6DJU: Mtb ClpB

Mtb ClpB in complex with ATPgammaS and casein, Conformer 1. Determined by electron microscopy at 3.8 Å resolution. Released 26 Sept 2018.

Method: Electron microscopy
Resolution: 3.8 Å
Organisms: Mycobacterium tuberculosis, Bos taurus
Chains: 7
Atoms: 27,140
Mol. weight: 564.08 kDa
Ligands: AGS, ADP
Released: 26 Sept 2018

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

Secondary structure: helices and β-sheets

6DJU contains 187 α-helices and 118 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: 33 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	160-163	4
α-helix	168-172	5
α-helix	184-194	11
β-strand	202-206	5	1
α-helix	213-225	13
β-strand	238-239	2	2
α-helix	242-245	4
α-helix	255-267	13
β-strand	275-276	2	2
α-helix	280-282	3
α-helix	301-304	4
β-strand	312	1	2
β-strand	313-316	4	1
α-helix	317-323	7
α-helix	331-333	3
β-strand	335-338	4	1
α-helix	339-341	3
α-helix	344-352	9
α-helix	355-361	7
β-strand	365-366	2	3
α-helix	368-380	13
α-helix	387-406	20
α-helix	413-430	18
α-helix	445-468	24
β-strand	532-533	2	3
α-helix	535-544	10
α-helix	558-568	11
α-helix	576-582	7
α-helix	583-585	3
α-helix	586-590	5
β-strand	601-606	6	4
α-helix	617-620	4
β-strand	632-635	4	4
α-helix	643-647	5
α-helix	651-652	2
β-strand	655	1	5
α-helix	665-667	3
β-strand	675-679	5	4
α-helix	692-695	4
β-strand	700-702	3	6
β-strand	708-710	3	6
β-strand	715-719	5	4
α-helix	730-738	9
α-helix	741-744	4
β-strand	751-752	2	4
α-helix	759-761	3
α-helix	762-775	14
β-strand	783-785	3	7
α-helix	787-795	9
α-helix	805-823	19
β-strand	834-836	3	7

Chain B: 31 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	160-162	3
α-helix	168-172	5
α-helix	184-194	11
β-strand	202-206	5	8
α-helix	213-225	13
α-helix	230-232	3
β-strand	236-239	4	9
α-helix	244-246	3
α-helix	254-268	15
β-strand	273-276	4	9
α-helix	280-282	3
α-helix	301-306	6
β-strand	310-312	3	9
β-strand	313-316	4	8
α-helix	317-323	7
α-helix	331-333	3
β-strand	335-338	4	8
α-helix	344-353	10
α-helix	355-361	7
β-strand	365-366	2	10
α-helix	368-376	9
α-helix	390-406	17
α-helix	413-430	18
α-helix	445-468	24
β-strand	532-533	2	10
α-helix	535-544	10
α-helix	558-562	5
α-helix	568-570	3
α-helix	576-578	3
α-helix	587-591	5
β-strand	601-606	6	11
β-strand	632-635	4	11
α-helix	645-647	3
β-strand	655	1	12
β-strand	676-679	4	11
α-helix	681-683	3
α-helix	688-692	5
β-strand	700-701	2	13
β-strand	709-710	2	13
β-strand	715-719	5	11
α-helix	732-738	7
α-helix	741-744	4
β-strand	751-752	2	11
α-helix	759-761	3
α-helix	762-775	14
β-strand	782-785	4	14
α-helix	787-796	10
α-helix	807-823	17
β-strand	833-836	4	14
β-strand	838	1	15
β-strand	843	1	15

Chain C: 33 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	160-164	5
α-helix	169-173	5
α-helix	178-180	3
α-helix	184-194	11
β-strand	202-206	5	16
α-helix	214-225	12
β-strand	238-239	2	16
β-strand	251	1	17
α-helix	254-268	15
β-strand	275-278	4	16
α-helix	280-283	4
α-helix	301-304	4
β-strand	312-316	5	16
α-helix	325-327	3
β-strand	335-338	4	16
α-helix	344-353	10
α-helix	357-361	5
β-strand	365-366	2	18
α-helix	368-381	14
α-helix	389-404	16
α-helix	412-430	19
α-helix	445-468	24
β-strand	532-533	2	18
α-helix	537-544	8
α-helix	558-562	5
α-helix	564-568	5
α-helix	576-578	3
α-helix	580-587	8
β-strand	601-604	4	19
β-strand	605-606	2	20
α-helix	613-625	13
β-strand	632-635	4	19
α-helix	642-648	7
α-helix	651-652	2
α-helix	664-668	5
β-strand	675-679	5	19
α-helix	693-697	5
β-strand	700-702	3	21
β-strand	708-710	3	21
β-strand	715-718	4	19
α-helix	731-738	8
α-helix	749-750	2
β-strand	751-752	2	20
α-helix	761-775	15
α-helix	776-778	3
β-strand	783-784	2	22
α-helix	787-795	9
α-helix	806-811	6
α-helix	812-816	5
α-helix	817-823	7
β-strand	824	1	23
β-strand	826	1	23
β-strand	834-835	2	22
β-strand	837-839	3	24
β-strand	842-844	3	24

Chain D: 28 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	160-162	3
β-strand	165	1	25
α-helix	168-174	7
α-helix	184-194	11
β-strand	202-206	5	26
α-helix	214-225	12
β-strand	238-239	2	26
β-strand	240	1	25
α-helix	254-268	15
β-strand	275-278	4	26
α-helix	280-282	3
α-helix	301-304	4
β-strand	312-314	3	26
β-strand	316	1	26
α-helix	317-323	7
β-strand	335-339	5	26
α-helix	344-353	10
α-helix	355-361	7
α-helix	368-377	10
α-helix	387-406	20
α-helix	537-544	8
α-helix	557-562	6
α-helix	568-570	3
α-helix	580-591	12
β-strand	605-606	2	27
α-helix	613-623	11
β-strand	632-635	4	28
α-helix	643-647	5
α-helix	651-652	2
β-strand	655	1	29
α-helix	663-669	7
β-strand	675-679	5	28
α-helix	692-695	4
β-strand	700-702	3	30
β-strand	708-710	3	30
β-strand	715-717	3	28
α-helix	732-738	7
α-helix	741-744	4
β-strand	751-752	2	27
α-helix	761-775	15
β-strand	783-784	2	31
α-helix	787-795	9
α-helix	808-811	4
α-helix	812-816	5
α-helix	817-820	4
β-strand	834-835	2	31
β-strand	837	1	32
β-strand	844	1	32

Chain E: 30 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	166-167	2	33
α-helix	170-174	5
α-helix	186-193	8
β-strand	203-205	3	34
α-helix	212-225	14
α-helix	230-232	3
β-strand	237	1	35
β-strand	238-239	2	33
α-helix	255-269	15
β-strand	274	1	35
α-helix	301-304	4
β-strand	313-315	3	34
α-helix	317-320	4
α-helix	331-333	3
β-strand	336-338	3	34
α-helix	344-353	10
α-helix	358-361	4
α-helix	368-381	14
α-helix	387-405	19
α-helix	536-546	11
α-helix	558-562	5
α-helix	568-570	3
α-helix	576-587	12
β-strand	601	1	36
β-strand	606	1	37
α-helix	615-621	7
β-strand	631-635	5	36
α-helix	646-648	3
α-helix	665-667	3
β-strand	675-679	5	36
α-helix	681-683	3
α-helix	689-695	7
β-strand	701-702	2	38
β-strand	708-709	2	38
β-strand	715-718	4	36
α-helix	730-738	9
α-helix	743-746	4
β-strand	752	1	37
α-helix	755-757	3
α-helix	759-761	3
α-helix	762-772	11
α-helix	787-790	4
α-helix	791-793	3
α-helix	794-797	4
α-helix	809-825	17

Chain F: 32 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	165	1	39
α-helix	170-174	5
α-helix	184-194	11
β-strand	203-205	3	40
β-strand	206	1	41
α-helix	212-225	14
α-helix	230-232	3
β-strand	238-239	2	42
β-strand	240	1	39
α-helix	241	1
α-helix	259-262	4
α-helix	264-267	4
β-strand	275-276	2	42
α-helix	280-282	3
α-helix	301-304	4
β-strand	312	1	42
β-strand	313	1	40
β-strand	316	1	41
α-helix	317-322	6
β-strand	336-338	3	40
α-helix	344-349	6
α-helix	351-353	3
β-strand	365	1	43
α-helix	368-374	7
α-helix	388-405	18
β-strand	532	1	43
α-helix	535-542	8
α-helix	557-561	5
α-helix	568-571	4
α-helix	576-589	14
β-strand	601-605	5	44
α-helix	613-618	6
α-helix	621-624	4
β-strand	631-633	3	44
α-helix	636-638	3
α-helix	644-647	4
α-helix	664-670	7
β-strand	675-678	4	44
α-helix	686-695	10
β-strand	715-719	5	44
α-helix	729-737	9
β-strand	750-751	2	44
α-helix	759-761	3
α-helix	762-776	15
β-strand	782-784	3	45
α-helix	787-792	6
α-helix	795-797	3
α-helix	805-810	6
α-helix	811-815	5
α-helix	816-824	9
β-strand	833-835	3	45

Chain N: 0 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	7	1	17
β-strand	16	1	5
β-strand	18	1	12
β-strand	22	1	29

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)
casein polyAlanine model	N	protein	26	Bos taurus

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

>6DJU_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

>6DJU_2 casein polyAlanine model (chains N)
AAAAAAAAAAAAAAAAAAAAAAAAAA

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

ATP hydrolysis-coupled peptide translocation mechanism ofMycobacterium tuberculosisClpB. Yu, H., Lupoli, T.J., Kovach, A. et al. Proc Natl Acad Sci U S A (2018) 115:E9560-E9569. DOI 10.1073/pnas.1810648115 · 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…
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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