	301	1	9
β-strand	302-303	2	7
β-strand	306	1	8
β-strand	308-309	2	5
β-strand	326	1	10
β-strand	337	1	10
α-helix	347-349	3
β-strand	356-360	5	11
β-strand	363-364	2	11
α-helix	368-374	7
β-strand	384-387	4	11
β-strand	392-395	4	11

Chain B: 15 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	400	1	12
α-helix	402-408	7
α-helix	409-411	3
β-strand	412-423	12	13
α-helix	424-427	4
β-strand	430	1	14
β-strand	439-453	15	13
β-strand	458-462	5	13
α-helix	463-466	4
β-strand	469-475	7	13
β-strand	481-490	10	13
β-strand	495-501	7	13
α-helix	509-510	2
β-strand	511	1	15
α-helix	512	1
α-helix	514-516	3
β-strand	521	1	1
β-strand	522-527	6	15
β-strand	535-544	10	15
β-strand	550-552	3	15
β-strand	564-566	3	15
β-strand	572-577	6	15
β-strand	590-594	5	15
α-helix	595-608	14
β-strand	614-615	2	16
β-strand	618-621	4	17
α-helix	626-629	4
β-strand	631	1	18
β-strand	639-644	6	17
α-helix	645	1
α-helix	649-653	5
β-strand	660-661	2	17
β-strand	663-664	2	19
β-strand	667-668	2	19
α-helix	672-678	7
α-helix	679-681	3
β-strand	687	1	20
β-strand	690-691	2	19
β-strand	694-695	2	21
β-strand	698-699	2	19
β-strand	702	1	20
β-strand	704-705	2	16
β-strand	722	1	22
β-strand	733	1	22
α-helix	743-745	3
β-strand	752-756	5	23
β-strand	759-760	2	23
α-helix	764-770	7
β-strand	780-783	4	23
β-strand	788-791	4	23

Chain C: 15 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	796	1	4
α-helix	798-804	7
α-helix	805-807	3
β-strand	808-819	12	24
α-helix	820-823	4
β-strand	835-849	15	24
β-strand	854-858	5	24
α-helix	859-862	4
β-strand	865-871	7	24
β-strand	877-886	10	24
β-strand	891-897	7	24
α-helix	905-906	2
β-strand	907	1	25
α-helix	908	1
α-helix	910-912	3
β-strand	917	1	12
β-strand	918-923	6	25
β-strand	931-940	10	25
β-strand	946-948	3	25
β-strand	960-962	3	25
β-strand	968-973	6	25
β-strand	986-990	5	25
α-helix	991-1004	14
β-strand	1010-1011	2	26
β-strand	1014-1017	4	27
α-helix	1022-1025	4
β-strand	1026	1	28
β-strand	1030-1031	2	29
β-strand	1035-1040	6	27
α-helix	1041	1
α-helix	1045-1049	5
β-strand	1055	1	30
β-strand	1056-1057	2	27
β-strand	1059-1060	2	31
β-strand	1063-1064	2	31
α-helix	1068-1074	7
α-helix	1075-1077	3
β-strand	1083	1	32
β-strand	1086-1087	2	31
β-strand	1089	1	33
β-strand	1094-1095	2	31
β-strand	1098	1	32
β-strand	1100-1101	2	26
β-strand	1118	1	34
β-strand	1129	1	34
α-helix	1139-1141	3
β-strand	1148-1152	5	35
β-strand	1155-1156	2	35
α-helix	1160-1166	7
β-strand	1176-1179	4	35
β-strand	1184-1187	4	35

Chain D: 5 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	1190-1194	5	14
β-strand	1197-1211	15	14
β-strand	1219-1220	2	14
β-strand	1223-1233	11	14
β-strand	1238-1249	12	14
β-strand	1259-1270	12	14
β-strand	1274-1282	9	14
α-helix	1286-1289	4
α-helix	1290-1292	3
β-strand	1312-1322	11	14
β-strand	1325-1326	2	36
β-strand	1331-1340	10	14
β-strand	1341	1	37
β-strand	1343	1	38
α-helix	1344	1
β-strand	1353	1	38
β-strand	1360	1	39
β-strand	1364	1	37
β-strand	1367-1376	10	14
β-strand	1379-1389	11	14
α-helix	1390-1391	2
β-strand	1393	1	40
β-strand	1400	1	41
β-strand	1405-1417	13	14
β-strand	1420-1430	11	14
β-strand	1434	1	42
β-strand	1439	1	41
β-strand	1440	1	42
β-strand	1443-1453	11	14
β-strand	1459-1471	13	14
β-strand	1480-1493	14	14
β-strand	1498-1507	10	14
α-helix	1513-1518	6
β-strand	1523	1	43
β-strand	1525-1533	9	14

Chain E: 15 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	1538	1	44
α-helix	1540-1546	7
α-helix	1547-1549	3
β-strand	1550-1561	12	45
α-helix	1562-1565	4
β-strand	1577-1591	15	45
β-strand	1596-1600	5	45
α-helix	1601-1604	4
β-strand	1607-1613	7	45
β-strand	1619-1628	10	45
β-strand	1633-1639	7	45
α-helix	1647-1648	2
β-strand	1649	1	46
α-helix	1650	1
α-helix	1652-1654	3
β-strand	1659	1	47
β-strand	1660-1665	6	46
β-strand	1673-1682	10	46
β-strand	1688-1690	3	46
β-strand	1702-1704	3	46
β-strand	1710-1715	6	46
β-strand	1728-1732	5	46
α-helix	1733-1746	14
β-strand	1752-1753	2	48
β-strand	1756-1759	4	49
α-helix	1764-1767	4
β-strand	1777-1782	6	49
α-helix	1783	1
α-helix	1787-1791	5
β-strand	1793	1	29
β-strand	1798-1799	2	49
β-strand	1801-1802	2	50
β-strand	1805-1806	2	50
α-helix	1810-1816	7
α-helix	1817-1819	3
β-strand	1825	1	51
β-strand	1828-1829	2	50
β-strand	1832	1	30
β-strand	1835	1	33
β-strand	1836-1837	2	50
β-strand	1840	1	51
β-strand	1842-1843	2	48
β-strand	1860	1	52
β-strand	1871	1	52
α-helix	1881-1883	3
β-strand	1890-1894	5	53
β-strand	1897-1898	2	53
α-helix	1902-1908	7
β-strand	1918-1921	4	53
β-strand	1926-1929	4	53

Chain F: 15 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	1934	1	54
α-helix	1936-1942	7
α-helix	1943-1945	3
β-strand	1946-1957	12	55
α-helix	1958-1961	4
β-strand	1965	1	14
β-strand	1967-1970	4	14
β-strand	1973-1987	15	55
β-strand	1992-1996	5	55
α-helix	1997-2000	4
β-strand	2003-2009	7	55
β-strand	2015-2024	10	55
β-strand	2029-2035	7	55
α-helix	2043-2044	2
β-strand	2045	1	56
α-helix	2046	1
α-helix	2048-2050	3
β-strand	2055	1	44
β-strand	2056-2061	6	56
β-strand	2069-2078	10	56
β-strand	2084-2086	3	56
β-strand	2098-2100	3	56
β-strand	2106-2111	6	56
β-strand	2124-2128	5	56
α-helix	2129-2142	14
β-strand	2148-2149	2	57
β-strand	2152-2155	4	58
α-helix	2160-2163	4
β-strand	2173-2178	6	58
α-helix	2179	1
α-helix	2183-2187	5
β-strand	2189	1	59
β-strand	2190-2192	3	60
β-strand	2194-2195	2	58
β-strand	2196	1	61
β-strand	2197-2198	2	62
β-strand	2201-2202	2	62
α-helix	2206-2212	7
α-helix	2213-2215	3
β-strand	2221	1	63
β-strand	2224-2225	2	62
β-strand	2232-2233	2	62
β-strand	2236	1	63
β-strand	2238-2239	2	57
β-strand	2256	1	64
β-strand	2267	1	64
α-helix	2277-2279	3
β-strand	2286-2290	5	65
β-strand	2293-2294	2	65
α-helix	2298-2304	7
β-strand	2314-2317	4	65
β-strand	2322-2325	4	65

Chain G: 15 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	2330	1	47
α-helix	2332-2338	7
α-helix	2339-2341	3
β-strand	2342-2353	12	66
α-helix	2354-2357	4
β-strand	2358	1	36
β-strand	2360	1	14
β-strand	2369-2383	15	66
β-strand	2388-2392	5	66
α-helix	2393-2396	4
β-strand	2399-2405	7	66
β-strand	2411-2420	10	66
β-strand	2425-2431	7	66
α-helix	2439-2440	2
β-strand	2441	1	67
α-helix	2442	1
α-helix	2444-2446	3
β-strand	2451	1	54
β-strand	2452-2457	6	67
β-strand	2465-2474	10	67
β-strand	2480-2482	3	67
β-strand	2494-2496	3	67
β-strand	2502-2507	6	67
β-strand	2520-2524	5	67
α-helix	2525-2538	14
β-strand	2544-2545	2	68
β-strand	2548-2551	4	69
α-helix	2556-2559	4
β-strand	2560	1	70
β-strand	2569-2574	6	69
α-helix	2575	1
α-helix	2579-2583	5
β-strand	2590-2591	2	69
β-strand	2593-2594	2	71
β-strand	2597-2598	2	71
α-helix	2602-2608	7
α-helix	2609-2611	3
β-strand	2617	1	72
β-strand	2620-2621	2	71
β-strand	2624-2625	2	73
β-strand	2628-2629	2	71
β-strand	2632	1	72
β-strand	2634-2635	2	68
β-strand	2652	1	74
β-strand	2663	1	74
α-helix	2673-2675	3
β-strand	2682-2686	5	75
β-strand	2689-2690	2	75
α-helix	2694-2700	7
β-strand	2710-2713	4	75
β-strand	2718-2721	4	75

Chain H: 15 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	2726	1	76
α-helix	2728-2734	7
α-helix	2735-2737	3
β-strand	2738-2749	12	77
α-helix	2750-2753	4
β-strand	2754	1	40
β-strand	2757	1	39
β-strand	2765-2779	15	77
β-strand	2784-2788	5	77
α-helix	2789-2792	4
β-strand	2795-2801	7	77
β-strand	2807-2816	10	77
β-strand	2821-2827	7	77
α-helix	2835-2836	2
β-strand	2837	1	78
α-helix	2838	1
α-helix	2840-2842	3
β-strand	2847	1	79
β-strand	2848-2853	6	78
β-strand	2861-2870	10	78
β-strand	2876-2878	3	78
β-strand	2890-2892	3	78
β-strand	2898-2903	6	78
β-strand	2916-2920	5	78
α-helix	2921-2934	14
β-strand	2940-2941	2	80
β-strand	2944-2947	4	81
α-helix	2952-2955	4
β-strand	2965-2970	6	81
α-helix	2971	1
α-helix	2975-2979	5
β-strand	2986-2987	2	81
β-strand	2989-2990	2	82
β-strand	2993-2994	2	82
α-helix	2998-3004	7
α-helix	3005-3007	3
β-strand	3013	1	83
β-strand	3016-3017	2	82
β-strand	3020-3021	2	84
β-strand	3024-3025	2	82
β-strand	3028	1	83
β-strand	3030-3031	2	80
β-strand	3048	1	85
β-strand	3059	1	85
α-helix	3069-3071	3
β-strand	3078-3082	5	86
β-strand	3085-3086	2	86
α-helix	3090-3096	7
β-strand	3106-3109	4	86
β-strand	3114-3117	4	86

5 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
Protease do	A, B, C, E, F, G, H, I, J, K, L, M	protein	448	Escherichia coli	P0C0V0 (AlphaFold model)
Outer membrane protein C	D	protein	346	Escherichia coli	P06996 (AlphaFold model)

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

>2ZLE_1 Protease do (chains A, B, C, E, F, G, H, I, J, K, L, M)
AETSSATTAQQMPSLAPMLEKVMPSVVSINVEGSTTVNTPRMPRNFQQFFGDDSPFCQEG
SPFQSSPFCQGGQGGNGGGQQQKFMALGSGVIIDADKGYVVTNNHVVDNATVIKVQLSDG
RKFDAKMVGKDPRSDIALIQIQNPKNLTAIKMADSDALRVGDYTVAIGNPFGLGETVTSG
IVSALGRSGLNAENYENFIQTDAAINRGNSGGALVNLNGELIGINTAILAPDGGNIGIGF
AIPSNMVKNLTSQMVEYGQVKRGELGIMGTELNSELAKAMKVDAQRGAFVSQVLPNSSAA
KAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKLTLGLLRDGKQVNVNLELQQSSQN
QVDSSSIFNGIEGAEMSNKGKDQGVVVNNVKTGTPAAQIGLKKGDVIIGANQQAVKNIAE
LRKVLDSKPSVLALNIQRGDSTIYLLMQ

Sequence of entity 2 (D), FASTA

>2ZLE_2 Outer membrane protein C (chains D)
AEVYNKDGNKLDLYGKVDGLHYFSDNKDVDGDQTYMRLGFKGETQVTDQLTGYGQWEYQI
QGNSAENENNSWTRVAFAGLKFQDVGSFDYGRNYGVVYDVTSWTDVLPEFGGDTYGSDNF
MQQRGNGFATYRNTDFFGLVDGLNFAVQYQGKNGNPSGEGFTSGVTNNGRDALRQNGDGV
GGSITYDYEGFGIGGAISSSKRTDAQNTAAYIGNGDRAETYTGGLKYDANNIYLAAQYTQ
TYNATRVGSLGWANKAQNFEAVAQYQFDFGLRPSLAYLQSKGKNLGRGYDDEDILKYVDV
GATYYFNKNMSTYVDYKINLLDDNQFTRDAGINTDNIVALGLVYQF

Primary citation

Structural basis for the regulated protease and chaperone function of DegP. Krojer, T., Sawa, J., Saibil, H.R. et al. Nature (2008) 453:885-890. DOI 10.1038/nature07004 · 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

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