Structure of the Mycobacterium tuberculosis Hsp70 protein DnaK bound to the nucleotide exchange factor GrpE. Determined by electron microscopy at 3.7 Å resolution. Released 31 Jan 2024.
Explore 8GB3 in 3D Show helices and sheets RCSB PDB PDBe
8GB3 contains 23 α-helices and 31 β-strands across 3 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.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 4-8 | 5 | 1 |
| β-strand | 15-19 | 5 | 1 |
| β-strand | 24-27 | 4 | 1 |
| α-helix | 52-60 | 9 | |
| α-helix | 89-102 | 14 | |
| α-helix | 103-105 | 3 | |
| β-strand | 113-116 | 4 | 1 |
| β-strand | 118 | 1 | 2 |
| α-helix | 124-137 | 14 | |
| β-strand | 140 | 1 | 1 |
| β-strand | 146 | 1 | 2 |
| α-helix | 147-155 | 9 | |
| β-strand | 166-170 | 5 | 3 |
| β-strand | 177-181 | 5 | 3 |
| β-strand | 194 | 1 | 3 |
| α-helix | 201-219 | 19 | |
| α-helix | 228-244 | 17 | |
| β-strand | 253 | 1 | 4 |
| β-strand | 271 | 1 | 4 |
| α-helix | 275-287 | 13 | |
| α-helix | 290-299 | 10 | |
| β-strand | 309-313 | 5 | 3 |
| α-helix | 320-329 | 10 | |
| β-strand | 336 | 1 | 3 |
| α-helix | 341-343 | 3 | |
| α-helix | 344-356 | 13 | |
| β-strand | 373-377 | 5 | 5 |
| β-strand | 381-386 | 6 | 5 |
| β-strand | 399-400 | 2 | 6 |
| β-strand | 410-416 | 7 | 5 |
| β-strand | 421 | 1 | 5 |
| β-strand | 426-433 | 8 | 5 |
| β-strand | 446-452 | 7 | 6 |
| β-strand | 458-464 | 7 | 6 |
| β-strand | 470-473 | 4 | 6 |
| α-helix | 483-495 | 13 | |
| α-helix | 502-508 | 7 | |
| α-helix | 509-511 | 3 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 45-78 | 34 | |
| α-helix | 80-93 | 14 | |
| α-helix | 96-107 | 12 | |
| α-helix | 115-128 | 14 | |
| β-strand | 141 | 1 | 7 |
| β-strand | 147 | 1 | 8 |
| β-strand | 163 | 1 | 7 |
| β-strand | 164-169 | 6 | 9 |
| β-strand | 172-174 | 3 | 10 |
| β-strand | 177-180 | 4 | 10 |
| β-strand | 182 | 1 | 8 |
| β-strand | 183-186 | 4 | 9 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 48-82 | 35 | |
| α-helix | 84-88 | 5 | |
| α-helix | 91-106 | 16 | |
| α-helix | 116-129 | 14 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Chaperone protein DnaK | D | protein | 625 | Mycobacterium tuberculosis | P9WMJ9 (AlphaFold model) |
| Protein GrpE | E, F | protein | 235 | Mycobacterium tuberculosis | P9WMT5 (AlphaFold model) |
>8GB3_1 Chaperone protein DnaK (chains D) MARAVGIDLGTTNSVVSVLEGGDPVVVANSEGSRTTPSIVAFARNGEVLVGQPAKNQAVT NVDRTVRSVKRHMGSDWSIEIDGKKYTAPEISARILMKLKRDAEAYLGEDITDAVITTPA YFNDAQRQATKDAGQIAGLNVLRIVNEPTAAALAYGLDKGEKEQRILVFDLGGGTFDVSL LEIGEGVVEVRATSGDNHLGGDDWDQRVVDWLVDKFKGTSGIDLTKDKMAMQRLREAAEK AKIELSSSQSTSINLPYITVDADKNPLFLDEQLTRAEFQRITQDLLDRTRKPFQSVIADT GISVSEIDHVVLVGGSTRMPAVTDLVKELTGGKEPNKGVNPDEVVAVGAALQAGVLKGEV KDVLLLDVTPLSLGIETKGGVMTRLIERNTTIPTKRSETFTTADDNQPSVQIQVYQGERE IAAHNKLLGSFELTGIPPAPRGIPQIEVTFDIDANGIVHVTAKDKGTGKENTIRIQEGSG LSKEDIDRMIKDAEAHAEEDRKRREEADVRNQAETLVYQTEKFVKEQREAEGGSKVPEDT LNKVDAAVAEAKAALGGSDISAIKSAMEKLGQESQALGQAIYEAAQAASQATGAAHPGGE PGGAHPGSADDVVDAEVVDDGREAK
>8GB3_2 Protein GrpE (chains E, F) MTDGNQKPDGNSGEQVTVTDKRRIDPETGEVRHVPPGDMPGGTAAADAAHTEDKVAELTA DLQRVQADFANYRKRALRDQQAAADRAKASVVSQLLGVLDDLERARKHGDLESGPLKSVA DKLDSALTGLGLVAFGAEGEDFDPVLHEAVQHEGDGGQGSKPVIGTVMRQGYQLGEQVLR HALVGVVDTVVVDAAELESVDDGTAVADTAENDQADQGNSADTSGEQAESEPSGS
Structure of the M. tuberculosis DnaK-GrpE complex reveals how key DnaK roles are controlled. Xiao, X., Fay, A., Molina, P.S. et al. Nat Commun (2024) 15:660-660. DOI 10.1038/s41467-024-44933-9 · PubMed
Other PDB entries of the same protein (UniProt P9WMJ9 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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