7NWH: 60S ribosomal protein L8

Name: PDB 7NWH: Mammalian pre-termination 80S ribosome with eRF1 and eRF3 bound by Blasticidin S.
Published: 2021-07-07
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Mammalian pre-termination 80S ribosome with eRF1 and eRF3 bound by Blasticidin S. Determined by electron microscopy at 4.1 Å resolution. Released 7 Jul 2021.

Method: Electron microscopy
Resolution: 4.1 Å
Organism: Oryctolagus cuniculus
Chains: 84
Atoms: 219,378
Mol. weight: 3476.52 kDa
Ligands: BLS, GCP, MG, ZN
Released: 7 Jul 2021

Explore 7NWH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7NWH contains 579 α-helices and 595 β-strands across 79 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 a: 10 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	8-11	4
α-helix	42-48	7
β-strand	72-74	3	192
α-helix	75-77	3
α-helix	79-81	3
α-helix	84-92	9
α-helix	98-99	2
β-strand	100	1	193
α-helix	104-106	3
β-strand	110-112	3	192
α-helix	116-118	3
β-strand	123	1	193
β-strand	126	1	194
β-strand	128-129	2	192
α-helix	131-140	10
β-strand	146	1	194

Chain A: 8 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	6-12	7
α-helix	18-19	2
α-helix	28-32	5
α-helix	34-38	5
β-strand	40-49	10	1
α-helix	57	1
β-strand	58-62	5	1
β-strand	73-77	5	1
β-strand	79	1	2
β-strand	83	1	3
β-strand	87-91	5	1
β-strand	101-103	3	1
β-strand	112-114	3	1
β-strand	116	1	4
β-strand	126	1	4
β-strand	134-140	7	1
β-strand	145-149	5	1
β-strand	155-159	5	1
β-strand	163-166	4	1
β-strand	169	1	2
α-helix	174-176	3
α-helix	182-192	11
α-helix	201-203	3
β-strand	224-225	2	5
β-strand	237-238	2	5

Chain aa: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	20-22	3	24
β-strand	29-31	3	24
β-strand	38	1	25
β-strand	41-43	3	26
α-helix	48-56	9
β-strand	66-68	3	26
β-strand	71	1	25
α-helix	75-81	7
α-helix	91-93	3
α-helix	96-98	3

Chain AA: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	12-21	10
β-strand	25	1	11
β-strand	38-41	4	11
β-strand	47-49	3	11
α-helix	51-67	17
α-helix	71-73	3
β-strand	74-78	5	12
α-helix	81-83	3
α-helix	84-94	11
β-strand	97-100	4	12
β-strand	121-124	4	12
α-helix	131-139	9
β-strand	144-148	5	12
β-strand	159-162	4	12
α-helix	168-185	18
α-helix	194-195	2
α-helix	199-202	4
α-helix	207-217	11

Chain b: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	12-19	8
α-helix	22-24	3
α-helix	37-49	13
α-helix	51-53	3
α-helix	55-75	21
α-helix	91-100	10
α-helix	102-116	15

Chain B: 20 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	9-10	2
α-helix	14-16	3
α-helix	27-28	2
α-helix	40-41	2
β-strand	43	1	35
β-strand	45-54	10	36
β-strand	57-60	4	37
β-strand	63	1	38
β-strand	65	1	38
β-strand	70-73	4	37
β-strand	76-80	5	36
α-helix	82-83	2
β-strand	84-94	11	39
β-strand	99-106	8	39
α-helix	112-115	4
α-helix	116-118	3
α-helix	131-134	4
α-helix	135-137	3
α-helix	140-155	16
β-strand	159-165	7	39
α-helix	168-170	3
α-helix	177-180	4
β-strand	182-184	3	39
β-strand	185	1	35
α-helix	190-200	11
β-strand	204-205	2	39
α-helix	207-210	4
β-strand	216-222	7	36
α-helix	223-225	3
β-strand	228-229	2	40
α-helix	231-235	5
α-helix	238-241	4
α-helix	262-263	2
β-strand	270-271	2	40
β-strand	276-288	13	36
β-strand	292-293	2	41
β-strand	298-299	2	41
β-strand	320	1	42
β-strand	324	1	42
β-strand	330-334	5	36
β-strand	343-349	7	36
α-helix	361-363	3
β-strand	365-367	3	37
α-helix	382-389	8

Chain bb: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	12-16	5
β-strand	32-36	5	174
β-strand	44-47	4	174
β-strand	55	1	175
α-helix	57-59	3
β-strand	62	1	175
β-strand	64-65	2	176
α-helix	71	1
β-strand	72-73	2	176
α-helix	74	1
β-strand	78-80	3	174

Chain BB: 10 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	24-27	4
β-strand	28-34	7	136
β-strand	43-50	8	136
β-strand	53	1	137
β-strand	56	1	137
α-helix	58-63	6
β-strand	66-70	5	136
α-helix	71-73	3
β-strand	82-90	9	136
β-strand	95-105	11	136
α-helix	107-113	7
β-strand	120-128	9	136
β-strand	134-142	9	136
β-strand	143	1	138
α-helix	144-146	3
α-helix	155-157	3
α-helix	158-177	20
α-helix	181-188	8
α-helix	192-201	10
β-strand	207	1	138
β-strand	211-217	7	136
α-helix	225-231	7

71 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
60S ribosomal protein L8	A	protein	249	Oryctolagus cuniculus	Q3T0S6 (AlphaFold model)
uL4	C	protein	378	Oryctolagus cuniculus	G1SVW5 (AlphaFold model)
eL31	d	protein	108	Oryctolagus cuniculus
40S ribosomal protein S3	DD	protein	281	Oryctolagus cuniculus	G1TNM3 (AlphaFold model)
S29	dd	protein	56	Oryctolagus cuniculus
60S ribosomal protein L5	D	protein	296	Oryctolagus cuniculus	P19949 (AlphaFold model)
Ribosomal protein L32	e	protein	129	Oryctolagus cuniculus	G1TUN8
40S ribosomal protein S4	EE	protein	263	Oryctolagus cuniculus
40S ribosomal protein S30	ee	protein	133	Oryctolagus cuniculus	G1T8A2
eL29	b	protein	226	Oryctolagus cuniculus	G1SGR6
60S ribosomal protein L6	E	protein	291	Oryctolagus cuniculus	G1SKF7
eL33	f	protein	110	Oryctolagus cuniculus	G1SF08

72 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>7NWH_1 60S ribosomal protein L8 (chains A)
MGRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAK
VVFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKP
GDRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPIL
KAGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAA
RRTGRLRGT

Sequence of entity 2 (C), FASTA

>7NWH_2 uL4 (chains C)
MACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGH
QTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQK
RYAICSALAASALPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDI
KKVYASQRMRAGKGKMRNRRRIQRRGPCVIYNEDNGIVKAFRNIPGITLLNVTKLNILKL
APGGHVGRFCIWTESAFRKLDDLYGTWRKAASLKSNYNLPMHKMLNTDLSRILKSPEIQR
ALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLRVERAAAALAA
KSDPKEAPAKKKPVVGKK

Sequence of entity 3 (d), FASTA

>7NWH_3 eL31 (chains d)
MNEVVTREYTINIHKRIHGVGFKKRAPRALKEIRKFAMKEMGTPDVRIDTRLNKAVWAKG
IRNVPYRIRVRLSRKRNEDEDSPNKLYTLVTYVPVTTFKNLQTVNVDE

Sequence of entity 4 (DD), FASTA

>7NWH_4 40S ribosomal protein S3 (chains DD)
MSARRRRRRAAFRRRAEPFIPISVREPLPFLSAARGGKMAVQISKKRKFVADGIFKAELN
EFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLGEKGRRIRELTAVVQKRFGFPEG
SVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVVVSGKL
RGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQGVLGIKVKIMLPWDPSGKIGPKK
PLPDHVSIVEPKDEILPTTPISEQKGGKPEPPAMPQPVPTA

Sequence of entity 5 (dd), FASTA

>7NWH_5 S29 (chains dd)
MGHQQLYWSHPRKFGQGSRSCRVCSNRHGLIRKYGLNMCRQCFRQYAKDIGFIKLD

Sequence of entity 6 (D), FASTA

>7NWH_6 60S ribosomal protein L5 (chains D)
GFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDII
CQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYEG
QVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRFP
GYDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNNVTPDMMEEMYK
KAHAAIRENPVYEKKPKREVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAAES

Sequence of entity 7 (e), FASTA

>7NWH_7 Ribosomal protein L32 (chains e)
MAALRPLVKPKIVKKRTKKFIRHQSDRYVKIKRNWRKPRGIDNRVRRRFKGQILMPNIGY
GSNKKTKHMLPSGFRKFLVHNVKELEVLLMCNKSYCAEIAHNVSSKNRKAIVERAAQLAI
RVTNPNARL

Sequence of entity 8 (EE), FASTA

>7NWH_8 40S ribosomal protein S4 (chains EE)
MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDE
VKKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAK
YKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNL
CMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPR
GKGIRLTIAEERDKRLAAKQSSG

Sequence of entity 9 (ee), FASTA

>7NWH_9 40S ribosomal protein S30 (chains ee)
MQLFVRAQELHTLEVTGRETVAQIKAHVASLEGIAPEDQVVLLAGTPLEDEATLGQCGVE
ALSTLEVAGRMLGGKVHGSLARVGKVRGQTLKVAKQEKKKKRTGRAKRRMQYNRRFVNVV
PTFGKKKGPNANS

Sequence of entity 10 (b), FASTA

>7NWH_10 eL29 (chains b)
MAKSKNHTTHNQSRKWHRNGIKKPRSQRYESLKGVDPKFLRNMRFAKKHNKKGLKKMQAN
NAKAMAARAEAIKALVKPKEVKPTIPKGVSRKLHRLAYIAHPKLGRRARARIARGLRLSR
PQTKAKAKTEPQIKGKVKAQIKAQAQAQIKSKGKGKAQAETKPKAQAETKPKAQAQAKPK
AQAQGKPKAQAQGKPKAQAQAKPKAQAQAKPKAQAQTKPKAQATPA

Sequence of entity 11 (E), FASTA

>7NWH_11 60S ribosomal protein L6 (chains E)
MAGEKAPAAKPDATKKSPAKKADHARGKAKKKTLAEKKPKKGKPHCSRNPVLVRGIGRYS
RSAMYSRKALYKRKYAAPKSRIERKKKREKVLATVTKPVGGDKNGGTRVVKLRKMPRYYP
TEDVPRKLLSHGKKPFSQHVRKLRASITPGTILIILTGRHRGKRVVFLKQLSSGLLLVTG
PLSLNRVPLRRTHQKFVIATSTKIDISGVKIPKHLTDAYFKKKKLRKPRHQEGEIFDTEK
EKYEITEQRKVDQKAVDSQILPKIKAVPQLQGYLRSVFALTNGVYPHKLVF

Sequence of entity 12 (f), FASTA

>7NWH_12 eL33 (chains f)
MSGRLWCKAIFAGYKRGLRNQREHTALLKIEGVYARDETEFYLGKRCAYVYKAKNNTVTP
GGKPNKTRVIWGKVTRAHGNSGMVRAKFRSNLPAKAIGHRIRVMLYPSRI

Ligands and cofactors

ID	Name	Formula	Copies
BLS	Blasticidin S	C17 H26 N8 O5	1
GCP	Phosphomethylphosphonic acid guanylate ester	C11 H18 N5 O13 P3	1
MG	Magnesium ion	Mg	281
ZN	Zinc ion	Zn	8

Primary citation

Blasticidin S inhibits mammalian translation and enhances production of protein encoded by nonsense mRNA. Powers, K.T., Stevenson-Jones, F., Yadav, S.K.N. et al. Nucleic Acids Res (2021) 49:7665-7679. DOI 10.1093/nar/gkab532 · PubMed

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