5V8I: 50S ribosomal protein L2

Name: PDB 5V8I: Thermus thermophilus 70S ribosome lacking ribosomal protein uS17
Published: 2018-03-28
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Thermus thermophilus 70S ribosome lacking ribosomal protein uS17. Determined by X-ray diffraction at 3.25 Å resolution. Released 28 Mar 2018.

Method: X-ray diffraction
Resolution: 3.25 Å
Organisms: Thermus thermophilus HB27, Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039), Thermus thermophilus (strain HB27/ATCC BAA-163 / DSM 7039)
Chains: 104
Atoms: 290,709
Mol. weight: 4380.61 kDa
Ligands: MG, ARG, ZN, SF4
Released: 28 Mar 2018

Explore 5V8I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5V8I contains 497 α-helices and 652 β-strands across 98 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: 1 helix, 8 β-strands

Element	Residues	Length	Sheet
β-strand	22-23	2	188
β-strand	30-31	2	189
β-strand	36-39	4	188
β-strand	46-47	2	189
β-strand	51-53	3	188
β-strand	59-61	3	188
β-strand	65-71	7	189
α-helix	73-75	3
β-strand	77-83	7	189

Chain 11: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	13-21	9	194
β-strand	33-42	10	194
β-strand	46-53	8	195
β-strand	56-63	8	195
α-helix	64-66	3
α-helix	67-76	10
α-helix	77-79	3
α-helix	87-96	10

Chain 12: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	3-15	13
α-helix	18-40	23
α-helix	48-68	21

Chain 13: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	3-8	6	202
α-helix	17-26	10
β-strand	34-38	5	202
α-helix	41-49	9
β-strand	54-59	6	202

Chains 14 and 24: 1 helix, 3 β-strands

Element	Residues	Length	Sheet
α-helix	7-9	3
β-strand	10-15	6	204
β-strand	21-26	6	204
β-strand	30-32	3	204

Chain 15: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	10-12	3
α-helix	13-20	8
α-helix	24-28	5
β-strand	31-32	2	1
β-strand	39-40	2	1
β-strand	44	1	120
β-strand	51	1	2
β-strand	56	1	2

Chain 16: 1 helix, 4 β-strands

Element	Residues	Length	Sheet
β-strand	6-13	8	5
β-strand	19-26	8	5
α-helix	33-34	2
β-strand	35-40	6	5
β-strand	45-53	9	5

Chain 17: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-16	8
α-helix	18-23	6
α-helix	25-36	12

88 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	2894	Thermus thermophilus HB27
5S Ribosomal RNA	1B, 2B	RNA	120	Thermus thermophilus HB27
50S ribosomal protein L2	1D, 2D	protein	276	Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)	Q72I07 (AlphaFold model)
50S ribosomal protein L3	1E, 2E	protein	206	Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)	Q72I04 (AlphaFold model)
50S ribosomal protein L4	1F, 2F	protein	210	Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)	Q72I05 (AlphaFold model)
50S ribosomal protein L5	1G, 2G	protein	182	Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)	Q72I16 (AlphaFold model)
50S ribosomal protein L6	1H, 2H	protein	180	Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)	Q72I19
50S ribosomal protein L9	1I, 2I	protein	148	Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)	Q72GV5
50S ribosomal protein L13	1N, 2N	protein	140	Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)	Q72IN1
50S ribosomal protein L14	1O, 2O	protein	122	Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)	Q72I14
50S ribosomal protein L15	1P, 2P	protein	150	Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)	Q72I23
50S ribosomal protein L16	1Q, 2Q	protein	141	Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)	Q72I11

40 more molecules are not listed.

Sequence of entity 1 (1A, 2A), FASTA

>5V8I_1 23S Ribosomal RNA (chains 1A, 2A)
GGUCAAGAUGGUAAGGGCCCACGGUGGAUGCCUCGGCACCCGAGCCGAUGAAGGACGUGG
CUACCUGCGAUAAGCCAGGGGGAGCCGGUAGCGGGCGUGGAUCCCUGGAUGUCCGAAUGG
GGGAACCCGGCCGGCGGGAACGCCGGUCACCGCGCUUUUUGCGCGGGGGGAACCUGGGGA
ACUGAAACAUCUCAGUACCCAGAGGAGAGGAAAGAGAAAUCGACUCCCUGAGUAGCGGCG
AGCGAAAGGGGACCAGCCUAAACCGUCCGGCUUGUCCGGGCGGGGUCGUGGGGCCCUCGG
ACACCGAAUCCCCAGCCUAGCCGAAGCUGUUGGGAAGCAGCGCCAGAGAGGGUGAAAGCC
CCGUAGGCGAAAGGUGGGGGGAUAGGUGAGGGUACCCGAGUACCCCGUGGUUCGUGGAGC
CAUGGGGGAAUCUGGGCGGACCACCGCCUAAGGCUAAGUACUCCGGGUGACCGAUAGCGC
ACCAGUACCGUGAGGGAAAGGUGAAAAGAACCCCGGGAGGGGAGUGAAAUAGAGCCUGAA
ACCGUGGGCUUACAAGCAGUCACGGCCCCGCAAGGGGUUGUGGCGUGCCUAUUGAAGCAU
GAGCCGGCGACUCACGGUCGUGGGCGAGCUUAAGCCGUUGAGGCGGAGGCGUAGGGAAAC
CGAGUCCGAACAGGGCGUCUAGUCCGCGGCCGUGGACCCGAAACCGGGCGAGCUAGCCCU
GGCCAGGGUGAAGCUGGGGUGAGACCCAGUGGAGGCCCGAACCGGUGGGGGAUGCAAACC
CCUCGGAUGAGCUGGGGCUAGGAGUGAAAAGCUAACCGAGCCCGGAGAUAGCUGGUUCUC
CCCGAAAUGACUUUAGGGUCAGCCUCAGGCGCUGACUGGGGCCUGUAGAGCACUGAUAGG
GCUAGGGGGCCCACCAGCCUACCAAACCCUGUCAAACUCCGAAGGGUCCCAGGUGGAGCC
UGGGAGUGAGGGCGCGAGCGAUAACGUCCGCGUCCGAGCGCGGGAACAACCGAGACCGCC
AGCUAAGGCCCCCAAGUCUGGGCUAAGUGGUAAAGGAUGUGGCGCCGCGAAGACAGCCAG
GAGGUUGGCUUAGAAGCAGCCAUCCUUUAAAGAGUGCGUAAUAGCUCACUGGUCGAGUGG
CGCCGCGCCGAAAAUGAUCGGGGCUCAAGCCCAGCGCCGAAGCUGCGGGUCUGGGGGAUG
ACCCCAGGCGGUAGGGGAGCGUUCCCGAUGCCGAUGAAGGCCGACCCGCGAGGGCGGCUG
GAGGUAAGGGAAGUGCGAAUGCCGGCAUGAGUAACGAUAAAGAGGGUGAGAAUCCCUCUC
GCCGUAAGCCCAAGGGUUCCUACGCAAUGGUCGUCAGCGUAGGGUUAGGCGGGACCUAAG
GUGAAGCCGAAAGGCGUAGCCGAAGGGCAGCCGGUUAAUAUUCCGGCCCUUCCCGCAGGU
GCGAUGGGGGGACGCUCUAGGCUAGGGGGACCGGAGCCAUGGACGAGCCCGGCCAGAAGC
GCAGGGUGGGAGGUAGGCAAAUCCGCCUCCCAAAAGCUCUGCGUGGUGGGGAAGCCCGUA
CGGGUGACAACCCCCCGAAGCCAGGGAGCCAAGAAAAGCCUCUAAGCACAACCUGCGGGA
ACCCGUACCGCAAACCGACACAGGUGGGCGGGUGCAAGAGCACUCAGGCGCGCGGGAGAA
CCCUCGCCAAGGAACUCUGCAAGUUGGCCCCGUAACUUCGGGAGAAGGGGUGCUCCCUGG
GGUGAUGAGCUCCGGGGAGCCGCAGUGAACAGGCUCUGGCGACUGUUUACCAAAAACACA
GCUCUCUGCGAACUCGUAAGAGGAGGUAUAGGGAGCGACGCUUGCCCGGUGCCGGAAGGU
CAAGGGGAGGGGUGCAAGCCCCGAACCGAAGCCCCGGUGAACGGCGGCCGUAACUAUAAC
GGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAAAGCGUAACG
ACCGGAGCGCUGUCUCGGCGAGGGACCCGGUGAAAUUGAACUGGCCGUGAAGAUGCGGCC
UACCCGUGGCAGGACGAAAAGACCCCGUGGAGCUUUACUGCAGCCUGGUGUUGGCUCUUG
GUCGCGCCUGCGUAGGAUAGGUGGGAGCCUGUGAACCCCCGCCUCCGGGUGGGGGGGAGG
CGCCGGUGAAAUACCACCCUGGCGCGGCUGGGGGCCUAACCCUCGGAUGGGGGGACAGCG
CUUGGCGGGCAGUUUGACUGGGGCGGUCGCCUCCUAAAAGGUAACGGAGGCGCCCAAAGG
UCCCCUCAGGCGGGACGGAAAUCCGCCGGAGAGCGCAAGGGUAGAAGGGGGCCUGACUGC
GAGGCCUGCAAGCCGAGCAGGGGCGAAAGCCGGGCCUAGUGAACCGGUGGUCCCGUGUGG
AAGGGCCAUCGAUCAACGGAUAAAAGUUACCCCGGGGAUAACAGGCUGAUCUCCCCCGAG
CGUCCACAGCGGCGGGGAGGUUUGGCACCUCGAUGUCGGCUCGUCGCAUCCUGGGGCUGA
AGAAGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGCACGCGAGCUGGGUUCAGAA
CGUCGUGAGACAGUUCGGUCUCUAUCCGCCACGGGCGCAGGAGGCUUGAGGGGGGCUCUU
CCUAGUACGAGAGGACCGGAAGGGACGCACCUCUGGUUUCCCAGCUGUCCCUCCAGGGGC
AUAAGCUGGGUAGCCAUGUGCGGAAGGGAUAACCGCUGAAAGCAUCUAAGCGGGAAGCCC
GCCCCAAGAUGAGGCCUCCCACGGCGUCAAGCCGGUAAGGACCCGGGAAGACGACCCGGU
GGAUGGGCCGGGGGUGUAAGCGCCGCGAGGCGUUGAGCCGACCGGUCCCAAUCGUCCGAG
GUCUUGACCCCUCC

Sequence of entity 2 (1B, 2B), FASTA

>5V8I_2 5S Ribosomal RNA (chains 1B, 2B)
UCCCCCGUGCCCAUAGCGGCGUGGAACCACCCGUUCCCAUUCCGAACACGGAAGUGAAAC
GCGCCAGCGCCGAUGGUACUGGGCGGGCGACCGCCUGGGAGAGUAGGUCGGUGCGGGGGA

Sequence of entity 3 (1D, 2D), FASTA

>5V8I_3 50S ribosomal protein L2 (chains 1D, 2D)
MAVKKFKPYTPSRRFMTVADFSEITKTEPEKSLVKPLKKTGGRNNQGRITVRFRGGGHKR
LYRIIDFKRWDKVGIPAKVAAIEYDPNRSARIALLHYVDGEKRYIIAPDGLQVGQQVVAG
PDAPIQVGNALPLRFIPVGTVVHAVELEPKKGAKLARAAGTSAQIQGREGDYVILRLPSG
ELRKVHGECYATVGAVGNADHKNIVLGKAGRSRWLGRRPHVRGAAMNPVDHPHGGGEGRA
PRGRPPASPWGWQTKGLKTRKRRKPSSRFIIARRKK

Sequence of entity 4 (1E, 2E), FASTA

>5V8I_4 50S ribosomal protein L3 (chains 1E, 2E)
MKGILGVKVGMTRIFRDDRAVPVTVILAGPCPVVQRRTPEKDGYTAVQLGFLPQNPKRVN
RPLKGHFAKAGVEPVRILREIRDFNPEGDTVTVEIFKPGERVDVTGTSKGRGFAGVMKRW
NFAGGPDSHGAHKIHRHPGSIGNRKTPGRVYKGKKMAGHYGAERVTVMNLEVVDVIPEEN
LLLVKGAVPGPNGGLVIVRETKKAAK

Sequence of entity 5 (1F, 2F), FASTA

>5V8I_5 50S ribosomal protein L4 (chains 1F, 2F)
MKEVAVYQIPVLSPSGRRELAADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYS
GRKIWPQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKVRKKGLAMAVADRARE
GKLLLVEAFAGVNGKTKEFLAWAKEAGLDGSESVLLVTGNELVRRAARNLPWVVTLAPEG
LNVYDIVRTERLVMDLDAWEVFQNRIGGEA

Sequence of entity 6 (1G, 2G), FASTA

>5V8I_6 50S ribosomal protein L5 (chains 1G, 2G)
MPLDLALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDARILEKAAQEL
ALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWIFLEKLLNVALPRIRDFRGL
NPNSFDGRGNYNLGLREQLIFPEITYDMVDALRGMDIAVVTTAETDEEARALLELLGFPF
RK

Sequence of entity 7 (1H, 2H), FASTA

>5V8I_7 50S ribosomal protein L6 (chains 1H, 2H)
MSRIGRLPIPVPKGVSVEVAPGRVKVKGPKGELEVPVSPEMRVVVEEGVVRVERPSDERR
HKSLHGLTRTLIANAVKGVSEGYSKELLIKGIGYRARLVGRALELTVGFSHPVVVEPPEG
ITFEVPEPTRVRVSGIDKQKVGQVAANIRAIRKPSAYHEKGIYYAGEPVRLKPGKAGAKK

Sequence of entity 8 (1I, 2I), FASTA

>5V8I_8 50S ribosomal protein L9 (chains 1I, 2I)
MKVILLEPLENLGDVGQVVDVKPGYARNYLLPRGLAVLATESNLKALEARIRAQAKRLAE
RKAEAERLKEILENLTLTIPVRAGETKIYGSVTAKDIAEALSRQHGITIDPKRLALEKPI
KELGEYVLTYKPHPEVPIQLKVSVVAQE

Sequence of entity 9 (1N, 2N), FASTA

>5V8I_9 50S ribosomal protein L13 (chains 1N, 2N)
MKTYVPKQVEPRWVLIDAEGKTLGRLATKIATLLRGKHRPDWTPNVAMGDFVVVVNADKI
RVTGKKLEQKIYTRYSGYPGGLKKIPLEKMLATHPERVLEHAVKGMLPKGPLGRRLFKRL
KVYAGPDHPHQAQRPEKLEV

Sequence of entity 10 (1O, 2O), FASTA

>5V8I_10 50S ribosomal protein L14 (chains 1O, 2O)
MIQPQTYLEVADNTGARKIMCIRVLKGSNAKYATVGDVIVASVKEAIPRGAVKEGDVVKA
VVVRTKKEVKRPDGSAIRFDDNAAVIINNQLEPRGTRVFGPVARELREKGFMKIVSLAPE
VL

Sequence of entity 11 (1P, 2P), FASTA

>5V8I_11 50S ribosomal protein L15 (chains 1P, 2P)
MKLSDLRPNPGANKRRKRVGRGPGSGHGKTATRGHKGQKSRSGGLKDPRRFEGGRSTTLM
RLPKRGMQGQVPGEIKRPRYQGVNLKDLARFEGEVTPELLVRAGLLKKGYRLKILGEGEA
KPLKVVAHAFSKSALEKLKAAGGEPVLLEA

Sequence of entity 12 (1Q, 2Q), FASTA

>5V8I_12 50S ribosomal protein L16 (chains 1Q, 2Q)
MLMPRRMKYRKQQRGRLKGATKGGDYVAFGDFGLVALEPAWITAQQIEAARVAMVRHFRR
GGKIFIRIFPDKPYTKKPLEVRMGKGKGNVEGYVAVVKPGRVMFEVAGVTEEQAMEALRI
AGHKLPIKTKIVRRDAYDEAQ

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2176
ARG	Arginine	C6 H15 N4 O2	2
ZN	Zinc ion	Zn	12
SF4	Iron/sulfur cluster	Fe4 S4	2

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

Primary citation

Structural robustness of the ribosome inferred from X-ray crystal structures of the 30S ribosomal subunit and the 70S ribosome lacking ribosomal protein uS17. Murphy, E., Connetti, J.L., Dahlberg, A.E. et al. To be published.

Other PDB entries of the same protein (UniProt Q72I07 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5J4D 3.1 Å, E. coli release factor 1 bound to the 70S ribosome in response to a pseudouridylated…
6N1D 3.2 Å, X-ray Crystal complex showing Spontaneous Ribosomal Translocation of mRNA and tRNAs into…
4V63 3.21 Å, Structural basis for translation termination on the 70S ribosome.
4V84 3.4 Å, Crystal structure of a complex containing domain 3 of CrPV IGR IRES RNA bound to the 70S…
4V9N 3.4 Å, Crystal structure of the 70S ribosome bound with the Q253P mutant of release factor RF2.
4V9Q 3.4 Å, Crystal Structure of Blasticidin S Bound to Thermus Thermophilus 70S Ribosome.
6B4V 3.4 Å, Antibiotic blasticidin S and E. coli release factor 1 bound to the 70S ribosome
6BOH 3.4 Å, Antibiotic blasticidin S and E. coli release factor 1 (containing deletion 302-304)…
4V83 3.5 Å, Crystal structure of a complex containing domain 3 from the PSIV IGR IRES RNA bound to…
4V9K 3.5 Å, 70S ribosome translocation intermediate GDPNP-I containing elongation factor EFG/GDPNP,…
4V9L 3.5 Å, 70S Ribosome translocation intermediate FA-3.6A containing elongation factor EFG/FUSIDIC…
6BOK 3.55 Å, E. coli release factor 1 (containing deletion 302-304) bound to the 70S ribosome

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