6W6G: Chaperone protein ClpB

Name: PDB 6W6G: The Mycobacterium tuberculosis ClpB disaggregase hexamer structure in conformation I in the presence of DnaK chaperone and a model substrate
Published: 2021-03-17
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: chaperone

The Mycobacterium tuberculosis ClpB disaggregase hexamer structure in conformation I in the presence of DnaK chaperone and a model substrate. Determined by electron microscopy at 3.1 Å resolution. Released 17 Mar 2021.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Mycobacterium tuberculosis
Chains: 7
Atoms: 27,581
Mol. weight: 565.04 kDa
Ligands: ADP, AGS
Released: 17 Mar 2021

Explore 6W6G in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6W6G contains 189 α-helices and 129 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: 34 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	160-164	5
β-strand	166-167	2	1
α-helix	169-173	5
α-helix	184-194	11
β-strand	202-206	5	1
α-helix	213-225	13
α-helix	230-232	3
β-strand	238-239	2	1
α-helix	242-245	4
β-strand	251	1	2
α-helix	255-268	14
β-strand	275-278	4	1
α-helix	280-282	3
α-helix	301-305	5
β-strand	312-316	5	1
α-helix	317-323	7
α-helix	328-331	4
β-strand	335-338	4	1
α-helix	344-361	18
β-strand	365-366	2	3
α-helix	368-380	13
α-helix	387-390	4
α-helix	392-406	15
α-helix	416-427	12
α-helix	438-468	31
β-strand	532-533	2	3
α-helix	537-544	8
α-helix	557-568	12
α-helix	576-590	15
β-strand	602-606	5	4
α-helix	615-623	9
β-strand	632-635	4	4
α-helix	636-638	3
α-helix	643-647	5
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	689-695	7
β-strand	700-702	3	6
β-strand	708-710	3	6
β-strand	715-720	6	4
α-helix	730-738	9
α-helix	741-744	4
β-strand	751-752	2	4
α-helix	762-775	14
β-strand	783-785	3	7
α-helix	787-796	10
α-helix	805-811	7
α-helix	812-816	5
α-helix	817-823	7
β-strand	824	1	8
β-strand	826	1	8
β-strand	834-836	3	7
β-strand	837-838	2	9
β-strand	843-844	2	9

Chain B: 33 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	160-163	4
β-strand	165-167	3	10
α-helix	168-173	6
α-helix	178-179	2
α-helix	184-194	11
β-strand	202-206	5	10
α-helix	213-225	13
α-helix	230-232	3
β-strand	236-240	5	10
α-helix	254-267	14
β-strand	273-278	6	10
α-helix	280-283	4
α-helix	301-304	4
β-strand	310-316	7	10
α-helix	320-324	5
α-helix	331-333	3
β-strand	335-339	5	10
α-helix	344-361	18
β-strand	365-366	2	11
α-helix	368-380	13
α-helix	389-406	18
α-helix	414-430	17
α-helix	442-468	27
β-strand	532-533	2	11
α-helix	537-544	8
α-helix	558-561	4
α-helix	576-590	15
β-strand	601-606	6	12
α-helix	613-624	12
β-strand	632-635	4	12
α-helix	642-647	6
β-strand	655	1	13
α-helix	665-668	4
β-strand	675-679	5	12
α-helix	681-683	3
α-helix	688-691	4
α-helix	695-698	4
β-strand	701-702	2	14
β-strand	708-709	2	14
β-strand	715-720	6	12
α-helix	732-738	7
α-helix	741-744	4
β-strand	750-752	3	12
α-helix	762-776	15
α-helix	777-779	3
β-strand	782	1	15
β-strand	785	1	16
α-helix	787-795	9
α-helix	805-811	7
α-helix	812-816	5
α-helix	817-823	7
β-strand	833	1	15
β-strand	836	1	16
β-strand	837-838	2	17
β-strand	843-844	2	17

Chain C: 35 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	161-164	4
β-strand	165-167	3	18
α-helix	168-173	6
α-helix	184-194	11
β-strand	202-206	5	19
α-helix	213-225	13
α-helix	230-232	3
β-strand	237	1	20
β-strand	238-240	3	18
β-strand	251	1	21
α-helix	254-268	15
β-strand	274	1	20
β-strand	276-278	3	19
α-helix	280-283	4
α-helix	301-306	6
β-strand	312-316	5	19
α-helix	320-323	4
α-helix	331-333	3
β-strand	335-339	5	19
α-helix	344-354	11
α-helix	357-361	5
β-strand	365-366	2	22
α-helix	368-380	13
α-helix	387-390	4
α-helix	392-406	15
α-helix	414-430	17
α-helix	438-468	31
β-strand	532-533	2	22
α-helix	537-544	8
α-helix	558-568	11
α-helix	576-590	15
β-strand	602-606	5	23
α-helix	613-625	13
α-helix	628-630	3
β-strand	632-635	4	23
α-helix	642-647	6
α-helix	651-652	2
α-helix	664-669	6
β-strand	675-679	5	23
α-helix	681-683	3
α-helix	690-692	3
α-helix	693-697	5
β-strand	700-702	3	24
β-strand	708-710	3	24
β-strand	715-720	6	23
α-helix	731-738	8
β-strand	750-752	3	23
α-helix	760-776	17
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	184-193	10
β-strand	202-206	5	28
α-helix	213-225	13
α-helix	230-232	3
β-strand	238-240	3	28
α-helix	255-268	14
β-strand	275-278	4	28
α-helix	280-283	4
α-helix	301-304	4
β-strand	312-316	5	28
α-helix	317-319	3
α-helix	320-324	5
α-helix	328-331	4
β-strand	335-338	4	28
α-helix	344-361	18
β-strand	365-366	2	29
α-helix	368-380	13
α-helix	387-406	20
β-strand	532-533	2	29
α-helix	537-544	8
α-helix	558-562	5
α-helix	576-590	15
β-strand	602-603	2	30
β-strand	604-606	3	31
α-helix	613-625	13
β-strand	632-635	4	30
α-helix	636-638	3
α-helix	642-647	6
β-strand	655	1	32
α-helix	663-669	7
β-strand	675-679	5	30
α-helix	688-690	3
α-helix	692-695	4
β-strand	701-702	2	33
β-strand	708-709	2	33
β-strand	715-718	4	30
β-strand	720	1	31
α-helix	732-738	7
α-helix	741-744	4
β-strand	750-752	3	31
α-helix	753-757	5
α-helix	761-775	15
β-strand	782-785	4	34
α-helix	787-795	9
α-helix	805-807	3
α-helix	808-811	4
α-helix	812-816	5
α-helix	817-824	8
β-strand	833-836	4	34
β-strand	837	1	35
β-strand	844	1	35

Chain E: 29 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	165	1	36
α-helix	168-174	7
α-helix	178-179	2
α-helix	186-193	8
β-strand	202-205	4	37
α-helix	212-225	14
β-strand	237-240	4	36
α-helix	242-245	4
α-helix	255-269	15
β-strand	274-277	4	36
α-helix	280-282	3
α-helix	301-304	4
β-strand	311-312	2	36
β-strand	313-315	3	37
α-helix	317-323	7
α-helix	331-333	3
β-strand	335-338	4	37
α-helix	344-353	10
α-helix	356-361	6
β-strand	366	1	38
α-helix	368-381	14
α-helix	387-405	19
β-strand	533	1	38
α-helix	536-546	11
α-helix	576-589	14
β-strand	601-604	4	39
β-strand	606	1	40
α-helix	613-624	12
β-strand	631-635	5	39
α-helix	646-648	3
α-helix	666-669	4
β-strand	675-679	5	39
α-helix	681-683	3
α-helix	688-694	7
β-strand	700-702	3	41
β-strand	708-710	3	41
β-strand	715-718	4	39
α-helix	731-738	8
α-helix	741-744	4
β-strand	752	1	40
α-helix	755-757	3
α-helix	759-761	3
α-helix	762-772	11
α-helix	787-790	4
α-helix	792-798	7
α-helix	806-825	20

Chain F: 27 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	160-162	3
α-helix	171-174	4
α-helix	184-194	11
β-strand	203-206	4	42
α-helix	212-225	14
α-helix	256-267	12
β-strand	276	1	43
α-helix	301-306	6
β-strand	312	1	43
β-strand	313-316	4	42
α-helix	317-324	8
β-strand	336-338	3	42
α-helix	344-350	7
α-helix	351-353	3
α-helix	364	1
β-strand	365	1	44
α-helix	366	1
α-helix	368-376	9
α-helix	390-405	16
β-strand	532	1	44
α-helix	535-543	9
α-helix	568-571	4
α-helix	576-589	14
β-strand	602-606	5	45
α-helix	613-624	12
β-strand	631-634	4	45
α-helix	665-670	6
β-strand	675-678	4	45
α-helix	686-695	10
β-strand	716-720	5	45
α-helix	729-738	10
β-strand	750-751	2	45
α-helix	758-761	4
α-helix	762-776	15
α-helix	777-779	3
β-strand	782-784	3	46
α-helix	787-796	10
α-helix	804-811	8
α-helix	812-817	6
α-helix	818-824	7
β-strand	833-835	3	46
β-strand	837-838	2	47
β-strand	843-844	2	47

Chain N: 0 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	2
β-strand	7	1	21
β-strand	16	1	5
β-strand	18	1	13
β-strand	22	1	32

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

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

>6W6G_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

>6W6G_2 Substrate (chains N)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

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:

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

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