7L6N: Chaperone protein ClpB

Name: PDB 7L6N: The Mycobacterium tuberculosis ClpB disaggregase hexamer structure with three locally refined ClpB middle domains and three DnaK nucleotide binding domains
Published: 2021-05-26
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: chaperone

The Mycobacterium tuberculosis ClpB disaggregase hexamer structure with three locally refined ClpB middle domains and three DnaK nucleotide binding domains. Determined by electron microscopy at 7.0 Å resolution. Released 26 May 2021.

Method: Electron microscopy
Resolution: 7.0 Å
Organism: Mycobacterium tuberculosis
Chains: 10
Atoms: 36,999
Mol. weight: 765.78 kDa
Ligands: AGS, ADP
Released: 26 May 2021

Explore 7L6N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7L6N contains 250 α-helices and 196 β-strands across 10 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: 42 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	160-164	5
β-strand	166-167	2	1
α-helix	169-173	5
α-helix	178-179	2
α-helix	184-194	11
β-strand	202-205	4	1
α-helix	213-225	13
α-helix	230-232	3
β-strand	238-239	2	1
α-helix	242-245	4
α-helix	255-268	14
β-strand	275-278	4	1
α-helix	280-283	4
α-helix	301-304	4
β-strand	312-315	4	1
α-helix	317-323	7
α-helix	325-327	3
α-helix	328-332	5
β-strand	335-338	4	1
α-helix	340-342	3
α-helix	344-361	18
β-strand	365-366	2	2
α-helix	368-376	9
α-helix	387-390	4
α-helix	392-406	15
α-helix	416-430	15
α-helix	437-460	24
α-helix	462-492	31
α-helix	496-500	5
α-helix	501-506	6
α-helix	507-517	11
β-strand	532-533	2	2
α-helix	537-544	8
α-helix	557-560	4
α-helix	564-568	5
α-helix	576-583	8
α-helix	587-590	4
β-strand	602-604	3	3
β-strand	605-606	2	4
α-helix	615-623	9
α-helix	628-630	3
β-strand	633-635	3	3
α-helix	642-647	6
α-helix	665-668	4
β-strand	677-679	3	3
α-helix	681-683	3
α-helix	689-695	7
β-strand	700-702	3	5
β-strand	708-710	3	5
β-strand	716-718	3	3
α-helix	729-738	10
α-helix	741-744	4
β-strand	751-752	2	4
α-helix	762-775	14
β-strand	783-784	2	6
α-helix	787-796	10
α-helix	805-811	7
α-helix	812-816	5
α-helix	817-823	7
β-strand	824	1	7
β-strand	826	1	7
β-strand	834-835	2	6
β-strand	837-838	2	8
β-strand	843-844	2	8

Chain B: 41 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	161-164	4
β-strand	165-167	3	9
α-helix	168-173	6
α-helix	184-194	11
β-strand	202-206	5	10
α-helix	214-225	12
β-strand	236-240	5	9
α-helix	243-245	3
α-helix	254-268	15
β-strand	273-276	4	9
α-helix	280-284	5
α-helix	301-305	5
β-strand	310-312	3	9
β-strand	313-316	4	10
α-helix	317-323	7
α-helix	325-327	3
α-helix	328-331	4
β-strand	335-338	4	10
α-helix	344-361	18
β-strand	366	1	11
α-helix	368-376	9
α-helix	377-379	3
α-helix	389-407	19
α-helix	409-410	2
α-helix	415-430	16
α-helix	439-467	29
α-helix	469-492	24
α-helix	496-500	5
α-helix	501-506	6
α-helix	507-517	11
β-strand	533	1	11
α-helix	537-544	8
α-helix	557-562	6
α-helix	568-570	3
α-helix	576-582	7
α-helix	584-590	7
β-strand	601-604	4	12
β-strand	605-606	2	13
α-helix	615-625	11
β-strand	633-635	3	12
α-helix	642-647	6
α-helix	651-652	2
β-strand	655	1	14
α-helix	665-668	4
β-strand	677-679	3	12
α-helix	681-683	3
α-helix	688-692	5
β-strand	700-702	3	15
β-strand	708-710	3	15
β-strand	715-718	4	12
α-helix	741-744	4
β-strand	751-752	2	13
α-helix	759-761	3
α-helix	762-775	14
α-helix	776-779	4
β-strand	782-785	4	16
α-helix	787-795	9
α-helix	806-811	6
α-helix	812-816	5
α-helix	817-823	7
β-strand	833-836	4	16
β-strand	837-838	2	17
β-strand	843-844	2	17

Chain C: 42 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	161-164	4
α-helix	169-173	5
α-helix	178-179	2
α-helix	184-194	11
β-strand	202-205	4	18
α-helix	214-225	12
α-helix	230-232	3
β-strand	238-239	2	18
β-strand	251	1	19
α-helix	256-268	13
β-strand	275-278	4	18
α-helix	280-282	3
α-helix	301-305	5
β-strand	312-314	3	18
α-helix	320-324	5
α-helix	325-327	3
α-helix	328-331	4
β-strand	335-338	4	18
α-helix	340-342	3
α-helix	344-354	11
α-helix	357-361	5
β-strand	365-366	2	20
α-helix	368-380	13
α-helix	387-406	20
α-helix	414-431	18
α-helix	439-468	30
α-helix	472-492	21
α-helix	496-500	5
α-helix	501-506	6
α-helix	507-515	9
β-strand	532-533	2	20
α-helix	537-544	8
α-helix	558-568	11
α-helix	576-590	15
β-strand	602-603	2	21
β-strand	606	1	22
α-helix	613-625	13
α-helix	628-630	3
β-strand	632-635	4	23
α-helix	642-648	7
α-helix	651-652	2
α-helix	664-668	5
β-strand	676-679	4	23
α-helix	681-683	3
α-helix	688-690	3
α-helix	692-697	6
β-strand	700-702	3	24
β-strand	708-710	3	24
β-strand	716-717	2	21
β-strand	718	1	23
α-helix	731-738	8
α-helix	741-744	4
β-strand	752	1	22
α-helix	761-776	16
α-helix	777-779	3
β-strand	783-785	3	25
α-helix	787-795	9
α-helix	805-811	7
α-helix	812-816	5
α-helix	817-823	7
β-strand	824	1	26
β-strand	826	1	26
β-strand	834-836	3	25
β-strand	837-838	2	27
β-strand	843-844	2	27

Chain D: 31 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	165-167	3	28
α-helix	168-173	6
α-helix	184-194	11
β-strand	202-205	4	29
α-helix	214-225	12
α-helix	230-232	3
β-strand	238-240	3	28
α-helix	255-268	14
β-strand	275-277	3	28
α-helix	280-282	3
α-helix	301-304	4
β-strand	312	1	28
β-strand	313-315	3	29
α-helix	317-323	7
α-helix	328-331	4
β-strand	335-338	4	29
α-helix	340-342	3
α-helix	344-361	18
β-strand	365-366	2	30
α-helix	368-380	13
α-helix	387-406	20
β-strand	532-533	2	30
α-helix	537-544	8
α-helix	557-562	6
α-helix	565-569	5
α-helix	576-591	16
β-strand	602-603	2	31
β-strand	606	1	32
α-helix	613-625	13
β-strand	633-635	3	31
α-helix	643-648	6
β-strand	655	1	33
α-helix	663-669	7
β-strand	677-679	3	31
α-helix	688-690	3
α-helix	692-695	4
β-strand	700-701	2	34
β-strand	709-710	2	34
β-strand	716-718	3	31
α-helix	728-738	11
α-helix	741-744	4
β-strand	752	1	32
α-helix	755-757	3
α-helix	761-775	15
β-strand	782-784	3	35
α-helix	787-795	9
α-helix	805-807	3
α-helix	808-811	4
α-helix	812-816	5
α-helix	817-823	7
β-strand	833-835	3	35
β-strand	837	1	36
β-strand	844	1	36

Chain E: 26 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	167	1	37
α-helix	171-173	3
α-helix	184-193	10
β-strand	202-206	5	38
α-helix	212-225	14
β-strand	237	1	39
β-strand	238	1	37
α-helix	242-244	3
α-helix	255-269	15
β-strand	274	1	39
β-strand	277-278	2	38
α-helix	280-282	3
α-helix	301-304	4
β-strand	313-315	3	38
α-helix	317-323	7
α-helix	331-333	3
β-strand	335-339	5	38
α-helix	344-353	10
α-helix	356-361	6
α-helix	368-381	14
α-helix	387-404	18
α-helix	535-546	12
α-helix	558-561	4
α-helix	576-589	14
β-strand	602-603	2	40
β-strand	606	1	41
α-helix	613-625	13
β-strand	632-635	4	40
α-helix	643-648	6
β-strand	675-679	5	40
α-helix	688-695	8
β-strand	700-702	3	42
β-strand	708-710	3	42
β-strand	715-717	3	40
α-helix	730-738	9
α-helix	743-746	4
β-strand	752	1	41
α-helix	753-757	5
α-helix	762-772	11
α-helix	787-797	11
α-helix	809-819	11
α-helix	822-825	4

Chain F: 26 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	167	1	43
α-helix	170-174	5
α-helix	184-194	11
β-strand	204	1	44
α-helix	212-225	14
β-strand	238-239	2	43
α-helix	256-268	13
β-strand	275-278	4	43
α-helix	300-305	6
β-strand	312-314	3	43
α-helix	317-323	7
β-strand	337	1	44
α-helix	344-354	11
α-helix	355-358	4
β-strand	366	1	45
α-helix	368-376	9
α-helix	387-405	19
β-strand	533	1	45
α-helix	537-543	7
α-helix	557-562	6
α-helix	564-568	5
α-helix	576-590	15
β-strand	601-606	6	46
α-helix	615-625	11
β-strand	632-635	4	46
α-helix	642-647	6
α-helix	651-652	2
α-helix	665-669	5
β-strand	675-679	5	46
α-helix	681-683	3
α-helix	688-695	8
β-strand	700-702	3	47
β-strand	708-710	3	47
β-strand	715-719	5	46
α-helix	729-738	10
β-strand	751-752	2	46
α-helix	761-775	15
β-strand	783-784	2	48
α-helix	787-796	10
α-helix	805-811	7
α-helix	812-816	5
α-helix	817-823	7
β-strand	834-835	2	48
β-strand	837-838	2	49
β-strand	843-844	2	49

Chain I: 14 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	62	1	50
β-strand	64-67	4	51
β-strand	72-78	7	51
β-strand	81-84	4	51
α-helix	85-87	3
β-strand	93-94	2	51
β-strand	97-99	3	52
β-strand	107-108	2	52
α-helix	110-118	9
β-strand	123-125	3	52
β-strand	137-138	2	53
β-strand	143-144	2	53
α-helix	146-165	20
β-strand	171	1	50
β-strand	172	1	54
β-strand	174	1	51
α-helix	182-195	14
β-strand	199	1	54
α-helix	205-212	8
β-strand	222-230	9	55
β-strand	233-242	10	55
β-strand	245-254	10	55
α-helix	259-277	19
α-helix	282-284	3
α-helix	286-303	18
β-strand	308-319	12	56
β-strand	323-332	10	56
α-helix	333-339	7
α-helix	341-358	18
β-strand	367	1	55
β-strand	368-369	2	57
β-strand	370-371	2	55
α-helix	373-375	3
α-helix	378-387	10
α-helix	391-392	2
β-strand	393-394	2	57
α-helix	399-414	16

Chains J and K: 14 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	62	1	58
β-strand	64-67	4	59
β-strand	72-78	7	59
β-strand	81-84	4	59
α-helix	85-87	3
β-strand	93-94	2	59
β-strand	97-99	3	60
β-strand	107-108	2	60
α-helix	110-118	9
β-strand	123-125	3	60
β-strand	137-138	2	61
β-strand	143-144	2	61
α-helix	146-165	20
β-strand	171	1	58
β-strand	172	1	62
β-strand	174	1	59
α-helix	182-195	14
β-strand	199	1	62
α-helix	205-212	8
β-strand	222-230	9	63
β-strand	233-242	10	63
β-strand	245-254	10	63
α-helix	259-277	19
α-helix	282-284	3
α-helix	286-303	18
β-strand	308-318	11	64
β-strand	324-332	9	64
α-helix	333-339	7
α-helix	341-358	18
β-strand	367	1	63
β-strand	368-369	2	65
β-strand	370-371	2	63
α-helix	373-375	3
α-helix	378-387	10
α-helix	391-392	2
β-strand	393-394	2	65
α-helix	399-414	16

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
Chaperone protein ClpB	A, B, C, D, E, F	protein	848	Mycobacterium tuberculosis	P9WPD1 (AlphaFold model)
Substrate	N	protein	33	Mycobacterium tuberculosis
Chaperone protein DnaK	I, J, K	protein	625	Mycobacterium tuberculosis	P9WMJ9 (AlphaFold model)

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

>7L6N_1 Chaperone protein ClpB (chains A, B, C, D, E, F)
MDSFNPTTKTQAALTAALQAASTAGNPEIRPAHLLMALLTQNDGIAAPLLEAVGVEPATV
RAETQRLLDRLPQATGASTQPQLSRESLAAITTAQQLATELDDEYVSTEHVMVGLATGDS
DVAKLLTGHGASPQALREAFVKVRGSARVTSPEPEATYQALQKYSTDLTARAREGKLDPV
IGRDNEIRRVVQVLSRRTKNNPVLIGEPGVGKTAIVEGLAQRIVAGDVPESLRDKTIVAL
DLGSMVAGSKYRGEFEERLKAVLDDIKNSAGQIITFIDELHTIVGAGATGEGAMDAGNMI
KPMLARGELRLVGATTLDEYRKHIEKDAALERRFQQVYVGEPSVEDTIGILRGLKDRYEV
HHGVRITDSALVAAATLSDRYITARFLPDKAIDLVDEAASRLRMEIDSRPVEIDEVERLV
RRLEIEEMALSKEEDEASAERLAKLRSELADQKEKLAELTTRWQNEKNAIEIVRDLKEQL
EALRGESERAERDGDLAKAAELRYGRIPEVEKKLDAALPQAQAREQVMLKEEVGPDDIAD
VVSAWTGIPAGRLLEGETAKLLRMEDELGKRVIGQKAAVTAVSDAVRRSRAGVSDPNRPT
GAFMFLGPTGVGKTELAKALADFLFDDERAMVRIDMSEYGEKHTVARLIGAPPGYVGYEA
GGQLTEAVRRRPYTVVLFDEIEKAHPDVFDVLLQVLDEGRLTDGHGRTVDFRNTILILTS
NLGSGGSAEQVLAAVRATFKPEFINRLDDVLIFEGLNPEELVRIVDIQLAQLGKRLAQRR
LQLQVSLPAKRWLAQRGFDPVYGARPLRRLVQQAIGDQLAKMLLAGQVHDGDTVPVNVSP
DADSLILG

Sequence of entity 2 (N), FASTA

>7L6N_2 Substrate (chains N)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Sequence of entity 3 (I, J, K), FASTA

>7L6N_3 Chaperone protein DnaK (chains I, J, K)
MARAVGIDLGTTNSVVSVLEGGDPVVVANSEGSRTTPSIVAFARNGEVLVGQPAKNQAVT
NVDRTVRSVKRHMGSDWSIEIDGKKYTAPEISARILMKLKRDAEAYLGEDITDAVITTPA
YFNDAQRQATKDAGQIAGLNVLRIVNEPTAAALAYGLDKGEKEQRILVFDLGGGTFDVSL
LEIGEGVVEVRATSGDNHLGGDDWDQRVVDWLVDKFKGTSGIDLTKDKMAMQRLREAAEK
AKIELSSSQSTSINLPYITVDADKNPLFLDEQLTRAEFQRITQDLLDRTRKPFQSVIADT
GISVSEIDHVVLVGGSTRMPAVTDLVKELTGGKEPNKGVNPDEVVAVGAALQAGVLKGEV
KDVLLLDVTPLSLGIETKGGVMTRLIERNTTIPTKRSETFTTADDNQPSVQIQVYQGERE
IAAHNKLLGSFELTGIPPAPRGIPQIEVTFDIDANGIVHVTAKDKGTGKENTIRIQEGSG
LSKEDIDRMIKDAEAHAEEDRKRREEADVRNQAETLVYQTEKFVKEQREAEGGSKVPEDT
LNKVDAAVAEAKAALGGSDISAIKSAMEKLGQESQALGQAIYEAAQAASQATGAAHPGGE
PGGAHPGSADDVVDAEVVDDGREAK

Ligands and cofactors

ID	Name	Formula	Copies
AGS	Phosphothiophosphoric acid-adenylate ester	C10 H16 N5 O12 P3 S	10
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	2

Primary citation

Structural basis for aggregate dissolution and refolding by the Mycobacterium tuberculosis ClpB-DnaK bi-chaperone system. Yin, Y., Feng, X., Yu, H. et al. Cell Rep (2021) 35:109166-109166. DOI 10.1016/j.celrep.2021.109166 · PubMed

Other PDB entries of the same protein (UniProt P9WPD1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6W6G 3.1 Å, The Mycobacterium tuberculosis ClpB disaggregase hexamer structure in conformation I in…
6W6J 3.2 Å, The Mycobacterium tuberculosis ClpB disaggregase hexamer structure with a locally…
6W6H 3.3 Å, The Mycobacterium tuberculosis ClpB disaggregase hexamer structure in conformation II in…
6W6I 3.5 Å, The Mycobacterium tuberculosis ClpB disaggregase hexamer structure in conformation T in…
6W6E 3.7 Å, The Mycobacterium tuberculosis ClpB disaggregase hexamer structure with a locally…
6DJU 3.8 Å, Mtb ClpB in complex with ATPgammaS and casein, Conformer 1
6DJV 3.9 Å, Mtb ClpB in complex with ATPgammaS and casein, Conformer 2
6ED3 6.3 Å, Mtb ClpB in complex with AMPPNP

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