6D90: Ribosomal protein L8

Name: PDB 6D90: Mammalian 80S ribosome with a double translocated CrPV-IRES, P-site tRNA and eRF1.
Published: 2018-06-06
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Mammalian 80S ribosome with a double translocated CrPV-IRES, P-site tRNA and eRF1. Determined by electron microscopy at 3.2 Å resolution. Released 6 Jun 2018.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Oryctolagus cuniculus, Escherichia coli, Homo sapiens
Chains: 85
Atoms: 223,875
Mol. weight: 3465.65 kDa
Released: 6 Jun 2018

Explore 6D90 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6D90 contains 510 α-helices and 611 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: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	210
β-strand	14	1	210
α-helix	42-48	7
α-helix	65-68	4
β-strand	72-73	2	211
β-strand	100-102	3	212
β-strand	110-111	2	211
α-helix	112	1
β-strand	123-126	4	212
β-strand	128-129	2	211
α-helix	131-140	10
β-strand	144-146	3	212

Chain A: 5 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	34-38	5
β-strand	40-50	11	1
β-strand	57-63	7	1
α-helix	64-65	2
β-strand	72-77	6	1
α-helix	78	1
β-strand	79	1	2
β-strand	80	1	3
β-strand	82	1	3
β-strand	83	1	4
β-strand	87-91	5	1
β-strand	102-103	2	5
β-strand	113-114	2	6
β-strand	116	1	7
β-strand	126	1	7
β-strand	135-140	6	8
β-strand	145-149	5	8
β-strand	155-158	4	8
β-strand	163-164	2	5
β-strand	165-166	2	6
β-strand	169	1	2
α-helix	182-189	8
α-helix	198-200	3
β-strand	224-225	2	9
β-strand	237-238	2	9

Chain aa: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	47	1	200
β-strand	50	1	159
β-strand	68	1	201
α-helix	73-76	4
β-strand	79	1	200
α-helix	88-94	7
β-strand	98-99	2	201
β-strand	103	1	202
β-strand	106	1	202
β-strand	109-110	2	201
α-helix	111-113	3

Chain b: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	12-17	6
α-helix	30-32	3
α-helix	40-43	4
α-helix	45-48	4
α-helix	54-68	15
α-helix	93-100	8
α-helix	107-109	3

Chain B: 12 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	40-41	2
β-strand	42-43	2	14
β-strand	47-50	4	15
β-strand	54-55	2	15
β-strand	56-59	4	16
β-strand	71-72	2	16
β-strand	75-80	6	15
α-helix	82-83	2
β-strand	84-94	11	17
β-strand	99-104	6	17
α-helix	112-115	4
α-helix	134-138	5
α-helix	145-156	12
β-strand	159-165	7	17
α-helix	178-179	2
β-strand	180-184	5	17
β-strand	185-186	2	14
α-helix	190-199	10
β-strand	204-205	2	17
α-helix	207-210	4
β-strand	216-222	7	15
α-helix	223-224	2
β-strand	225-229	5	18
α-helix	231-234	4
β-strand	270-273	4	18
β-strand	276-287	12	15
β-strand	293	1	19
β-strand	298	1	19
α-helix	315-316	2
β-strand	330-334	5	15
β-strand	344-346	3	15
β-strand	365-368	4	16
α-helix	382-389	8

Chain bb: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	20-22	3	208
β-strand	29-31	3	208
β-strand	36-43	8	209
α-helix	52-55	4
β-strand	57	1	126
α-helix	64-65	2
β-strand	66-73	8	209
α-helix	75-80	6
α-helix	91-93	3
α-helix	97-99	3

Chain BB: 13 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	12-14	3
α-helix	18-21	4
β-strand	25	1	205
α-helix	34-36	3
β-strand	38-41	4	206
β-strand	47-49	3	206
α-helix	50	1
α-helix	52-55	4
α-helix	61-67	7
β-strand	74-78	5	207
α-helix	91-94	4
β-strand	97-100	4	207
β-strand	121-124	4	207
α-helix	131-139	9
β-strand	144-146	3	207
β-strand	160	1	207
α-helix	171-186	16
α-helix	194-195	2
α-helix	199-202	4
α-helix	204-206	3
α-helix	210-216	7

Chain c: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	15-22	8
β-strand	26-29	4	20
α-helix	33-40	8
β-strand	45-47	3	20
β-strand	49	1	21
α-helix	54-63	10
β-strand	74	1	21
α-helix	78-82	5
α-helix	83-85	3
β-strand	94-98	5	20
α-helix	103-105	3

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
Ribosomal protein L8	A	protein	257	Oryctolagus cuniculus	G1TT27 (AlphaFold model)
uL3	B	protein	403	Oryctolagus cuniculus	G1TL06 (AlphaFold model)
Ribosomal protein L4	C	protein	392	Oryctolagus cuniculus	G1SVW5 (AlphaFold model)
Large ribosomal subunit protein uL18	D	protein	297	Oryctolagus cuniculus	P19949 (AlphaFold model)
60S ribosomal protein L6	E	protein	291	Oryctolagus cuniculus	G1SKF7
uL30	F	protein	249	Oryctolagus cuniculus	G1SV32
eL8	G	protein	242	Oryctolagus cuniculus	G1STW0
60S ribosomal protein L9	H	protein	192	Oryctolagus cuniculus	G1SWI6
60S ribosomal protein L10	I	protein	214	Oryctolagus cuniculus	B7NZQ2
Ribosomal protein L11	J	protein	178	Oryctolagus cuniculus	G1TUB8
eL13	L	protein	211	Oryctolagus cuniculus
Large ribosomal subunit protein eL14	M	protein	198	Oryctolagus cuniculus	G1SZ12

73 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>6D90_1 Ribosomal protein L8 (chains A)
MGRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAK
VVFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKP
GDRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPIL
KAGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAA
RRTGRLRGTKTVQEKEN

Sequence of entity 2 (B), FASTA

>6D90_2 uL3 (chains B)
QSHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREV
DRPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYK
NWHKSKKKAFTKYCKKWQDDAGKRQLDKDFSSMKKYCQVIRVLAHTQMRLLPLRQKKAHL
MEIQVNGGTVAEKLDWARERLEQQVPVSQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKL
PRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIK
NNASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRAL
EKIDLKFIDTTSKFGHGRFQTVEEKKAFMGPLKKDRIAKEEGA

Sequence of entity 3 (C), FASTA

>6D90_3 Ribosomal protein L4 (chains C)
AAGRRGAWLSPLPAMACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRK
NNRQPYAVSELAGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTK
TWRRWHRRVNTTQKRYAICSALAASALPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKE
AVLLLKKLKAWNDIKKVYASQRMRAGKGKMRNRRRIQRRGPCVIYNEDNGIVKAFRNIPG
ITLLNVTKLNILKLAPGGHVGRFCIWTESAFRKLDDLYGTWRKAASLKSNYNLPMHKMLN
TDLSRILKSPEIQRALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARN
HKLRVERAAAALAAKSDPKEAPAKKKPVVGKK

Sequence of entity 4 (D), FASTA

>6D90_4 Large ribosomal subunit protein uL18 (chains D)
KGFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDI
ICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYE
GQVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRF
PGYDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNNVTPDMMEEMY
KKAHAAIRENPVYEKKPKREVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAAES

Sequence of entity 5 (E), FASTA

>6D90_5 60S ribosomal protein L6 (chains E)
MAGEKAPAAKPDATKKSPAKKADHARGKAKKKTLAEKKPKKGKPHCSRNPVLVRGIGRYS
RSAMYSRKALYKRKYAAPKSRIERKKKREKVLATVTKPVGGDKNGGTRVVKLRKMPRYYP
TEDVPRKLLSHGKKPFSQHVRKLRASITPGTILIILTGRHRGKRVVFLKQLSSGLLLVTG
PLSLNRVPLRRTHQKFVIATSTKIDISGVKIPKHLTDAYFKKKKLRKPRHQEGEIFDTEK
EKYEITEQRKVDQKAVDSQILPKIKAVPQLQGYLRSVFALTNGVYPHKLVF

Sequence of entity 6 (F), FASTA

>6D90_6 uL30 (chains F)
LFANNIREKKKVPAVPETLKKKRRNFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHK
EYRQMYRTEIRMARMARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFN
GTFVKLNKASINMLRIVEPYIAWGYPNLKSVNELIYKRGYGKINKKRIALTDNTLIARSL
GKYNIICMEDLIHEIYTVGKHFKEANNFLWPFKLSSPRGGMKKKTTHFVEGGDAGNREDQ
INRLIRRMN

Sequence of entity 7 (G), FASTA

>6D90_7 eL8 (chains G)
KKVVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQRAILYKRLKVPPAINQFT
QVLDRQTATQLLKLAHKYRPETKQEKKQRLLARAEKKAAGKGDVPTKRPPVLRAGVNTVT
TLVENKKAQLVVIAHDVDPIELVVFLPALCRKMGVPYCILKGKARLCRLVHRKTCTTVAF
TQVNSEDKGALAKLVEAIRTNYNDRYDEIRRHWGGNVLGPKSVARIAKLEKAKAKELATK
LG

Sequence of entity 8 (H), FASTA

>6D90_8 60S ribosomal protein L9 (chains H)
MKTILSNQTVDIPENVDISLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKW
WGNRKELATVRTICSHVQNMIKGVTLGFRYKMRSVYAHFPINVVIQENGSLVEIRNFLGE
KYIRRVRMRPGVACSVSQAQKDELVLEGNDIELVSNSAALIQQATTVKNKDIRKFLDGIY
VSEKGTVQQADE

Sequence of entity 9 (I), FASTA

>6D90_9 60S ribosomal protein L10 (chains I)
MGRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQL
SSEALEAARICANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFG
KPQGTVARVHIGQVIMSIRTKLQNKEHVVEALRRAKFKFPGRQKIHISKKWGFTKFNADE
FEDMVAEKRLIPDGCGVKYIPNRGPLDKWRALHS

Sequence of entity 10 (J), FASTA

>6D90_10 Ribosomal protein L11 (chains J)
MAQDQGEKENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVRSF
GIRRNEKIAVHCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGFGIQEHIDLGIKYD
PSIGIYGLDFYVVLGRPGFSIADKKRRTGCIGAKHRISKEEAMRWFQQKYDGIILPGK

Sequence of entity 11 (L), FASTA

>6D90_11 eL13 (chains L)
MAPSRNGMILKPHFHKDWQRRVATWFNQPARKIRRRKARQARARRIAPRPAAGPIRPIVR
CPTVRYHTKVRAGRGFSLEELRVAGIHKKVARTIGISVDPRRRNKSTESLQANVQRLKEY
RSKLVLFPRKPSAPKKGDSSAEELKLATQLTGPVMPIRNVFKKEKARVITEEEKNFKAFA
SLRMARANARLFGIRAKRAKEAAEQDVEKKK

Sequence of entity 12 (M), FASTA

>6D90_12 Large ribosomal subunit protein eL14 (chains M)
MVFRRFVEVGRVAYVSFGPHAGKLVAIVDVIDQNRALVDGPCTRVRRQAMPFKCMQLTDF
ILKFPHSARQKYVRKAWEKADINTKWAATRWAKKIEARERKAKMTDFDRYKVMKAKKMRN
RIIKNEVKKLQRAALLKASPKKAPVAKGAVAAAAAAAKVPAKKATAAGKKAAQPPKAQKG
QKPPAQKAPAPKASGKKA

Primary citation

Dual tRNA mimicry in the Cricket Paralysis Virus IRES uncovers an unexpected similarity with the Hepatitis C Virus IRES. Pisareva, V.P., Pisarev, A.V., Fernandez, I.S. Elife (2018) 7. DOI 10.7554/eLife.34062 · 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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