6W6J: Chaperone protein ClpB
The Mycobacterium tuberculosis ClpB disaggregase hexamer structure with a locally refined N-terminal domain in the presence of DnaK chaperone and a model substrate. Determined by electron microscopy at 3.2 Å resolution. Released 26 May 2021.
- Method
- Electron microscopy
- Resolution
- 3.2 Å
- Organism
- Mycobacterium tuberculosis
- Chains
- 7
- Atoms
- 29,240
- Mol. weight
- 564.7 kDa
- Ligands
- ADP, AGS
- Released
- 26 May 2021
Explore 6W6J in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6W6J contains 216 α-helices and 115 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: 37 helices, 21 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 160-163 | 4 | |
| 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 | 237-239 | 3 | 1 |
| α-helix | 242-245 | 4 | |
| β-strand | 251 | 1 | 2 |
| α-helix | 255-268 | 14 | |
| β-strand | 274-278 | 5 | 1 |
| α-helix | 280-283 | 4 | |
| α-helix | 301-305 | 5 | |
| β-strand | 312-316 | 5 | 1 |
| α-helix | 317-323 | 7 | |
| α-helix | 325-327 | 3 | |
| α-helix | 328-331 | 4 | |
| 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 | 387-390 | 4 | |
| α-helix | 392-406 | 15 | |
| α-helix | 416-430 | 15 | |
| α-helix | 439-468 | 30 | |
| β-strand | 532-533 | 2 | 3 |
| α-helix | 536-544 | 9 | |
| α-helix | 557-560 | 4 | |
| α-helix | 564-568 | 5 | |
| α-helix | 576-590 | 15 | |
| β-strand | 602-604 | 3 | 4 |
| β-strand | 605-606 | 2 | 5 |
| α-helix | 615-625 | 11 | |
| β-strand | 632-635 | 4 | 4 |
| α-helix | 642-647 | 6 | |
| α-helix | 665-667 | 3 | |
| β-strand | 675-679 | 5 | 4 |
| α-helix | 681-683 | 3 | |
| α-helix | 688-690 | 3 | |
| α-helix | 692-695 | 4 | |
| β-strand | 700-702 | 3 | 6 |
| β-strand | 708-710 | 3 | 6 |
| β-strand | 715-718 | 4 | 4 |
| α-helix | 729-738 | 10 | |
| α-helix | 741-744 | 4 | |
| β-strand | 751-752 | 2 | 5 |
| α-helix | 758-761 | 4 | |
| α-helix | 762-775 | 14 | |
| β-strand | 784-785 | 2 | 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 | 835-836 | 2 | 7 |
Chain B: 35 helices, 21 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 165-167 | 3 | 9 |
| α-helix | 168-173 | 6 | |
| α-helix | 184-194 | 11 | |
| β-strand | 202-205 | 4 | 9 |
| α-helix | 213-225 | 13 | |
| β-strand | 236-240 | 5 | 9 |
| α-helix | 242-245 | 4 | |
| α-helix | 254-268 | 15 | |
| β-strand | 273-278 | 6 | 9 |
| α-helix | 280-283 | 4 | |
| α-helix | 300-306 | 7 | |
| β-strand | 312-315 | 4 | 9 |
| α-helix | 317-319 | 3 | |
| α-helix | 320-324 | 5 | |
| α-helix | 331-333 | 3 | |
| β-strand | 335-338 | 4 | 9 |
| α-helix | 344-361 | 18 | |
| β-strand | 366 | 1 | 10 |
| α-helix | 368-376 | 9 | |
| α-helix | 377-379 | 3 | |
| α-helix | 389-407 | 19 | |
| α-helix | 409-410 | 2 | |
| α-helix | 415-430 | 16 | |
| α-helix | 439-468 | 30 | |
| β-strand | 533 | 1 | 10 |
| α-helix | 537-544 | 8 | |
| α-helix | 557-562 | 6 | |
| α-helix | 576-582 | 7 | |
| α-helix | 584-590 | 7 | |
| β-strand | 601-604 | 4 | 11 |
| β-strand | 605-606 | 2 | 12 |
| α-helix | 616-625 | 10 | |
| β-strand | 632-635 | 4 | 11 |
| α-helix | 642-647 | 6 | |
| β-strand | 655 | 1 | 13 |
| α-helix | 665-668 | 4 | |
| β-strand | 676-679 | 4 | 11 |
| α-helix | 681-683 | 3 | |
| α-helix | 688-692 | 5 | |
| β-strand | 700-702 | 3 | 14 |
| β-strand | 708-710 | 3 | 14 |
| β-strand | 715-718 | 4 | 11 |
| α-helix | 732-735 | 4 | |
| α-helix | 741-744 | 4 | |
| β-strand | 751-752 | 2 | 12 |
| α-helix | 759-761 | 3 | |
| α-helix | 762-776 | 15 | |
| α-helix | 777-779 | 3 | |
| β-strand | 782-785 | 4 | 15 |
| α-helix | 787-795 | 9 | |
| α-helix | 806-811 | 6 | |
| α-helix | 812-816 | 5 | |
| α-helix | 817-823 | 7 | |
| 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 | 166-167 | 2 | 17 |
| α-helix | 168-173 | 6 | |
| α-helix | 184-194 | 11 | |
| β-strand | 202-205 | 4 | 17 |
| α-helix | 213-225 | 13 | |
| α-helix | 230-232 | 3 | |
| β-strand | 237-239 | 3 | 17 |
| β-strand | 251 | 1 | 18 |
| α-helix | 254-268 | 15 | |
| β-strand | 274-278 | 5 | 17 |
| α-helix | 280-282 | 3 | |
| α-helix | 301-305 | 5 | |
| β-strand | 312-315 | 4 | 17 |
| α-helix | 328-331 | 4 | |
| β-strand | 335-338 | 4 | 17 |
| α-helix | 340-342 | 3 | |
| α-helix | 344-354 | 11 | |
| α-helix | 357-361 | 5 | |
| β-strand | 365-366 | 2 | 19 |
| α-helix | 368-380 | 13 | |
| α-helix | 387-390 | 4 | |
| α-helix | 392-406 | 15 | |
| α-helix | 414-430 | 17 | |
| α-helix | 437-468 | 32 | |
| β-strand | 532-533 | 2 | 19 |
| α-helix | 537-544 | 8 | |
| α-helix | 558-568 | 11 | |
| α-helix | 576-590 | 15 | |
| β-strand | 602-603 | 2 | 20 |
| β-strand | 606 | 1 | 21 |
| α-helix | 613-625 | 13 | |
| α-helix | 628-630 | 3 | |
| 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 | 693-697 | 5 | |
| β-strand | 700-702 | 3 | 22 |
| β-strand | 708-710 | 3 | 22 |
| β-strand | 715-718 | 4 | 20 |
| β-strand | 720 | 1 | 21 |
| α-helix | 731-738 | 8 | |
| α-helix | 741-744 | 4 | |
| β-strand | 752 | 1 | 21 |
| α-helix | 755-757 | 3 | |
| α-helix | 758-776 | 19 | |
| α-helix | 777-779 | 3 | |
| β-strand | 783-785 | 3 | 23 |
| α-helix | 787-795 | 9 | |
| α-helix | 806-811 | 6 | |
| α-helix | 812-816 | 5 | |
| α-helix | 817-823 | 7 | |
| β-strand | 824 | 1 | 24 |
| β-strand | 826 | 1 | 24 |
| β-strand | 834-836 | 3 | 23 |
| β-strand | 837-838 | 2 | 25 |
| β-strand | 843-844 | 2 | 25 |
Chain D: 47 helices, 19 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-22 | 15 | |
| β-strand | 28-29 | 2 | 26 |
| α-helix | 31-39 | 9 | |
| α-helix | 47-52 | 6 | |
| α-helix | 65-67 | 3 | |
| β-strand | 82-83 | 2 | 26 |
| α-helix | 85-97 | 13 | |
| α-helix | 108-118 | 11 | |
| α-helix | 120-129 | 10 | |
| α-helix | 133-136 | 4 | |
| α-helix | 141-144 | 4 | |
| α-helix | 160-163 | 4 | |
| β-strand | 165-167 | 3 | 27 |
| α-helix | 168-173 | 6 | |
| α-helix | 184-194 | 11 | |
| β-strand | 202-206 | 5 | 27 |
| α-helix | 213-224 | 12 | |
| α-helix | 230-232 | 3 | |
| β-strand | 238-240 | 3 | 27 |
| α-helix | 255-267 | 13 | |
| β-strand | 275-278 | 4 | 27 |
| α-helix | 280-283 | 4 | |
| α-helix | 301-304 | 4 | |
| β-strand | 312-316 | 5 | 27 |
| α-helix | 317-322 | 6 | |
| α-helix | 324-326 | 3 | |
| α-helix | 328-331 | 4 | |
| β-strand | 335-338 | 4 | 27 |
| α-helix | 340-342 | 3 | |
| α-helix | 344-361 | 18 | |
| β-strand | 365-366 | 2 | 28 |
| α-helix | 368-380 | 13 | |
| α-helix | 387-406 | 20 | |
| β-strand | 532-533 | 2 | 28 |
| α-helix | 535-544 | 10 | |
| α-helix | 558-562 | 5 | |
| α-helix | 564-567 | 4 | |
| α-helix | 568-570 | 3 | |
| α-helix | 576-591 | 16 | |
| β-strand | 602-606 | 5 | 29 |
| α-helix | 613-625 | 13 | |
| β-strand | 632-635 | 4 | 29 |
| α-helix | 636-638 | 3 | |
| α-helix | 643-647 | 5 | |
| α-helix | 651-652 | 2 | |
| α-helix | 663-669 | 7 | |
| α-helix | 674 | 1 | |
| β-strand | 675-679 | 5 | 29 |
| α-helix | 689-695 | 7 | |
| β-strand | 700-702 | 3 | 30 |
| β-strand | 708-710 | 3 | 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 | 753 | 1 | |
| α-helix | 755-757 | 3 | |
| α-helix | 758-761 | 4 | |
| α-helix | 762-775 | 14 | |
| β-strand | 782-784 | 3 | 31 |
| α-helix | 787-795 | 9 | |
| α-helix | 808-811 | 4 | |
| α-helix | 812-816 | 5 | |
| α-helix | 817-820 | 4 | |
| β-strand | 833-835 | 3 | 31 |
| α-helix | 843-844 | 2 | |
Chain E: 28 helices, 14 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 167 | 1 | 32 |
| α-helix | 171-173 | 3 | |
| α-helix | 185-193 | 9 | |
| β-strand | 203-205 | 3 | 33 |
| α-helix | 212-225 | 14 | |
| β-strand | 237-240 | 4 | 32 |
| α-helix | 242-244 | 3 | |
| α-helix | 255-268 | 14 | |
| β-strand | 274-277 | 4 | 32 |
| α-helix | 280-282 | 3 | |
| α-helix | 301-304 | 4 | |
| β-strand | 313-315 | 3 | 33 |
| α-helix | 317-323 | 7 | |
| α-helix | 331-333 | 3 | |
| β-strand | 336-338 | 3 | 33 |
| α-helix | 344-353 | 10 | |
| α-helix | 356-361 | 6 | |
| α-helix | 368-381 | 14 | |
| α-helix | 387-404 | 18 | |
| α-helix | 536-546 | 11 | |
| α-helix | 558-561 | 4 | |
| α-helix | 576-589 | 14 | |
| β-strand | 602-604 | 3 | 34 |
| β-strand | 606 | 1 | 35 |
| α-helix | 613-624 | 12 | |
| β-strand | 631-633 | 3 | 34 |
| α-helix | 643-648 | 6 | |
| β-strand | 675-677 | 3 | 34 |
| α-helix | 681-683 | 3 | |
| α-helix | 688-697 | 10 | |
| β-strand | 701-702 | 2 | 36 |
| β-strand | 708-709 | 2 | 36 |
| β-strand | 715-718 | 4 | 34 |
| α-helix | 730-738 | 9 | |
| β-strand | 752 | 1 | 35 |
| α-helix | 753-757 | 5 | |
| α-helix | 762-772 | 11 | |
| α-helix | 775-777 | 3 | |
| α-helix | 787-792 | 6 | |
| α-helix | 794-797 | 4 | |
| α-helix | 809-819 | 11 | |
| α-helix | 822-825 | 4 | |
Chain F: 34 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 171-174 | 4 | |
| α-helix | 184-194 | 11 | |
| β-strand | 203-206 | 4 | 37 |
| α-helix | 212-225 | 14 | |
| α-helix | 258-268 | 11 | |
| β-strand | 276-278 | 3 | 37 |
| α-helix | 280-282 | 3 | |
| α-helix | 302-305 | 4 | |
| β-strand | 312-316 | 5 | 37 |
| α-helix | 317-324 | 8 | |
| α-helix | 331-333 | 3 | |
| β-strand | 336-338 | 3 | 37 |
| α-helix | 344-358 | 15 | |
| α-helix | 368-374 | 7 | |
| α-helix | 378-381 | 4 | |
| α-helix | 387-406 | 20 | |
| α-helix | 416-427 | 12 | |
| α-helix | 439-468 | 30 | |
| α-helix | 536-543 | 8 | |
| α-helix | 558-562 | 5 | |
| α-helix | 564-567 | 4 | |
| α-helix | 568-570 | 3 | |
| α-helix | 576-583 | 8 | |
| α-helix | 587-590 | 4 | |
| β-strand | 601-606 | 6 | 38 |
| α-helix | 615-625 | 11 | |
| α-helix | 628-630 | 3 | |
| β-strand | 632-635 | 4 | 38 |
| α-helix | 642-647 | 6 | |
| α-helix | 651-652 | 2 | |
| α-helix | 665-668 | 4 | |
| β-strand | 675-679 | 5 | 38 |
| α-helix | 681-683 | 3 | |
| α-helix | 689-698 | 10 | |
| β-strand | 700-702 | 3 | 39 |
| β-strand | 708-710 | 3 | 39 |
| β-strand | 715-720 | 6 | 38 |
| α-helix | 729-738 | 10 | |
| β-strand | 751-752 | 2 | 38 |
| α-helix | 758-760 | 3 | |
| α-helix | 762-775 | 14 | |
| β-strand | 783-784 | 2 | 40 |
| α-helix | 787-796 | 10 | |
| α-helix | 805-811 | 7 | |
| α-helix | 812-816 | 5 | |
| α-helix | 817-823 | 7 | |
| β-strand | 834-835 | 2 | 40 |
Chain N: 0 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3 | 1 | 2 |
| β-strand | 7 | 1 | 18 |
| 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 | 29 | Mycobacterium tuberculosis | |
Sequence of entity 1 (A, B, C, D, E, F), FASTA
>6W6J_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
>6W6J_2 Substrate (chains N)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXX
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…
- 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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