5HAU: Antimicrobial peptide Bac7(1-19)
Crystal structure of antimicrobial peptide Bac7(1-19) bound to the Thermus thermophilus 70S ribosome. Determined by X-ray diffraction at 3.0 Å resolution. Released 6 Apr 2016.
- Method
- X-ray diffraction
- Resolution
- 3.0 Å
- Organisms
- Thermus thermophilus HB8, Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579), Thermus thermophilus
- Chains
- 116
- Atoms
- 306,384
- Mol. weight
- 4713.15 kDa
- Ligands
- MG, ZN, SF4, GDP
- Released
- 6 Apr 2016
Explore 5HAU in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5HAU contains 540 α-helices and 753 β-strands across 106 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 10: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-13 | 11 | |
| α-helix | 18-41 | 24 | |
| α-helix | 48-67 | 20 | |
Chains 11 and 21: 2 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-8 | 6 | 1 |
| α-helix | 17-26 | 10 | |
| β-strand | 34-38 | 5 | 1 |
| α-helix | 41-49 | 9 | |
| β-strand | 54-59 | 6 | 1 |
Chains 12 and 22: 1 helix, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-8 | 2 | |
| β-strand | 10-16 | 7 | 5 |
| β-strand | 21-26 | 6 | 5 |
| β-strand | 30-33 | 4 | 5 |
Chain 13: 4 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-12 | 3 | |
| α-helix | 13-19 | 7 | |
| α-helix | 20-22 | 3 | |
| α-helix | 27-29 | 3 | |
| β-strand | 31-32 | 2 | 14 |
| β-strand | 39-40 | 2 | 14 |
| β-strand | 44-45 | 2 | 146 |
| β-strand | 51-52 | 2 | 15 |
| β-strand | 55-56 | 2 | 15 |
Chain 14: 1 helix, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-13 | 8 | 42 |
| β-strand | 19-26 | 8 | 42 |
| α-helix | 33-34 | 2 | |
| β-strand | 35-40 | 6 | 42 |
| β-strand | 45-52 | 8 | 42 |
Chain 15: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-16 | 8 | |
| α-helix | 18-22 | 5 | |
| α-helix | 25-37 | 13 | |
Chain 16: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 8-11 | 4 | |
| β-strand | 15-16 | 2 | 55 |
| β-strand | 22-25 | 4 | 55 |
| α-helix | 26 | 1 | |
| α-helix | 38-44 | 7 | |
| β-strand | 47-49 | 3 | 55 |
| α-helix | 52-60 | 9 | |
Chains 17 and 27: 1 helix, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 61 |
| β-strand | 15-19 | 5 | 61 |
| β-strand | 22-26 | 5 | 61 |
| α-helix | 30-32 | 3 | |
| β-strand | 34-36 | 3 | 61 |
89 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| 23S Ribosomal RNA | 1A, 2A | RNA | 2915 | Thermus thermophilus HB8 | |
| 5S Ribosomal RNA | 1B, 2B | RNA | 121 | Thermus thermophilus HB8 | |
| 50S ribosomal protein L1 | 1C, 2C | protein | 229 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Q5SLP7 (AlphaFold model) |
| 50S ribosomal protein L2 | 1D, 2D | protein | 276 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | P60405 (AlphaFold model) |
| 50S ribosomal protein L3 | 1E, 2E | protein | 206 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Q5SHN8 (AlphaFold model) |
| 50S ribosomal protein L4 | 1F, 2F | protein | 210 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Q5SHN9 (AlphaFold model) |
| 50S ribosomal protein L5 | 1G, 2G | protein | 182 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Q5SHQ0 |
| 50S ribosomal protein L6 | 1H, 2H | protein | 180 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | P0DOY8 |
| 50S ribosomal protein L10 | 1J, 2J | protein | 173 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Q8VVE3 |
| 50S ribosomal protein L11 | 1K, 2K | protein | 147 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Q5SLP6 |
| 50S ribosomal protein L13 | 1L, 2L | protein | 140 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | P60488 |
| 50S ribosomal protein L14 | 1M, 2M | protein | 122 | Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) | Q5SHP8 |
46 more molecules are not listed.
Sequence of entity 1 (1A, 2A), FASTA
>5HAU_1 23S Ribosomal RNA (chains 1A, 2A)
GUCAAGAUGGUAAGGGCCCACGGUGGAUGCCUCGGCACCCGAGCCGAUGAAGGACGUGGC
UACCUGCGAUAAGCCAGGGGGAGCCGGUAGCGGGCGUGGAUCCCUGGAUGUCCGAAUGGG
GGAACCCGGCCGGCGGGAACGCCGGUCACCGCGCUUUUGCGCGGGGGGAACCUGGGGAAC
UGAAACAUCUCAGUACCCAGAGGAGAGGAAAGAGAAAUCGACUCCCUGAGUAGCGGCGAG
CGAAAGGGGACCAGCCUAAACCGUCCGGCUUGUCCGGGCGGGGUCGUGGGGCCCUCGGAC
ACCGAAUCCCCAGCCUAGCCGAAGCUGUUGGGAAGCAGCGCCAGAGAGGGUGAAAGCCCC
GUAGGCGAAAGGUGGGGGGAUAGGUGAGGGUACCCGAGUACCCCGUGGUUCGUGGAGCCA
UGGGGGAAUCUGGGCGGACCACCGCCUAAGGCUAAGUACUCCGGGUGACCGAUAGCGCAC
CAGUACCGUGAGGGAAAGGUGAAAAGAACCCCGGGAGGGGAGUGAAAUAGAGCCUGAAAC
CGUGGGCUUACAAGCAGUCACGGCCCCGCAAGGGGUUGUGGCGUGCCUAUUGAAGCAUGA
GCCGGCGACUCACGGUCGUGGGCGAGCUUAAGCCGUUGAGGCGGAGGCGUAGGGAAACCG
AGUCCGAACAGGGCGCAAGCGGGCCGCACGCGGCCCGCAAAGUCCGCGGCCGUGGACCCG
AAACCGGGCGAGCUAGCCCUGGCCAGGGUGAAGCUGGGGUGAGACCCAGUGGAGGCCCGA
ACCGGUGGGGGAUGCAAACCCCUCGGAUGAGCUGGGGCUAGGAGUGAAAAGCUAACCGAG
CCCGGAGAUAGCUGGUUCUCCCCGAAAUGACUUUAGGGUCAGCCUCAGGCGCUGACUGGG
GCCUGUAGAGCACUGAUAGGGCUAGGGGGCCCACCAGCCUACCAAACCCUGUCAAACUCC
GAAGGGUCCCAGGUGGAGCCUGGGAGUGAGGGCGCGAGCGAUAACGUCCGCGUCCGAGCG
CGGGAACAACCGAGACCGCCAGCUAAGGCCCCCAAGUCUGGGCUAAGUGGUAAAGGAUGU
GGCGCCGCGAAGACAGCCAGGAGGUUGGCUUAGAAGCAGCCAUCCUUUAAAGAGUGCGUA
AUAGCUCACUGGUCGAGUGGCGCCGCGCCGAAAAUGAUCGGGGCUUAAGCCCAGCGCCGA
AGCUGCGGGUCUGGGGGAUGACCCCAGGCGGUAGGGGAGCGUUCCCGAUGCCGAUGAAGG
CCGACCCGCGAGGGCGGCUGGAGGUAAGGGAAGUGCGAAUGCCGGCAUGAGUAACGAUAA
AGAGGGUGAGAAUCCCUCUCGCCGUAAGCCCAAGGGUUCCUACGCAAUGGUCGUCAGCGU
AGGGUUAGGCGGGACCUAAGGUGAAGCCGAAAGGCGUAGCCGAAGGGCAGCCGGUUAAUA
UUCCGGCCCUUCCCGCAGGUGCGAUGGGGGGACGCUCUAGGCUAGGGGGACCGGAGCCAU
GGACGAGCCCGGCCAGAAGCGCAGGGUGGGAGGUAGGCAAAUCCGCCUCCCAACAAGCUC
UGCGUGGUGGGGAAGCCCGUACGGGUGACAACCCCCCGAAGCCAGGGAGCCAAGAAAAGC
CUCUAAGCACAACCUGCGGGAACCCGUACCGCAAACCGACACAGGUGGGCGGGUGCAAGA
GCACUCAGGCGCGCGGGAGAACCCUCGCCAAGGAACUCUGCAAGUUGGCCCCGUAACUUC
GGGAGAAGGGGUGCUCCCUGGGGUGAUGAGCCCCGGGGAGCCGCAGUGAACAGGCUCUGG
CGACUGUUUACCAAAAACACAGCUCUCUGCGAACUCGUAAGAGGAGGUAUAGGGAGCGAC
GCUUGCCCGGUGCCGGAAGGUCAAGGGGAGGGGUGCAAGCCCCGAACCGAAGCCCCGGUG
AACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCG
ACCUGCACGAAAAGCGUAACGACCGGAGCGCUGUCUCGGCGAGGGACCCGGUGAAAUUGA
ACUGGCCGUGAAGAUGCGGCCUACCCGUGGCAGGACGAAAAGACCCCGUGGAGCUUUACU
GCAGCCUGGUGUUGGCUCUUGGUCGCGCCUGCGUAGGAUAGGUGGGAGCCUGUGAACCCC
CGCCUCCGGGUGGGGGGGAGGCGCCGGUGAAAUACCACCCUGGCGCGGCUGGGGGCCUAA
CCCUCGGAUGGGGGGACAGCGCUUGGCGGGCAGUUUGACUGGGGCGGUCGCCUCCUAAAA
GGUAACGGAGGCGCCCAAAGGUCCCCUCAGGCGGGACGGAAAUCCGCCGGAGAGCGCAAG
GGUAGAAGGGGGCCUGACUGCGAGGCCUGCAAGCCGAGCAGGGGCGAAAGCCGGGCCUAG
UGAACCGGUGGUCCCGUGUGGAAGGGCCAUCGAUCAACGGAUAAAAGUUACCCCGGGGAU
AACAGGCUGAUCUCCCCCGAGCGUCCACAGCGGCGGGGAGGUUUGGCACCUCGAUGUCGG
CUCGUCGCAUCCUGGGGCUGAAGAAGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCG
GCACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCUCUAUCCGCCACGGGCGCA
GGAGGCUUGAGGGGGGCUCUUCCUAGUACGAGAGGACCGGAAGGGACGCACCUCUGGUUU
CCCAGCUGUCCCUCCAGGGGCAUAAGCUGGGUAGCCAUGUGCGGAAGGGAUAACCGCUGA
AAGCAUCUAAGCGGGAAGCCCGCCCCAAGAUGAGGCCUCCCACGGCGUCAAGCCGGUAAG
GACCCGGGAAGACCACCCGGUGGAUGGGCCGGGGGUGUAAGCGCCGCGAGGCGUUGAGCC
GACCGGUCCCAAUCGUCCGAGGUCUUGACCCCUCC
Sequence of entity 2 (1B, 2B), FASTA
>5HAU_2 5S Ribosomal RNA (chains 1B, 2B)
UCCCCCGUGCCCAUAGCGGCGUGGAACCACCCGUUCCCAUUCCGAACACGGAAGUGAAAC
GCGCCAGCGCCGAUGGUACUGGGCGGGCGACCGCCUGGGAGAGUAGGUCGGUGCGGGGGA
U
Sequence of entity 3 (1C, 2C), FASTA
>5HAU_3 50S ribosomal protein L1 (chains 1C, 2C)
MPKHGKRYRALLEKVDPNKVYTIDEAARLVKELATAKFDETVEVHAKLGIDPRRSDQNVR
GTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMDFDAVVATPDV
MGAVGSKLGRILGPRGLLPNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKAS
FPPEKLADNIRAFIRALEAHKPEGAKGTFLRSVYVTTTMGPSVRINPHS
Sequence of entity 4 (1D, 2D), FASTA
>5HAU_4 50S ribosomal protein L2 (chains 1D, 2D)
MAVKKFKPYTPSRRFMTVADFSEITKTEPEKSLVKPLKKTGGRNNQGRITVRFRGGGHKR
LYRIIDFKRWDKVGIPAKVAAIEYDPNRSARIALLHYVDGEKRYIIAPDGLQVGQQVVAG
PDAPIQVGNALPLRFIPVGTVVHAVELEPKKGAKLARAAGTSAQIQGREGDYVILRLPSG
ELRKVHGECYATVGAVGNADHKNIVLGKAGRSRWLGRRPHVRGAAMNPVDHPHGGGEGRA
PRGRPPASPWGWQTKGLKTRKRRKPSSRFIIARRKK
Sequence of entity 5 (1E, 2E), FASTA
>5HAU_5 50S ribosomal protein L3 (chains 1E, 2E)
MKGILGVKVGMTRIFRDDRAVPVTVILAGPCPVVQRRTPEKDGYTAVQLGFLPQNPKRVN
RPLKGHFAKAGVEPVRILREIRDFNPEGDTVTVEIFKPGERVDVTGTSKGRGFAGVMKRW
NFAGGPDSHGAHKIHRHPGSIGNRKTPGRVYKGKKMAGHYGAERVTVMNLEVVDVIPEEN
LLLVKGAVPGPNGGLVIVRETKKAAK
Sequence of entity 6 (1F, 2F), FASTA
>5HAU_6 50S ribosomal protein L4 (chains 1F, 2F)
MKEVAVYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYS
GRKIWPQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKVRKKGLAMAVADRARE
GKLLLVEAFAGVNGKTKEFLAWAKEAGLDGSESVLLVTGNELVRRAARNLPWVVTLAPEG
LNVYDIVRTERLVMDLDAWEVFQNRIGGEA
Sequence of entity 7 (1G, 2G), FASTA
>5HAU_7 50S ribosomal protein L5 (chains 1G, 2G)
MPLDVALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDARILEKAAQEL
ALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWIFLEKLLNVALPRIRDFRGL
NPNSFDGRGNYNLGLREQLIFPEITYDMVDALRGMDIAVVTTAETDEEARALLELLGFPF
RK
Sequence of entity 8 (1H, 2H), FASTA
>5HAU_8 50S ribosomal protein L6 (chains 1H, 2H)
MSRIGRLPIPVPKGVSVEVAPGRVKVKGPKGELEVPVSPEMRVVVEEGVVRVERPSDERR
HKSLHGLTRTLIANAVKGVSEGYSKELLIKGIGYRARLVGRALELTVGFSHPVVVEPPEG
ITFEVPEPTRVRVSGIDKQKVGQVAANIRAIRKPSAYHEKGIYYAGEPVRLKPGKAGAKK
Sequence of entity 9 (1J, 2J), FASTA
>5HAU_9 50S ribosomal protein L10 (chains 1J, 2J)
MPNKRNVELLATLKENLERAQGSFFLVNYQGLPAKETHALRQALKQNGARLFVAKNTLIR
LALKELGLPELDGLQGPSAVVFYEDPVAAAKTLVQFAKSNPKGIPQVKSGLLQGQILTAK
DVEALAELPTMDELRAELVGVLQAPMAELVGVLGGVARELVGILEAYAEKKAA
Sequence of entity 10 (1K, 2K), FASTA
>5HAU_10 50S ribosomal protein L11 (chains 1K, 2K)
MKKVVAVVKLQLPAGKATPAPPVGPALGQHGANIMEFVKAFNAATANMGDAIVPVEITIY
ADRSFTFVTKTPPASYLIRKAAGLEKGAHKPGREKVGRITWEQVLEIAKQKMPDLNTTDL
EAAARMIAGSARSMGVEVVGAPEVKDA
Sequence of entity 11 (1L, 2L), FASTA
>5HAU_11 50S ribosomal protein L13 (chains 1L, 2L)
MKTYVPKQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKI
RVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRRLFKRL
KVYAGPDHPHQAQRPEKLEV
Sequence of entity 12 (1M, 2M), FASTA
>5HAU_12 50S ribosomal protein L14 (chains 1M, 2M)
MIQPQTYLEVADNTGARKIMCIRVLKGSNAKYATVGDVIVASVKEAIPRGAVKEGDVVKA
VVVRTKKEIKRPDGSAIRFDDNAAVIINNQLEPRGTRVFGPVARELREKGFMKIVSLAPE
VL
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 1929 |
| ZN | Zinc ion | Zn | 12 |
| SF4 | Iron/sulfur cluster | Fe4 S4 | 2 |
| GDP | Guanosine-5'-diphosphate | C10 H15 N5 O11 P2 | 2 |
Primary citation
Structures of proline-rich peptides bound to the ribosome reveal a common mechanism of protein synthesis inhibition. Gagnon, M.G., Roy, R.N., Lomakin, I.B. et al. Nucleic Acids Res (2016) 44:2439-2450. DOI 10.1093/nar/gkw018 · PubMed
Other PDB entries of the same protein (UniProt Q5SLP7 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 3TG8 1.95 Å, Mutant ribosomal protein L1 lacking ala158 from thermus thermophilus
- 2OV7 2.3 Å, The first domain of the ribosomal protein L1 from Thermus thermophilus
- 2OUM 2.55 Å, The first domain of L1 from Thermus thermophilus
- 5NPM 2.7 Å, Crystal structure of mutant ribosomal protein TTHL1 lacking 8 N-terminal residues in…
- 4U26 2.8 Å, Crystal structure of the E. coli ribosome bound to dalfopristin and quinupristin.
- 4U27 2.8 Å, Crystal structure of the E. coli ribosome bound to flopristin and linopristin.
- 4V51 2.8 Å, Structure of the Thermus thermophilus 70S ribosome complexed with mRNA, tRNA and…
- 4WPO 2.8 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with elongation…
- 4WQF 2.8 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with elongation…
- 4WQU 2.8 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with elongation…
- 4WQY 2.8 Å, Crystal structure of the Thermus thermophilus 70S ribosome in complex with elongation…
- 4V9H 2.86 Å, Crystal structure of the ribosome bound to elongation factor G in the guanosine…
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