4WQU: Thermus thermophilus 70S ribosome
Crystal structure of the Thermus thermophilus 70S ribosome in complex with elongation factor G trapped by the antibiotic dityromycin. Determined by X-ray diffraction at 2.8 Å resolution. Released 28 Jan 2015.
- Method
- X-ray diffraction
- Resolution
- 2.8 Å
- Organisms
- Thermus thermophilus HB8, Thermus thermophilus, synthetic construct
- Chains
- 118
- Atoms
- 310,038
- Mol. weight
- 4754.77 kDa
- Ligands
- MG, ZN, SF4, GDP
- Released
- 28 Jan 2015
Explore 4WQU in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
4WQU contains 521 α-helices and 778 β-strands across 104 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 A0: 2 helices, 8 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 16-18 | 3 | |
| β-strand | 22-23 | 2 | 236 |
| β-strand | 30-31 | 2 | 237 |
| β-strand | 36-39 | 4 | 236 |
| β-strand | 46-47 | 2 | 237 |
| β-strand | 51-53 | 3 | 236 |
| β-strand | 59-61 | 3 | 236 |
| β-strand | 65-71 | 7 | 237 |
| α-helix | 73-75 | 3 | |
| β-strand | 77-83 | 7 | 237 |
Chain A1: 5 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12 | 1 | |
| β-strand | 13-21 | 9 | 244 |
| α-helix | 25-27 | 3 | |
| β-strand | 33-42 | 10 | 244 |
| β-strand | 46-53 | 8 | 245 |
| β-strand | 56-63 | 8 | 245 |
| α-helix | 64-66 | 3 | |
| α-helix | 67-75 | 9 | |
| α-helix | 87-95 | 9 | |
Chain A2: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 3-14 | 12 | |
| α-helix | 18-40 | 23 | |
| α-helix | 48-69 | 22 | |
Chain A3: 3 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-8 | 6 | 1 |
| α-helix | 17-25 | 9 | |
| β-strand | 34-38 | 5 | 1 |
| α-helix | 41-49 | 9 | |
| α-helix | 51-53 | 3 | |
| β-strand | 54-59 | 6 | 1 |
Chain A4: 0 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 10-16 | 7 | 4 |
| β-strand | 21-26 | 6 | 4 |
| β-strand | 30-33 | 4 | 4 |
Chain A5: 4 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-12 | 3 | |
| α-helix | 13-19 | 7 | |
| α-helix | 20-22 | 3 | |
| α-helix | 24-29 | 6 | |
| β-strand | 31-32 | 2 | 11 |
| β-strand | 39-40 | 2 | 11 |
| β-strand | 51-52 | 2 | 12 |
| β-strand | 55-56 | 2 | 12 |
Chain A6: 1 helix, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-13 | 8 | 28 |
| β-strand | 19-26 | 8 | 28 |
| α-helix | 33-34 | 2 | |
| β-strand | 35-40 | 6 | 28 |
| β-strand | 45-52 | 8 | 28 |
Chain A7: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-16 | 8 | |
| α-helix | 18-23 | 6 | |
| α-helix | 25-36 | 12 | |
95 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 | AA, CA | RNA | 2915 | Thermus thermophilus HB8 | |
| 5S Ribosomal RNA | AB, CB | RNA | 121 | Thermus thermophilus HB8 | |
| 50S ribosomal protein L1 | AC, CC | protein | 228 | Thermus thermophilus | Q5SLP7 (AlphaFold model) |
| 50S ribosomal protein L2 | AD, CD | protein | 276 | Thermus thermophilus | P60405 (AlphaFold model) |
| 50S ribosomal protein L3 | AE, CE | protein | 206 | Thermus thermophilus | Q5SHN8 (AlphaFold model) |
| 50S ribosomal protein L4 | AF, CF | protein | 210 | Thermus thermophilus | Q5SHN9 (AlphaFold model) |
| 50S ribosomal protein L5 | AG, CG | protein | 182 | Thermus thermophilus | Q5SHQ0 |
| 50S ribosomal protein L6 | AH, CH | protein | 180 | Thermus thermophilus | P0DOY8 |
| 50S ribosomal protein L10 | AK, CK | protein | 173 | Thermus thermophilus | Q8VVE3 |
| 50S ribosomal protein L11 | AL, CL | protein | 147 | Thermus thermophilus | Q5SLP6 |
| 50S ribosomal protein L13 | AN, CN | protein | 140 | Thermus thermophilus | P60488 |
| 50S ribosomal protein L14 | AO, CO | protein | 122 | Thermus thermophilus | Q5SHP8 |
46 more molecules are not listed.
Sequence of entity 1 (AA, CA), FASTA
>4WQU_1 23S Ribosomal RNA (chains AA, CA)
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 (AB, CB), FASTA
>4WQU_2 5S Ribosomal RNA (chains AB, CB)
UCCCCCGUGCCCAUAGCGGCGUGGAACCACCCGUUCCCAUUCCGAACACGGAAGUGAAAC
GCGCCAGCGCCGAUGGUACUGGGCGGGCGACCGCCUGGGAGAGUAGGUCGGUGCGGGGGA
U
Sequence of entity 3 (AC, CC), FASTA
>4WQU_3 50S ribosomal protein L1 (chains AC, CC)
PKHGKRYRALLEKVDPNKVYTIDEAARLVKELATAKFDETVEVHAKLGIDPRRSDQNVRG
TVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMDFDAVVATPDVM
GAVGSKLGRILGPRGLLPNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASF
PPEKLADNIRAFIRALEAHKPEGAKGTFLRSVYVTTTMGPSVRINPHS
Sequence of entity 4 (AD, CD), FASTA
>4WQU_4 50S ribosomal protein L2 (chains AD, CD)
MAVKKFKPYTPSRRFMTVADFSEITKTEPEKSLVKPLKKTGGRNNQGRITVRFRGGGHKR
LYRIIDFKRWDKVGIPAKVAAIEYDPNRSARIALLHYVDGEKRYIIAPDGLQVGQQVVAG
PDAPIQVGNALPLRFIPVGTVVHAVELEPKKGAKLARAAGTSAQIQGREGDYVILRLPSG
ELRKVHGECYATVGAVGNADHKNIVLGKAGRSRWLGRRPHVRGAAMNPVDHPHGGGEGRA
PRGRPPASPWGWQTKGLKTRKRRKPSSRFIIARRKK
Sequence of entity 5 (AE, CE), FASTA
>4WQU_5 50S ribosomal protein L3 (chains AE, CE)
MKGILGVKVGMTRIFRDDRAVPVTVILAGPCPVVQRRTPEKDGYTAVQLGFLPQNPKRVN
RPLKGHFAKAGVEPVRILREIRDFNPEGDTVTVEIFKPGERVDVTGTSKGRGFAGVMKRW
NFAGGPDSHGAHKIHRHPGSIGNRKTPGRVYKGKKMAGHYGAERVTVMNLEVVDVIPEEN
LLLVKGAVPGPNGGLVIVRETKKAAK
Sequence of entity 6 (AF, CF), FASTA
>4WQU_6 50S ribosomal protein L4 (chains AF, CF)
MKEVAVYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYS
GRKIWPQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKVRKKGLAMAVADRARE
GKLLLVEAFAGVNGKTKEFLAWAKEAGLDGSESVLLVTGNELVRRAARNLPWVVTLAPEG
LNVYDIVRTERLVMDLDAWEVFQNRIGGEA
Sequence of entity 7 (AG, CG), FASTA
>4WQU_7 50S ribosomal protein L5 (chains AG, CG)
MPLDVALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDARILEKAAQEL
ALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWIFLEKLLNVALPRIRDFRGL
NPNSFDGRGNYNLGLREQLIFPEITYDMVDALRGMDIAVVTTAETDEEARALLELLGFPF
RK
Sequence of entity 8 (AH, CH), FASTA
>4WQU_8 50S ribosomal protein L6 (chains AH, CH)
MSRIGRLPIPVPKGVSVEVAPGRVKVKGPKGELEVPVSPEMRVVVEEGVVRVERPSDERR
HKSLHGLTRTLIANAVKGVSEGYSKELLIKGIGYRARLVGRALELTVGFSHPVVVEPPEG
ITFEVPEPTRVRVSGIDKQKVGQVAANIRAIRKPSAYHEKGIYYAGEPVRLKPGKAGAKK
Sequence of entity 9 (AK, CK), FASTA
>4WQU_9 50S ribosomal protein L10 (chains AK, CK)
MPNKRNVELLATLKENLERAQGSFFLVNYQGLPAKETHALRQALKQNGARLFVAKNTLIR
LALKELGLPELDGLQGPSAVVFYEDPVAAAKTLVQFAKSNPKGIPQVKSGLLQGQILTAK
DVEALAELPTMDELRAELVGVLQAPMAELVGVLGGVARELVGILEAYAEKKAA
Sequence of entity 10 (AL, CL), FASTA
>4WQU_10 50S ribosomal protein L11 (chains AL, CL)
MKKVVAVVKLQLPAGKATPAPPVGPALGQHGANIMEFVKAFNAATANMGDAIVPVEITIY
ADRSFTFVTKTPPASYLIRKAAGLEKGAHKPGREKVGRITWEQVLEIAKQKMPDLNTTDL
EAAARMIAGSARSMGVEVVGAPEVKDA
Sequence of entity 11 (AN, CN), FASTA
>4WQU_11 50S ribosomal protein L13 (chains AN, CN)
MKTYVPKQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKI
RVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRRLFKRL
KVYAGPDHPHQAQRPEKLEV
Sequence of entity 12 (AO, CO), FASTA
>4WQU_12 50S ribosomal protein L14 (chains AO, CO)
MIQPQTYLEVADNTGARKIMCIRVLKGSNAKYATVGDVIVASVKEAIPRGAVKEGDVVKA
VVVRTKKEIKRPDGSAIRFDDNAAVIINNQLEPRGTRVFGPVARELREKGFMKIVSLAPE
VL
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MG | Magnesium ion | Mg | 2040 |
| ZN | Zinc ion | Zn | 12 |
| SF4 | Iron/sulfur cluster | Fe4 S4 | 2 |
| GDP | Guanosine-5'-diphosphate | C10 H15 N5 O11 P2 | 2 |
Primary citation
Conformational Changes of Elongation Factor G on the Ribosome during tRNA Translocation. Lin, J., Gagnon, M.G., Bulkley, D. et al. Cell (2015) 160:219-227. DOI 10.1016/j.cell.2014.11.049 · 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…
- 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…
- 4U20 2.9 Å, Crystal structure of the E. coli ribosome bound to flopristin.
Browse structure collections
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