6D9J: Ribosomal protein L8

Name: PDB 6D9J: Mammalian 80S ribosome with a double translocated CrPV-IRES, P-sitetRNA 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-sitetRNA 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: 227,188
Mol. weight: 3493.89 kDa
Ligands: MG, ZN
Released: 6 Jun 2018

Explore 6D9J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6D9J contains 497 α-helices and 609 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 9: 35 helices, 44 β-strands

Element	Residues	Length	Sheet
α-helix	6-13	8
β-strand	19-26	8	79
α-helix	32-43	12
α-helix	63-66	4
β-strand	75-80	6	79
α-helix	83-88	6
β-strand	97-104	8	79
α-helix	113-120	8
β-strand	124-130	7	79
α-helix	137-148	12
β-strand	152-158	7	79
α-helix	161	1
α-helix	162-167	6
α-helix	171-191	21
β-strand	213	1	79
β-strand	214-215	2	80
β-strand	222-223	2	80
α-helix	225-235	11
α-helix	248-260	13
β-strand	265	1	81
β-strand	278	1	82
β-strand	284	1	82
β-strand	287	1	81
α-helix	288	1
α-helix	289-294	6
α-helix	295-306	12
α-helix	309-319	11
α-helix	333-343	11
α-helix	347-357	11
α-helix	359-360	2
α-helix	361-372	12
β-strand	373	1	83
α-helix	380-387	8
β-strand	395-402	8	84
α-helix	410	1
β-strand	411-418	8	84
β-strand	421	1	85
β-strand	426-430	5	84
β-strand	442-446	5	84
β-strand	451-454	4	84
β-strand	457-460	4	84
β-strand	464	1	85
β-strand	468-472	5	84
β-strand	484-486	3	84
β-strand	494	1	83
β-strand	505-509	5	86
α-helix	514-516	3
α-helix	517-530	14
β-strand	537-538	2	86
β-strand	544-548	5	86
α-helix	551-560	10
α-helix	561-565	5
β-strand	580-583	4	87
β-strand	591-593	3	88
β-strand	602-608	7	88
α-helix	609-610	2
α-helix	611-619	9
α-helix	628-637	10
β-strand	660-664	5	88
α-helix	672-688	17
β-strand	697	1	87
β-strand	700-707	8	88
α-helix	718-720	3
α-helix	722-735	14
β-strand	738-741	4	87
β-strand	743	1	89
β-strand	745	1	90
β-strand	747	1	91
β-strand	752	1	92
α-helix	756-765	10
β-strand	774-775	2	93
β-strand	781	1	92
β-strand	782-783	2	93
β-strand	788	1	90
α-helix	796-804	9
β-strand	812	1	91
β-strand	817	1	89
α-helix	830-842	13
α-helix	851-854	4

Chain a: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	42-48	7
α-helix	65-68	4
β-strand	72-74	3	198
α-helix	78-81	4
α-helix	84-92	9
β-strand	98	1	123
α-helix	99	1
β-strand	100-102	3	199
α-helix	103-106	4
β-strand	110-112	3	198
β-strand	122-125	4	199
β-strand	128-129	2	198
α-helix	131-140	10
β-strand	142-145	4	199

Chain A: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	18	1	1
α-helix	29-32	4
α-helix	34-37	4
β-strand	40-49	10	2
β-strand	58-62	5	2
β-strand	64	1	3
β-strand	71	1	3
β-strand	74-77	4	2
α-helix	78	1
β-strand	79	1	4
β-strand	82-83	2	5
β-strand	87-91	5	2
β-strand	102-103	2	6
β-strand	112-114	3	7
β-strand	116	1	8
β-strand	126	1	8
β-strand	134-140	7	7
β-strand	145-149	5	7
β-strand	155-158	4	7
β-strand	163-164	2	6
β-strand	165-166	2	7
α-helix	168	1
β-strand	169	1	4
α-helix	178-179	2
α-helix	182-192	11
β-strand	193	1	1
α-helix	198-200	3
β-strand	224-225	2	9
β-strand	237-238	2	9

Chain aa: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	47	1	185
β-strand	50	1	149
α-helix	52-60	9
β-strand	67-68	2	186
α-helix	70-77	8
β-strand	79	1	185
α-helix	81-94	14
β-strand	98-101	4	186
β-strand	108-110	3	186

Chain b: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	12-19	8
α-helix	21-24	4
α-helix	37-48	12
α-helix	55-75	21
α-helix	91-100	10
α-helix	106-116	11

Chain B: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	32-35	4
β-strand	42-43	2	15
β-strand	45-54	10	16
β-strand	57-60	4	17
β-strand	70-73	4	17
β-strand	76-80	5	16
β-strand	84-94	11	18
β-strand	99-106	8	18
α-helix	112-118	7
α-helix	133-137	5
α-helix	140-155	16
β-strand	157-166	10	18
α-helix	177-179	3
β-strand	180-184	5	18
β-strand	185-186	2	15
α-helix	190-199	10
β-strand	204	1	18
β-strand	217-222	6	16
α-helix	223-225	3
β-strand	227-229	3	19
α-helix	231-235	5
α-helix	238-240	3
β-strand	270-272	3	19
β-strand	276-282	7	16
β-strand	284-287	4	16
β-strand	292-294	3	20
β-strand	297-299	3	20
β-strand	330-334	5	16
β-strand	344-348	5	16
β-strand	367	1	17
α-helix	382-389	8

Chain bb: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	21-22	2	192
β-strand	29-30	2	192
β-strand	36-43	8	193
α-helix	49-55	7
β-strand	57	1	128
α-helix	62-65	4
β-strand	66-73	8	193
α-helix	75-80	6
α-helix	89-92	4
α-helix	96-99	4

Chain BB: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	15-21	7
β-strand	25	1	190
α-helix	32-34	3
β-strand	38-42	5	190
β-strand	46-49	4	190
α-helix	51-67	17
β-strand	74-78	5	191
α-helix	85-94	10
β-strand	97-100	4	191
β-strand	121-124	4	191
α-helix	136-139	4
β-strand	144-148	5	191
β-strand	159-162	4	191
α-helix	168-186	19
α-helix	199-201	3
α-helix	207-217	11

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
60S ribosomal protein L13	L	protein	211	Oryctolagus cuniculus	G1TPV0
Large ribosomal subunit protein eL14	M	protein	198	Oryctolagus cuniculus	G1SZ12

73 more molecules are not listed.

Sequence of entity 1 (A), FASTA

>6D9J_1 Ribosomal protein L8 (chains A)
MGRVIRGQRKGAGSVFRAHVKHRKGAARLRAVDFAERHGYIKGIVKDIIHDPGRGAPLAK
VVFRDPYRFKKRTELFIAAEGIHTGQFVYCGKKAQLNIGNVLPVGTMPEGTIVCCLEEKP
GDRGKLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPIL
KAGRAYHKYKAKRNCWPRVRGVAMNPVEHPFGGGNHQHIGKPSTIRRDAPAGRKVGLIAA
RRTGRLRGTKTVQEKEN

Sequence of entity 2 (B), FASTA

>6D9J_2 uL3 (chains B)
QSHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREV
DRPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYK
NWHKSKKKAFTKYCKKWQDDAGKRQLDKDFSSMKKYCQVIRVLAHTQMRLLPLRQKKAHL
MEIQVNGGTVAEKLDWARERLEQQVPVSQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKL
PRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIK
NNASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRAL
EKIDLKFIDTTSKFGHGRFQTVEEKKAFMGPLKKDRIAKEEGA

Sequence of entity 3 (C), FASTA

>6D9J_3 Ribosomal protein L4 (chains C)
AAGRRGAWLSPLPAMACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRK
NNRQPYAVSELAGHQTSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTK
TWRRWHRRVNTTQKRYAICSALAASALPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKE
AVLLLKKLKAWNDIKKVYASQRMRAGKGKMRNRRRIQRRGPCVIYNEDNGIVKAFRNIPG
ITLLNVTKLNILKLAPGGHVGRFCIWTESAFRKLDDLYGTWRKAASLKSNYNLPMHKMLN
TDLSRILKSPEIQRALRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARN
HKLRVERAAAALAAKSDPKEAPAKKKPVVGKK

Sequence of entity 4 (D), FASTA

>6D9J_4 Large ribosomal subunit protein uL18 (chains D)
KGFVKVVKNKAYFKRYQVKFRRRREGKTDYYARKRLVIQDKNKYNTPKYRMIVRVTNRDI
ICQIAYARIEGDMIVCAAYAHELPKYGVKVGLTNYAAAYCTGLLLARRLLNRFGMDKIYE
GQVEVTGDEYNVESIDGQPGAFTCYLDAGLARTTTGNKVFGALKGAVDGGLSIPHSTKRF
PGYDSESKEFNAEVHRKHIMGQNVADYMRYLMEEDEDAYKKQFSQYIKNNVTPDMMEEMY
KKAHAAIRENPVYEKKPKREVKKKRWNRPKMSLAQKKDRVAQKKASFLRAQERAAES

Sequence of entity 5 (E), FASTA

>6D9J_5 60S ribosomal protein L6 (chains E)
MAGEKAPAAKPDATKKSPAKKADHARGKAKKKTLAEKKPKKGKPHCSRNPVLVRGIGRYS
RSAMYSRKALYKRKYAAPKSRIERKKKREKVLATVTKPVGGDKNGGTRVVKLRKMPRYYP
TEDVPRKLLSHGKKPFSQHVRKLRASITPGTILIILTGRHRGKRVVFLKQLSSGLLLVTG
PLSLNRVPLRRTHQKFVIATSTKIDISGVKIPKHLTDAYFKKKKLRKPRHQEGEIFDTEK
EKYEITEQRKVDQKAVDSQILPKIKAVPQLQGYLRSVFALTNGVYPHKLVF

Sequence of entity 6 (F), FASTA

>6D9J_6 uL30 (chains F)
LFANNIREKKKVPAVPETLKKKRRNFAELKIKRLRKKFAQKMLRKARRKLIYEKAKHYHK
EYRQMYRTEIRMARMARKAGNFYVPAEPKLAFVIRIRGINGVSPKVRKVLQLLRLRQIFN
GTFVKLNKASINMLRIVEPYIAWGYPNLKSVNELIYKRGYGKINKKRIALTDNTLIARSL
GKYNIICMEDLIHEIYTVGKHFKEANNFLWPFKLSSPRGGMKKKTTHFVEGGDAGNREDQ
INRLIRRMN

Sequence of entity 7 (G), FASTA

>6D9J_7 eL8 (chains G)
KKVVNPLFEKRPKNFGIGQDIQPKRDLTRFVKWPRYIRLQRQRAILYKRLKVPPAINQFT
QVLDRQTATQLLKLAHKYRPETKQEKKQRLLARAEKKAAGKGDVPTKRPPVLRAGVNTVT
TLVENKKAQLVVIAHDVDPIELVVFLPALCRKMGVPYCILKGKARLCRLVHRKTCTTVAF
TQVNSEDKGALAKLVEAIRTNYNDRYDEIRRHWGGNVLGPKSVARIAKLEKAKAKELATK
LG

Sequence of entity 8 (H), FASTA

>6D9J_8 60S ribosomal protein L9 (chains H)
MKTILSNQTVDIPENVDISLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKW
WGNRKELATVRTICSHVQNMIKGVTLGFRYKMRSVYAHFPINVVIQENGSLVEIRNFLGE
KYIRRVRMRPGVACSVSQAQKDELVLEGNDIELVSNSAALIQQATTVKNKDIRKFLDGIY
VSEKGTVQQADE

Sequence of entity 9 (I), FASTA

>6D9J_9 60S ribosomal protein L10 (chains I)
MGRRPARCYRYCKNKPYPKSRFCRGVPDAKIRIFDLGRKKAKVDEFPLCGHMVSDEYEQL
SSEALEAARICANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFG
KPQGTVARVHIGQVIMSIRTKLQNKEHVVEALRRAKFKFPGRQKIHISKKWGFTKFNADE
FEDMVAEKRLIPDGCGVKYIPNRGPLDKWRALHS

Sequence of entity 10 (J), FASTA

>6D9J_10 Ribosomal protein L11 (chains J)
MAQDQGEKENPMRELRIRKLCLNICVGESGDRLTRAAKVLEQLTGQTPVFSKARYTVRSF
GIRRNEKIAVHCTVRGAKAEEILEKGLKVREYELRKNNFSDTGNFGFGIQEHIDLGIKYD
PSIGIYGLDFYVVLGRPGFSIADKKRRTGCIGAKHRISKEEAMRWFQQKYDGIILPGK

Sequence of entity 11 (L), FASTA

>6D9J_11 60S ribosomal protein L13 (chains L)
MAPSRNGMILKPHFHKDWQRRVATWFNQPARKIRRRKARQARARRIAPRPAAGPIRPIVR
CPTVRYHTKVRAGRGFSLEELRVAGIHKKVARTIGISVDPRRRNKSTESLQANVQRLKEY
RSKLVLFPRKPSAPKKGDSSAEELKLATQLTGPVMPIRNVFKKEKARVITEEEKNFKAFA
SLRMARANARLFGIRAKRAKEAAEQDVEKKK

Sequence of entity 12 (M), FASTA

>6D9J_12 Large ribosomal subunit protein eL14 (chains M)
MVFRRFVEVGRVAYVSFGPHAGKLVAIVDVIDQNRALVDGPCTRVRRQAMPFKCMQLTDF
ILKFPHSARQKYVRKAWEKADINTKWAATRWAKKIEARERKAKMTDFDRYKVMKAKKMRN
RIIKNEVKKLQRAALLKASPKKAPVAKGAVAAAAAAAKVPAKKATAAGKKAAQPPKAQKG
QKPPAQKAPAPKASGKKA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
ZN	Zinc ion	Zn	4

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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