4WPO: Thermus thermophilus 70S ribosome

Name: PDB 4WPO: Crystal structure of the Thermus thermophilus 70S ribosome in complex with elongation factor G in the pre-translocational state
Published: 2015-01-28
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Crystal structure of the Thermus thermophilus 70S ribosome in complex with elongation factor G in the pre-translocational state. 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: 313,372
Mol. weight: 4806.77 kDa
Ligands: MG, ZN, SF4, GDP
Released: 28 Jan 2015

Explore 4WPO in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4WPO contains 536 α-helices and 772 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	232
β-strand	30-31	2	233
β-strand	36-39	4	232
β-strand	45-47	3	233
β-strand	51-53	3	232
β-strand	59-61	3	232
β-strand	65-71	7	233
α-helix	73-75	3
β-strand	77-83	7	233

Chain A1: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	13-21	9	237
α-helix	25-27	3
β-strand	33-42	10	237
β-strand	46-53	8	238
β-strand	56-63	8	238
α-helix	64-66	3
α-helix	67-76	10
α-helix	87-95	9

Chain A2: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	3-13	11
α-helix	18-40	23
α-helix	48-68	21

Chains A3 and C3: 3 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
α-helix	51-53	3
β-strand	54-59	6	1

Chain A4: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
β-strand	10-16	7	4
β-strand	21-26	6	4
β-strand	30-33	4	4
α-helix	37-39	3

Chains A5 and C5: 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	27-29	3
β-strand	31-32	2	12
β-strand	39-40	2	12
β-strand	51-52	2	13
β-strand	55-56	2	13

Chain A6: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	6-13	8	29
β-strand	19-26	8	29
α-helix	33-34	2
β-strand	35-40	6	29
β-strand	45-53	9	29

Chain A7: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-16	8
α-helix	18-22	5
α-helix	25-37	13

91 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

47 more molecules are not listed.

Sequence of entity 1 (AA, CA), FASTA

>4WPO_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

>4WPO_2 5S Ribosomal RNA (chains AB, CB)
UCCCCCGUGCCCAUAGCGGCGUGGAACCACCCGUUCCCAUUCCGAACACGGAAGUGAAAC
GCGCCAGCGCCGAUGGUACUGGGCGGGCGACCGCCUGGGAGAGUAGGUCGGUGCGGGGGA
U

Sequence of entity 3 (AC, CC), FASTA

>4WPO_3 50S ribosomal protein L1 (chains AC, CC)
PKHGKRYRALLEKVDPNKVYTIDEAARLVKELATAKFDETVEVHAKLGIDPRRSDQNVRG
TVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMDFDAVVATPDVM
GAVGSKLGRILGPRGLLPNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASF
PPEKLADNIRAFIRALEAHKPEGAKGTFLRSVYVTTTMGPSVRINPHS

Sequence of entity 4 (AD, CD), FASTA

>4WPO_4 50S ribosomal protein L2 (chains AD, CD)
MAVKKFKPYTPSRRFMTVADFSEITKTEPEKSLVKPLKKTGGRNNQGRITVRFRGGGHKR
LYRIIDFKRWDKVGIPAKVAAIEYDPNRSARIALLHYVDGEKRYIIAPDGLQVGQQVVAG
PDAPIQVGNALPLRFIPVGTVVHAVELEPKKGAKLARAAGTSAQIQGREGDYVILRLPSG
ELRKVHGECYATVGAVGNADHKNIVLGKAGRSRWLGRRPHVRGAAMNPVDHPHGGGEGRA
PRGRPPASPWGWQTKGLKTRKRRKPSSRFIIARRKK

Sequence of entity 5 (AE, CE), FASTA

>4WPO_5 50S ribosomal protein L3 (chains AE, CE)
MKGILGVKVGMTRIFRDDRAVPVTVILAGPCPVVQRRTPEKDGYTAVQLGFLPQNPKRVN
RPLKGHFAKAGVEPVRILREIRDFNPEGDTVTVEIFKPGERVDVTGTSKGRGFAGVMKRW
NFAGGPDSHGAHKIHRHPGSIGNRKTPGRVYKGKKMAGHYGAERVTVMNLEVVDVIPEEN
LLLVKGAVPGPNGGLVIVRETKKAAK

Sequence of entity 6 (AF, CF), FASTA

>4WPO_6 50S ribosomal protein L4 (chains AF, CF)
MKEVAVYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYS
GRKIWPQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKVRKKGLAMAVADRARE
GKLLLVEAFAGVNGKTKEFLAWAKEAGLDGSESVLLVTGNELVRRAARNLPWVVTLAPEG
LNVYDIVRTERLVMDLDAWEVFQNRIGGEA

Sequence of entity 7 (AG, CG), FASTA

>4WPO_7 50S ribosomal protein L5 (chains AG, CG)
MPLDVALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDARILEKAAQEL
ALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWIFLEKLLNVALPRIRDFRGL
NPNSFDGRGNYNLGLREQLIFPEITYDMVDALRGMDIAVVTTAETDEEARALLELLGFPF
RK

Sequence of entity 8 (AH, CH), FASTA

>4WPO_8 50S ribosomal protein L6 (chains AH, CH)
MSRIGRLPIPVPKGVSVEVAPGRVKVKGPKGELEVPVSPEMRVVVEEGVVRVERPSDERR
HKSLHGLTRTLIANAVKGVSEGYSKELLIKGIGYRARLVGRALELTVGFSHPVVVEPPEG
ITFEVPEPTRVRVSGIDKQKVGQVAANIRAIRKPSAYHEKGIYYAGEPVRLKPGKAGAKK

Sequence of entity 9 (AK, CK), FASTA

>4WPO_9 50S ribosomal protein L10 (chains AK, CK)
MPNKRNVELLATLKENLERAQGSFFLVNYQGLPAKETHALRQALKQNGARLFVAKNTLIR
LALKELGLPELDGLQGPSAVVFYEDPVAAAKTLVQFAKSNPKGIPQVKSGLLQGQILTAK
DVEALAELPTMDELRAELVGVLQAPMAELVGVLGGVARELVGILEAYAEKKAA

Sequence of entity 10 (AL, CL), FASTA

>4WPO_10 50S ribosomal protein L11 (chains AL, CL)
MKKVVAVVKLQLPAGKATPAPPVGPALGQHGANIMEFVKAFNAATANMGDAIVPVEITIY
ADRSFTFVTKTPPASYLIRKAAGLEKGAHKPGREKVGRITWEQVLEIAKQKMPDLNTTDL
EAAARMIAGSARSMGVEVVGAPEVKDA

Sequence of entity 11 (AN, CN), FASTA

>4WPO_11 50S ribosomal protein L13 (chains AN, CN)
MKTYVPKQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKI
RVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRRLFKRL
KVYAGPDHPHQAQRPEKLEV

Sequence of entity 12 (AO, CO), FASTA

>4WPO_12 50S ribosomal protein L14 (chains AO, CO)
MIQPQTYLEVADNTGARKIMCIRVLKGSNAKYATVGDVIVASVKEAIPRGAVKEGDVVKA
VVVRTKKEIKRPDGSAIRFDDNAAVIINNQLEPRGTRVFGPVARELREKGFMKIVSLAPE
VL

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2056
ZN	Zinc ion	Zn	12
SF4	Iron/sulfur cluster	Fe4 S4	2
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2

Water and common crystallization additives (K) are not listed.

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…
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…
4U20 2.9 Å, Crystal structure of the E. coli ribosome bound to flopristin.

Browse structure collections

About this viewer

MolViewer shows 4WPO directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.