6DJV: Mtb ClpB

Mtb ClpB in complex with ATPgammaS and casein, Conformer 2. Determined by electron microscopy at 3.9 Å resolution. Released 26 Sept 2018.

Method: Electron microscopy
Resolution: 3.9 Å
Organisms: Mycobacterium tuberculosis, Bos taurus
Chains: 7
Atoms: 27,318
Mol. weight: 564.08 kDa
Ligands: AGS, ADP
Released: 26 Sept 2018

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

Secondary structure: helices and β-sheets

6DJV contains 180 α-helices and 133 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: 30 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	160-164	5
α-helix	168-173	6
α-helix	184-194	11
β-strand	203-205	3	1
α-helix	213-225	13
α-helix	230-232	3
β-strand	238-239	2	2
β-strand	251	1	3
α-helix	254-267	14
β-strand	275-276	2	2
α-helix	301-304	4
β-strand	312	1	2
β-strand	313-315	3	1
α-helix	318-323	6
α-helix	330-333	4
β-strand	337-338	2	1
α-helix	344-351	8
α-helix	355-361	7
β-strand	366	1	4
α-helix	368-380	13
α-helix	392-406	15
α-helix	412-430	19
α-helix	445-468	24
β-strand	533	1	4
α-helix	535-544	10
α-helix	558-561	4
α-helix	564-567	4
α-helix	568-570	3
α-helix	576-591	16
β-strand	602-606	5	5
α-helix	615-620	6
α-helix	628-630	3
β-strand	631-635	5	5
α-helix	643-648	6
β-strand	655	1	6
α-helix	665-667	3
β-strand	675-679	5	5
α-helix	688-690	3
β-strand	700-701	2	7
β-strand	709-710	2	7
β-strand	715-719	5	5
α-helix	729-738	10
α-helix	741-744	4
β-strand	751-752	2	5
α-helix	759-775	17
β-strand	783-785	3	8
α-helix	787-795	9
β-strand	799	1	9
β-strand	803	1	9
α-helix	805-823	19
β-strand	824	1	10
β-strand	826	1	10
β-strand	834-836	3	8
β-strand	837-838	2	11
β-strand	843-844	2	11

Chain B: 33 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	160-163	4
α-helix	169-172	4
α-helix	184-194	11
β-strand	202-206	5	12
α-helix	213-225	13
α-helix	230-232	3
β-strand	236-239	4	12
α-helix	244-246	3
α-helix	255-268	14
β-strand	273-278	6	12
α-helix	280-282	3
α-helix	301-306	6
β-strand	310-316	7	12
α-helix	317-323	7
α-helix	325-327	3
α-helix	330-333	4
β-strand	335-338	4	12
α-helix	340-342	3
α-helix	344-353	10
α-helix	355-361	7
β-strand	365-366	2	13
α-helix	369-377	9
α-helix	392-406	15
α-helix	412-430	19
α-helix	445-468	24
β-strand	532-533	2	13
α-helix	535-544	10
α-helix	558-562	5
α-helix	568-570	3
α-helix	576-590	15
β-strand	601-604	4	14
β-strand	605-606	2	15
β-strand	632-635	4	14
α-helix	645-647	3
α-helix	651-652	2
β-strand	655	1	16
α-helix	665-668	4
β-strand	675-679	5	14
α-helix	689-695	7
β-strand	700-701	2	17
β-strand	709-710	2	17
β-strand	715-718	4	14
α-helix	729-733	5
α-helix	735-738	4
β-strand	751-752	2	15
α-helix	760-775	16
β-strand	782-785	4	18
α-helix	787-796	10
β-strand	799	1	19
β-strand	803	1	19
α-helix	807-814	8
α-helix	816-824	9
β-strand	833-836	4	18
β-strand	837	1	20
β-strand	844	1	20

Chain C: 32 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	161-164	4
α-helix	170-173	4
α-helix	178-180	3
α-helix	184-193	10
β-strand	202-206	5	21
α-helix	213-225	13
β-strand	238	1	22
β-strand	251	1	23
α-helix	254-267	14
β-strand	275	1	22
β-strand	276-278	3	21
α-helix	280-282	3
α-helix	301-304	4
β-strand	312-316	5	21
α-helix	320-323	4
α-helix	325-327	3
β-strand	335-338	4	21
α-helix	344-351	8
α-helix	358-361	4
β-strand	365-366	2	24
α-helix	368-377	10
α-helix	392-406	15
α-helix	412-430	19
α-helix	445-468	24
β-strand	532-533	2	24
α-helix	535-543	9
α-helix	558-562	5
α-helix	568-570	3
α-helix	576-591	16
β-strand	601-606	6	25
α-helix	613-619	7
β-strand	632-635	4	25
α-helix	643-647	5
α-helix	665-667	3
β-strand	675-679	5	25
β-strand	700-702	3	26
β-strand	708-710	3	26
β-strand	715-719	5	25
α-helix	732-738	7
α-helix	741-744	4
β-strand	751-752	2	25
α-helix	758-775	18
α-helix	776-779	4
β-strand	783-785	3	27
α-helix	787-795	9
α-helix	807-811	5
α-helix	812-816	5
α-helix	817-823	7
β-strand	824	1	28
β-strand	826	1	28
α-helix	832-833	2
β-strand	834-836	3	27
β-strand	837-839	3	29
β-strand	842-844	3	29

Chain D: 29 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	166-167	2	30
α-helix	168-171	4
α-helix	184-194	11
β-strand	201	1	31
β-strand	203	1	32
β-strand	204-206	3	33
α-helix	214-224	11
α-helix	230-232	3
β-strand	238-239	2	30
α-helix	242-244	3
α-helix	255-268	14
β-strand	276-278	3	32
α-helix	280-283	4
α-helix	301-304	4
β-strand	312-314	3	32
β-strand	316	1	33
α-helix	317-319	3
α-helix	320-324	5
β-strand	334	1	31
β-strand	337-339	3	33
α-helix	344-353	10
α-helix	358-361	4
β-strand	366	1	34
α-helix	368-381	14
α-helix	392-406	15
β-strand	533	1	34
α-helix	537-544	8
α-helix	558-562	5
α-helix	565-568	4
α-helix	580-590	11
β-strand	604-606	3	35
α-helix	613-623	11
β-strand	632-635	4	35
α-helix	642-648	7
α-helix	663-669	7
β-strand	675-679	5	35
α-helix	688-690	3
α-helix	692-695	4
β-strand	700-701	2	36
β-strand	709-710	2	36
β-strand	715-719	5	35
α-helix	732-738	7
β-strand	751-752	2	35
α-helix	761-775	15
β-strand	783-784	2	37
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	37

Chain E: 29 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	171-173	3
α-helix	177-179	3
α-helix	186-194	9
β-strand	202-206	5	38
α-helix	212-225	14
α-helix	230-232	3
β-strand	236-237	2	39
α-helix	257-267	11
β-strand	273-274	2	39
β-strand	275-278	4	38
α-helix	280-282	3
α-helix	301-304	4
β-strand	311-316	6	38
α-helix	317-320	4
β-strand	335-338	4	38
α-helix	344-353	10
β-strand	365	1	40
α-helix	368-381	14
α-helix	387-390	4
α-helix	401-406	6
β-strand	532	1	40
α-helix	535-546	12
α-helix	576-585	10
α-helix	589-591	3
β-strand	601	1	41
β-strand	606	1	42
α-helix	615-624	10
β-strand	631-635	5	41
α-helix	645-648	4
α-helix	665-667	3
β-strand	675-679	5	41
α-helix	681-683	3
α-helix	689-695	7
β-strand	701-702	2	43
β-strand	708-709	2	43
β-strand	715-718	4	41
α-helix	729-738	10
α-helix	742-746	5
β-strand	752	1	42
α-helix	761-773	13
α-helix	775-777	3
β-strand	784	1	44
α-helix	787-795	9
α-helix	807-811	5
α-helix	812-816	5
α-helix	817-825	9
β-strand	835	1	44
β-strand	839	1	45
β-strand	842	1	45

Chain F: 27 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	169-173	5
α-helix	185-194	10
β-strand	203-206	4	46
α-helix	213-225	13
α-helix	230-232	3
β-strand	236-238	3	47
α-helix	254-266	13
β-strand	273-275	3	47
β-strand	276-278	3	46
α-helix	280-282	3
α-helix	301-304	4
β-strand	312-316	5	46
α-helix	319-321	3
α-helix	324-326	3
α-helix	328-331	4
β-strand	336-338	3	46
α-helix	344-353	10
α-helix	357-361	5
α-helix	368-377	10
α-helix	390-405	16
α-helix	535-542	8
α-helix	558-562	5
α-helix	568-570	3
α-helix	576-590	15
β-strand	601-606	6	48
α-helix	617-624	8
β-strand	632-635	4	48
α-helix	642-647	6
α-helix	651-652	2
α-helix	664-670	7
β-strand	675-679	5	48
α-helix	688-693	6
β-strand	700-702	3	49
β-strand	708-710	3	49
β-strand	715-719	5	48
α-helix	729-736	8
β-strand	751-752	2	48
α-helix	761-775	15
β-strand	783-784	2	50
α-helix	787-795	9
α-helix	805-823	19
β-strand	824	1	51
β-strand	826	1	51
β-strand	834-835	2	50
β-strand	837-839	3	52
β-strand	842-844	3	52

Chain N: 0 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	3
β-strand	7	1	23
β-strand	16	1	6
β-strand	18	1	16

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

>6DJV_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

>6DJV_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…
6DJU 3.8 Å, Mtb ClpB in complex with ATPgammaS and casein, Conformer 1
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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