6ED3: Mtb ClpB

Mtb ClpB in complex with AMPPNP. Determined by electron microscopy at 6.3 Å resolution. Released 26 Sept 2018.

Method: Electron microscopy
Resolution: 6.3 Å
Organism: Mycobacterium tuberculosis
Chains: 6
Atoms: 12,768
Mol. weight: 556.13 kDa
Released: 26 Sept 2018

Explore 6ED3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6ED3 contains 168 α-helices and 111 β-strands across 6 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: 28 helices, 16 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	1
α-helix	213-225	13
α-helix	230-232	3
α-helix	255-267	13
α-helix	280-282	3
α-helix	301-306	6
β-strand	313-316	4	1
α-helix	317-323	7
α-helix	331-333	3
β-strand	335-338	4	1
α-helix	344-353	10
α-helix	355-361	7
β-strand	365-366	2	2
α-helix	368-376	9
α-helix	390-406	17
β-strand	532-533	2	2
α-helix	535-544	10
α-helix	559-562	4
α-helix	568-570	3
α-helix	576-578	3
α-helix	587-591	5
β-strand	601-606	6	3
β-strand	632-635	4	3
α-helix	645-647	3
β-strand	676-679	4	3
α-helix	681-683	3
α-helix	688-692	5
β-strand	700-701	2	4
β-strand	709-710	2	4
β-strand	715-719	5	3
α-helix	732-738	7
α-helix	741-744	4
β-strand	751-752	2	3
α-helix	759-761	3
α-helix	762-775	14
β-strand	782-785	4	5
α-helix	787-796	10
α-helix	807-823	17
β-strand	833-836	4	5
β-strand	838	1	6
β-strand	843	1	6

Chains B, C, D and E: 28 helices, 19 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	7
α-helix	213-225	13
α-helix	230-232	3
β-strand	236-239	4	8
α-helix	255-268	14
β-strand	273-276	4	8
α-helix	280-282	3
α-helix	301-306	6
β-strand	310-312	3	8
β-strand	313-316	4	7
α-helix	317-323	7
α-helix	331-333	3
β-strand	335-338	4	7
α-helix	344-353	10
α-helix	355-361	7
β-strand	365-366	2	9
α-helix	368-376	9
α-helix	390-406	17
β-strand	532-533	2	9
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	10
β-strand	632-635	4	10
α-helix	645-647	3
β-strand	676-679	4	10
α-helix	681-683	3
α-helix	688-692	5
β-strand	700-701	2	11
β-strand	709-710	2	11
β-strand	715-719	5	10
α-helix	732-738	7
α-helix	741-744	4
β-strand	751-752	2	10
α-helix	759-761	3
α-helix	762-775	14
β-strand	782-785	4	12
α-helix	787-796	10
α-helix	807-823	17
β-strand	833-836	4	12
β-strand	838	1	13
β-strand	843	1	13

Chain F: 28 helices, 19 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	35
α-helix	213-225	13
α-helix	230-232	3
β-strand	236-239	4	36
α-helix	255-268	14
β-strand	273-276	4	36
α-helix	280-282	3
α-helix	301-306	6
β-strand	310-312	3	36
β-strand	313-316	4	35
α-helix	317-323	7
α-helix	331-333	3
β-strand	335-338	4	35
α-helix	345-353	9
α-helix	355-361	7
β-strand	365-366	2	37
α-helix	368-376	9
α-helix	390-406	17
β-strand	532-533	2	37
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	38
β-strand	632-635	4	38
α-helix	645-647	3
β-strand	676-679	4	38
α-helix	681-683	3
α-helix	688-692	5
β-strand	700-701	2	39
β-strand	709-710	2	39
β-strand	715-719	5	38
α-helix	732-738	7
α-helix	741-744	4
β-strand	751-752	2	38
α-helix	759-761	3
α-helix	762-775	14
β-strand	782-785	4	40
α-helix	787-796	10
α-helix	807-823	17
β-strand	833-836	4	40
β-strand	838	1	41
β-strand	843	1	41

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)

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

>6ED3_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

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
6DJV 3.9 Å, Mtb ClpB in complex with ATPgammaS and casein, Conformer 2
7L6N 7.0 Å, The Mycobacterium tuberculosis ClpB disaggregase hexamer structure with three locally…

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