7NWI: PDB entry 7NWI

Name: PDB 7NWI: Mammalian pre-termination 80S ribosome with Empty-A site bound by Blasticidin S
Published: 2021-07-07
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Mammalian pre-termination 80S ribosome with Empty-A site bound by Blasticidin S. Determined by electron microscopy at 3.13 Å resolution. Released 7 Jul 2021.

Method: Electron microscopy
Resolution: 3.13 Å
Organism: Oryctolagus cuniculus
Chains: 84
Atoms: 216,929
Mol. weight: 3414.47 kDa
Ligands: MG, ZN, BLS
Released: 7 Jul 2021

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

Secondary structure: helices and β-sheets

7NWI contains 434 α-helices and 530 β-strands across 77 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: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	42-47	6
β-strand	72-73	2	173
α-helix	84-89	6
β-strand	100-102	3	174
β-strand	110-111	2	173
β-strand	123-126	4	174
β-strand	128	1	173
α-helix	131-140	10
β-strand	143-146	4	174

Chain A: 6 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	10-12	3
α-helix	29-32	4
α-helix	34-38	5
β-strand	41-49	9	1
β-strand	58-64	7	1
β-strand	71-74	4	1
β-strand	77	1	1
α-helix	78	1
β-strand	79	1	2
β-strand	83	1	3
β-strand	87-90	4	1
β-strand	101-103	3	1
β-strand	112-113	2	4
β-strand	114	1	1
β-strand	116	1	5
β-strand	126	1	5
β-strand	134-140	7	4
β-strand	145-150	6	4
β-strand	154-159	6	4
β-strand	163-165	3	1
β-strand	169	1	2
α-helix	186-189	4
α-helix	201-203	3
β-strand	224-225	2	6
β-strand	237-238	2	6

Chain aa: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	20-22	3	117
β-strand	29-31	3	117
β-strand	37-40	4	118
α-helix	50-55	6
β-strand	69-72	4	118
α-helix	75-81	7
α-helix	90-93	4

Chain AA: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	13-21	9
β-strand	25	1	115
β-strand	38-41	4	115
β-strand	47-49	3	115
α-helix	50	1
α-helix	53-56	4
α-helix	58-67	10
α-helix	71-73	3
β-strand	74-77	4	116
α-helix	84-92	9
β-strand	97-99	3	116
β-strand	121-124	4	116
α-helix	131-136	6
β-strand	144-148	5	116
β-strand	159-162	4	116
α-helix	168-184	17
α-helix	194-195	2

Chain b: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	12-19	8
α-helix	22-24	3
α-helix	37-47	11
α-helix	54-75	22

Chain B: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	27-29	3
α-helix	32-34	3
β-strand	42	1	10
β-strand	47-60	14	11
β-strand	70-80	11	11
β-strand	84-95	12	12
β-strand	98-106	9	12
α-helix	112-115	4
α-helix	133-136	4
α-helix	141-155	15
β-strand	159-165	7	12
β-strand	180-184	5	12
β-strand	186	1	10
α-helix	190-200	11
β-strand	204-205	2	12
β-strand	216-222	7	11
β-strand	227-229	3	13
α-helix	231-234	4
α-helix	237-240	4
β-strand	270-272	3	13
β-strand	276-288	13	11
β-strand	292-293	2	14
β-strand	297-298	2	14
β-strand	320	1	15
β-strand	324	1	15
β-strand	330-334	5	11
β-strand	344-349	6	11
α-helix	357-360	4
β-strand	365-368	4	11
α-helix	382-389	8

Chain bb: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
α-helix	12-16	5
β-strand	32-35	4	126
β-strand	45-47	3	126
β-strand	55	1	127
β-strand	62	1	127
β-strand	79-80	2	126

Chain BB: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	28-34	7	121
β-strand	43-50	8	121
β-strand	53	1	122
β-strand	55	1	122
α-helix	58-62	5
β-strand	66	1	123
β-strand	69-70	2	124
α-helix	72-75	4
β-strand	82-84	3	124
β-strand	87	1	123
β-strand	88-91	4	121
β-strand	95-98	4	121
β-strand	103-105	3	124
α-helix	107-113	7
β-strand	120-128	9	125
β-strand	134-142	9	125
α-helix	158-176	19
α-helix	182-188	7
α-helix	192-201	10
β-strand	209-212	4	125
β-strand	217-219	3	125
α-helix	225-232	8

69 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
L8	A	protein	244	Oryctolagus cuniculus	G1TT27 (AlphaFold model)
uL3	B	protein	403	Oryctolagus cuniculus	G1TL06 (AlphaFold model)
60S ribosomal protein L4	C	protein	425	Oryctolagus cuniculus
60S ribosomal protein L5	D	protein	297	Oryctolagus cuniculus	P19949 (AlphaFold model)
60S ribosomal protein L6	E	protein	291	Oryctolagus cuniculus	G1SKF7 (AlphaFold model)
uL30	F	protein	249	Oryctolagus cuniculus	G1SV32
60S ribosomal protein L7a	G	protein	241	Oryctolagus cuniculus	G1STW0
L9	H	protein	190	Oryctolagus cuniculus	G1SWI6
60S ribosomal protein L10	I	protein	214	Oryctolagus cuniculus	B7NZQ2
Ribosomal protein L11	J	protein	181	Oryctolagus cuniculus
L13	L	protein	211	Oryctolagus cuniculus	G1TKB3
Ribosomal protein L14	M	protein	218	Oryctolagus cuniculus	G1SZ12

72 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>7NWI_1 L8 (chains A)
GRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAKV
VFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKPG
DRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPILK
AGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAAR
RTGR

Sequence of entity 2 (B), FASTA

>7NWI_2 uL3 (chains B)
MSHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREV
DRPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYK
NWHKSKKKAFTKYCKKWQDDAGKRQLDKDFSSMKKYCQVIRVLAHTQMRLLPLRQKKAHL
MEIQVNGGTVAEKLDWARERLEQQVPVSQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKL
PRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIK
NNASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRAL
EKIDLKFIDTTSKFGHGRFQTVEEKKAFMGPLKKDRIAKEEGA

Sequence of entity 3 (C), FASTA

>7NWI_3 60S ribosomal protein L4 (chains C)
MACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGH
QTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQK
RYAICSALAASALPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDI
KKVYASQRMRAGKGKMRNRRRIQRRGPCVIYNEDNGIVKAFRNIPGITLLNVTKLNILKL
APGGHVGRFCIWTESAFRKLDDLYGTWRKAASLKSNYNLPMHKMLNTDLSRILKSPEIQR
ALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLRVERAAAALAA
KSDPKEAPAKKKPVVGKKVKKPRAVGIKQKKKPVVGRKAAAAKKPAADKKAADKRAGPED
KKPAA

Sequence of entity 4 (D), FASTA

>7NWI_4 60S ribosomal protein L5 (chains D)
MGFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDI
ICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYE
GQVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRF
PGYDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNNVTPDMMEEMY
KKAHAAIRENPVYEKKPKREVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAAES

Sequence of entity 5 (E), FASTA

>7NWI_5 60S ribosomal protein L6 (chains E)
MAGEKAPAAKPDATKKSPAKKADHARGKAKKKTLAEKKPKKGKPHCSRNPVLVRGIGRYS
RSAMYSRKALYKRKYAAPKSRIERKKKREKVLATVTKPVGGDKNGGTRVVKLRKMPRYYP
TEDVPRKLLSHGRKPFSQHVRKLRASITPGTILIILTGRHRGKRVVFLKQLSSGLLLVTG
PLSLNRVPLRRTHQKFVIATSTKIDISGVKIPKHLTDAYFKKKQLRKPRHQEGEIFDTEK
EKYEITEQRKVDQKAVDSQILPKIKAVPQLQGYLRSVFALTNGVYPHKLVF

Sequence of entity 6 (F), FASTA

>7NWI_6 uL30 (chains F)
LFANNIREKKKVPAVPETLKKKRRNFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHK
EYRQMYRTEIRMARMARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFN
GTFVKLNKASINMLRIVEPYIAWGYPNLKSVNELIYKRGYGKINKKRIALTDNALIARSL
GKYGIICMEDLIHEIYTVGKRFKEANNFLWPFKLSSPRGGMKKKTTHFVEGEDAGNREDQ
INRLIRRMN

Sequence of entity 7 (G), FASTA

>7NWI_7 60S ribosomal protein L7a (chains G)
KVVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQRAILYKRLKVPPAINQFTQ
VLDRQTATQLLKLAHKYRPETKQEKKQRLLARAEKKAAGKGDVPTKRPPVLRAGVNTVTT
LVENKKAQLVVIAHDVDPIELVVFLPALCRKMGVPYCILKGKARLGRLVHRKTCTTVAFT
QVNSEDKGALAKLVEAIRTNYNDRYDEIRRHWGGNVLGPKSVARIAKLEKAKAKELATKL
G

Sequence of entity 8 (H), FASTA

>7NWI_8 L9 (chains H)
MKTILSNQTVDIPENVDISLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKW
WGNRKELATVRTICSHVQNMIKGVTLGFRYKMRSVYAHFPINVVIQENGSLVEIRNFLGE
KYIRRVRMRPGVACSVSQAQKDELVLEGNDIELVSNSAALIQQATTVKNKDIRKFLDGIY
VSEKGTVQQA

Sequence of entity 9 (I), FASTA

>7NWI_9 60S ribosomal protein L10 (chains I)
MGRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQL
SSEALEAARICANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFG
KPQGTVARVHIGQVIMSIRTKLQNKEHVVEALRRAKFKFPGRQKIHISKKWGFTKFNADE
FEDMVAEKRLIPDGCGVKYIPNRGPLDKWRALHS

Sequence of entity 10 (J), FASTA

>7NWI_10 Ribosomal protein L11 (chains J)
MAQRPQDQGEKENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTV
RSFGIRRNEKIAVHCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGFGIQEHIDLGI
KYDPSIGIYGLDFYVVLGRPGFSIADKKRRTGCIGAKHRISKEEAMRWFQQKYDGIILPG
K

Sequence of entity 11 (L), FASTA

>7NWI_11 L13 (chains L)
MAPSRNGMILKPHFHKDWQRRVATWFNQPARKIRRRKARQARARRIAPRPASGPLRPIVR
CPTVRYHTKVRAGRGFSLEELRVAGIHKKVARTIGISVDPRRRNKSTESLQANVQRLKEY
RSKLVLFPRKPSAPKKGDSSAEELKLATQLTGPVMPIRNVFKKEKARVITEEEKNFKAFA
SLRMARANARLFGIRAKRAKEAAEQDVEKKK

Sequence of entity 12 (M), FASTA

>7NWI_12 Ribosomal protein L14 (chains M)
MVFRRFVEVGRVAYVSFGPHAGKLVAIVDVIDQNRALVDGPCTRVRRQAMPFKCMQLTDF
ILKFPHSARQKYVRKAWEKADINTKWAATRWAKKIEARERKAKMTDFDRYKVMKAKKMRN
RIIKNEVKKLQRAALLKASPKKAPVAKGAVAAAAAAAKVPAKKATAAGKKAAAQKAPAQK
APAQKAAGQKAAQPPKAQKGQKPPAQKAPAPKASGKKA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	210
ZN	Zinc ion	Zn	5
BLS	Blasticidin S	C17 H26 N8 O5	1

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

Other PDB entries of the same protein (UniProt G1TT27 (AlphaFold model), which also has an AlphaFold model), best resolution first:

11IQ 2.4 Å, Rabbit 80S with eEF2,eIF5A and SERBP1
8SCB 2.5 Å, Terminating ribosome with SRI-41315
9MR4 2.65 Å, NAC: Ribosome nascent chain complex(Oxa1L)
9RHU 2.65 Å, Rabbit 80S ribosome in complex with eRF1-AAQ, stalled at the Stop codon in mutated F2A…
8RJB 2.69 Å, Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in…
8VVQ 2.7 Å, Codon sampling state of elongation inhibitor-treated mammalian ribosomes obtained from…
8RJD 2.79 Å, Structure of the rabbit 80S ribosome stalled on a 2-TMD rhodopsin intermediate in…
8B6C 2.79 Å, Cryo-EM structure of ribosome-Sec61 in complex with cyclotriazadisulfonamide derivative…
6SGC 2.8 Å, Rabbit 80S ribosome stalled on a poly(A) tail
7UCK 2.8 Å, 80S translation initiation complex with ac4c(-1) mRNA and Harringtonine
9BDL 2.8 Å, 80S ribosome with angiogenin
9QQA 2.8 Å, Ternary complex of translating ribosome, NAC and NMT1

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