6W6H: Chaperone protein ClpB

Name: PDB 6W6H: The Mycobacterium tuberculosis ClpB disaggregase hexamer structure in conformation II in the presence of DnaK chaperone and a model substrate
Published: 2021-05-26
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: chaperone

The Mycobacterium tuberculosis ClpB disaggregase hexamer structure in conformation II in the presence of DnaK chaperone and a model substrate. Determined by electron microscopy at 3.3 Å resolution. Released 26 May 2021.

Method: Electron microscopy
Resolution: 3.3 Å
Organism: Mycobacterium tuberculosis
Chains: 7
Atoms: 28,427
Mol. weight: 564.87 kDa
Ligands: ADP, AGS
Released: 26 May 2021

Explore 6W6H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6W6H contains 207 α-helices and 124 β-strands across 7 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: 38 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	161-164	4
β-strand	165-167	3	1
α-helix	168-173	6
α-helix	184-194	11
β-strand	202-206	5	1
α-helix	213-225	13
α-helix	230-232	3
β-strand	237-240	4	1
α-helix	242-245	4
β-strand	251	1	2
α-helix	254-268	15
β-strand	274-278	5	1
α-helix	280-283	4
α-helix	301-304	4
β-strand	312-316	5	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	3
α-helix	368-376	9
α-helix	392-406	15
α-helix	416-430	15
α-helix	439-468	30
β-strand	532-533	2	3
α-helix	535-544	10
α-helix	557-568	12
α-helix	576-591	16
β-strand	602-606	5	4
α-helix	613-620	8
α-helix	628-630	3
β-strand	632-635	4	4
α-helix	642-645	4
α-helix	646-649	4
α-helix	651-652	2
β-strand	655	1	5
α-helix	665-668	4
β-strand	675-679	5	4
α-helix	681-683	3
α-helix	692-698	7
β-strand	702	1	6
β-strand	708	1	6
β-strand	715-720	6	4
α-helix	729-738	10
α-helix	741-744	4
β-strand	752	1	4
α-helix	759-761	3
α-helix	762-776	15
α-helix	777-779	3
β-strand	783-785	3	7
α-helix	787-795	9
β-strand	799	1	8
β-strand	803	1	8
α-helix	805-811	7
α-helix	812-816	5
α-helix	817-824	8
β-strand	834-836	3	7
β-strand	837-838	2	9
β-strand	843-844	2	9

Chain B: 35 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	160-163	4
β-strand	165-167	3	10
α-helix	169-172	4
α-helix	184-193	10
β-strand	202-206	5	10
α-helix	213-225	13
α-helix	230-232	3
β-strand	236-240	5	10
α-helix	243-246	4
α-helix	254-268	15
β-strand	273-278	6	10
α-helix	280-283	4
α-helix	301-306	6
β-strand	310-316	7	10
α-helix	319	1
α-helix	320-324	5
α-helix	325-327	3
β-strand	335-338	4	10
α-helix	344-361	18
β-strand	366	1	11
α-helix	369-377	9
α-helix	392-406	15
α-helix	414-430	17
α-helix	438-476	39
β-strand	533	1	11
α-helix	535-544	10
α-helix	558-562	5
α-helix	568-570	3
α-helix	576-590	15
β-strand	601-606	6	12
α-helix	615-623	9
β-strand	632-635	4	12
α-helix	642-647	6
α-helix	651-652	2
β-strand	655	1	13
α-helix	665-668	4
β-strand	676-679	4	12
α-helix	681-683	3
α-helix	689-692	4
β-strand	701	1	14
β-strand	709	1	14
β-strand	715-720	6	12
α-helix	729-738	10
β-strand	751-752	2	12
α-helix	753	1
α-helix	760-776	17
α-helix	777-779	3
β-strand	782-785	4	15
α-helix	787-796	10
α-helix	806-811	6
α-helix	812-816	5
α-helix	817-825	9
β-strand	833-836	4	15
β-strand	837-838	2	16
β-strand	843-844	2	16

Chain C: 35 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	160-164	5
β-strand	165-167	3	17
α-helix	184-193	10
β-strand	202-205	4	17
α-helix	213-225	13
α-helix	230-232	3
β-strand	238-240	3	17
α-helix	242-244	3
β-strand	251	1	18
α-helix	254-267	14
β-strand	275-278	4	17
α-helix	280-283	4
α-helix	301-304	4
β-strand	312-315	4	17
α-helix	318-321	4
α-helix	325-327	3
α-helix	328-331	4
β-strand	335-338	4	17
α-helix	340-342	3
α-helix	344-354	11
α-helix	358-361	4
β-strand	365-366	2	19
α-helix	368-377	10
α-helix	392-406	15
α-helix	414-427	14
α-helix	439-475	37
β-strand	532-533	2	19
α-helix	537-543	7
α-helix	558-562	5
α-helix	576-590	15
β-strand	601-606	6	20
α-helix	613-623	11
β-strand	632-635	4	20
α-helix	642-648	7
α-helix	665-668	4
β-strand	675-679	5	20
α-helix	681-683	3
α-helix	693-696	4
β-strand	701-702	2	21
β-strand	708-709	2	21
β-strand	715-720	6	20
α-helix	732-738	7
α-helix	741-744	4
β-strand	751-752	2	20
α-helix	753	1
α-helix	760-776	17
β-strand	783-785	3	22
α-helix	787-795	9
β-strand	799	1	23
β-strand	803	1	23
α-helix	805-811	7
α-helix	812-816	5
α-helix	817-823	7
β-strand	824	1	24
β-strand	826	1	24
α-helix	833	1
β-strand	834-836	3	22
β-strand	837-838	2	25
β-strand	843-844	2	25

Chain D: 29 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	165	1	26
α-helix	168-172	5
α-helix	184-194	11
β-strand	202-206	5	27
α-helix	212-225	14
α-helix	230-232	3
β-strand	238-239	2	27
β-strand	240	1	26
α-helix	242-244	3
α-helix	255-268	14
β-strand	275-278	4	27
α-helix	280-284	5
α-helix	301-304	4
β-strand	312-316	5	27
α-helix	317-323	7
α-helix	331-333	3
β-strand	335-338	4	27
α-helix	344-354	11
α-helix	358-361	4
β-strand	366	1	28
α-helix	368-380	13
α-helix	392-406	15
β-strand	533	1	28
α-helix	537-544	8
α-helix	557-562	6
α-helix	565-568	4
α-helix	576-591	16
β-strand	601-606	6	29
α-helix	613-625	13
β-strand	632-634	3	29
α-helix	642-647	6
α-helix	663-669	7
β-strand	675-678	4	29
α-helix	689-692	4
β-strand	701-702	2	30
β-strand	708-709	2	30
β-strand	715-720	6	29
α-helix	730-738	9
α-helix	741-744	4
β-strand	750-752	3	29
α-helix	761-775	15
β-strand	783-784	2	31
α-helix	787-795	9
α-helix	807-811	5
α-helix	812-816	5
α-helix	817-824	8
β-strand	834-835	2	31

Chain E: 32 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	170-174	5
α-helix	178-179	2
α-helix	185-194	10
β-strand	202-205	4	32
α-helix	212-225	14
α-helix	230-232	3
β-strand	237-240	4	32
α-helix	242-244	3
α-helix	257-269	13
β-strand	274-278	5	32
α-helix	280-282	3
α-helix	301-304	4
β-strand	311-315	5	32
α-helix	317-319	3
α-helix	320-324	5
α-helix	331-333	3
β-strand	335-338	4	32
α-helix	344-353	10
α-helix	356-359	4
β-strand	365	1	33
α-helix	368-381	14
α-helix	387-390	4
α-helix	404-406	3
β-strand	532	1	33
α-helix	535-546	12
α-helix	566-569	4
α-helix	576-588	13
β-strand	601	1	34
β-strand	605-606	2	35
α-helix	613-624	12
β-strand	631-635	5	34
α-helix	642-648	7
α-helix	666-669	4
β-strand	675-679	5	34
α-helix	681-683	3
α-helix	688-695	8
β-strand	700-702	3	36
β-strand	708-710	3	36
β-strand	715-718	4	34
β-strand	719-720	2	35
α-helix	729-738	10
α-helix	741-746	6
β-strand	752	1	35
α-helix	758-773	16
β-strand	784	1	37
α-helix	787-795	9
α-helix	807-811	5
α-helix	812-817	6
α-helix	818-825	8
β-strand	835	1	37

Chain F: 38 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	165-167	3	38
α-helix	169-173	5
α-helix	184-194	11
β-strand	202-206	5	38
α-helix	213-225	13
α-helix	230-232	3
β-strand	236-240	5	38
α-helix	254-268	15
β-strand	273-278	6	38
α-helix	280-284	5
α-helix	301-304	4
β-strand	312-316	5	38
α-helix	317-323	7
α-helix	324-326	3
α-helix	328-331	4
β-strand	335-338	4	38
α-helix	340-342	3
α-helix	344-354	11
α-helix	357-361	5
β-strand	365	1	39
α-helix	368-377	10
α-helix	392-407	16
α-helix	414-430	17
α-helix	438-468	31
β-strand	532	1	39
α-helix	535-544	10
α-helix	555-562	8
α-helix	565-568	4
α-helix	576-590	15
β-strand	601-606	6	40
α-helix	613-624	12
β-strand	632-635	4	40
α-helix	642-644	3
α-helix	645-649	5
α-helix	658-660	3
α-helix	664-669	6
β-strand	675-679	5	40
α-helix	681-683	3
α-helix	688-692	5
α-helix	693-695	3
β-strand	700-702	3	41
β-strand	708-710	3	41
β-strand	715-720	6	40
α-helix	729-738	10
α-helix	741-744	4
β-strand	751-752	2	40
α-helix	753-756	4
α-helix	758-761	4
α-helix	762-775	14
β-strand	782-785	4	42
α-helix	787-795	9
α-helix	805-811	7
α-helix	812-816	5
α-helix	817-823	7
β-strand	833-836	4	42

Chain N: 0 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	2
β-strand	7	1	18
β-strand	16	1	5
β-strand	18	1	13

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	31	Mycobacterium tuberculosis

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

>6W6H_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

>6W6H_2 Substrate (chains N)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Ligands and cofactors

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

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…
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
7L6N 7.0 Å, The Mycobacterium tuberculosis ClpB disaggregase hexamer structure with three locally…

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