6SGC: Rabbit 80S ribosome stalled on a poly(A) tail

Name: PDB 6SGC: Rabbit 80S ribosome stalled on a poly(A) tail
Published: 2019-12-04
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Rabbit 80S ribosome stalled on a poly(A) tail. Determined by electron microscopy at 2.8 Å resolution. Released 4 Dec 2019.

Method: Electron microscopy
Resolution: 2.8 Å
Organisms: Oryctolagus cuniculus, Homo sapiens
Chains: 86
Atoms: 218,966
Mol. weight: 3468.05 kDa
Ligands: MG, ZN, SPD
Released: 4 Dec 2019

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

Secondary structure: helices and β-sheets

6SGC contains 579 α-helices and 585 β-strands across 78 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 a1: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	47	1	1
β-strand	50	1	144
α-helix	55-61	7
α-helix	62-64	3
β-strand	68	1	2
α-helix	70-76	7
β-strand	79	1	1
α-helix	81-93	13
β-strand	98-101	4	2
β-strand	108-110	3	2

Chain a2: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	7-9	3
α-helix	42-48	7
β-strand	72-74	3	79
α-helix	75-77	3
α-helix	85-92	8
β-strand	97-98	2	155
β-strand	100-102	3	80
β-strand	110-112	3	79
β-strand	122-126	5	80
β-strand	128-129	2	79
α-helix	131-139	9
β-strand	142-146	5	80

Chain A2: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	6-9	4
β-strand	18	1	84
α-helix	29-32	4
α-helix	34-38	5
β-strand	40-49	10	85
α-helix	50-51	2
β-strand	58-64	7	85
β-strand	71-77	7	85
β-strand	79	1	86
β-strand	83	1	87
β-strand	87-91	5	85
β-strand	101-103	3	85
α-helix	104-106	3
β-strand	112-114	3	85
β-strand	116	1	88
β-strand	126	1	88
β-strand	134-140	7	85
β-strand	145-149	5	85
β-strand	155-159	5	85
β-strand	163-166	4	85
β-strand	169	1	86
α-helix	174-176	3
α-helix	182-190	9
β-strand	193	1	84
α-helix	201-203	3
β-strand	224-225	2	89
α-helix	229-230	2
β-strand	237-238	2	89

Chain B: 10 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	8-18	11
α-helix	21-24	4
β-strand	32	1	49
β-strand	34-38	5	50
β-strand	50-54	5	51
β-strand	65-68	4	52
α-helix	74-79	6
β-strand	84	1	52
α-helix	87-94	8
α-helix	100-106	7
β-strand	109-112	4	52
α-helix	124-127	4
α-helix	134-135	2
β-strand	136-137	2	52
α-helix	147-151	5
β-strand	154-158	5	51
β-strand	164-167	4	50
α-helix	176-193	18
α-helix	198-200	3
β-strand	201-205	5	50
β-strand	208	1	49

Chain b1: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	20-22	3	11
β-strand	29-31	3	11
β-strand	36-43	8	12
α-helix	50-55	6
β-strand	57	1	123
α-helix	63-65	3
β-strand	66-73	8	12
α-helix	75-80	6
α-helix	96-99	4

Chain B1: 12 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	10-11	2
α-helix	12-21	10
β-strand	25	1	9
α-helix	32-34	3
β-strand	38-41	4	9
β-strand	47-49	3	9
α-helix	51-66	16
α-helix	71-73	3
β-strand	74-78	5	10
α-helix	81-83	3
α-helix	84-94	11
β-strand	97-100	4	10
β-strand	121-124	4	10
α-helix	131-136	6
β-strand	144-148	5	10
β-strand	159-162	4	10
α-helix	168-186	19
α-helix	194-195	2
α-helix	199-202	4
α-helix	207-215	9

Chain b2: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	12-18	7
α-helix	22-24	3
α-helix	37-48	12
α-helix	50-52	3
α-helix	54-72	19
α-helix	91-99	9
α-helix	106-116	11

Chain B2: 16 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	9-10	2
α-helix	14-16	3
α-helix	32-35	4
α-helix	40-41	2
β-strand	42-43	2	92
β-strand	45-59	15	93
β-strand	71-80	10	93
α-helix	82-83	2
β-strand	84-95	12	94
β-strand	98-106	9	94
α-helix	112-115	4
α-helix	116-118	3
α-helix	134-137	4
α-helix	140-156	17
β-strand	159-166	8	94
α-helix	168-170	3
β-strand	180-184	5	94
β-strand	185-186	2	92
α-helix	190-199	10
β-strand	204-205	2	94
α-helix	207-210	4
β-strand	216-222	7	93
α-helix	223-224	2
β-strand	225-229	5	95
α-helix	231-234	4
α-helix	237-241	5
β-strand	270-273	4	95
β-strand	276-288	13	93
β-strand	292-294	3	96
β-strand	297-299	3	96
β-strand	320	1	97
β-strand	324	1	97
β-strand	330-334	5	93
β-strand	344-349	6	93
β-strand	365-368	4	93
α-helix	382-389	8

70 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
18S ribosomal RNA	A1	RNA	1869	Oryctolagus cuniculus
uS2	B1	protein	295	Oryctolagus cuniculus
40S ribosomal protein S3a	C1	protein	264	Oryctolagus cuniculus	G1SS70 (AlphaFold model)
uS5	D1	protein	293	Oryctolagus cuniculus
uS5	E1	protein	243	Oryctolagus cuniculus	G1TNM3 (AlphaFold model)
40S ribosomal protein S4	F1	protein	263	Oryctolagus cuniculus	G1TK17 (AlphaFold model)
Ribosomal protein S5	G1	protein	204	Oryctolagus cuniculus	G1TFM5 (AlphaFold model)
40S ribosomal protein S6	H1	protein	249	Oryctolagus cuniculus	G1TM55
40S ribosomal protein S7	I1	protein	194	Oryctolagus cuniculus	G1SVB0
40S ribosomal protein S8	J1	protein	208	Oryctolagus cuniculus	G1TJW1
Ribosomal protein S9 (Predicted)	K1	protein	194	Oryctolagus cuniculus	B7NZS8
S10_plectin domain-ontaining protein	L1	protein	165	Oryctolagus cuniculus	G1TPV3

73 more molecules are not listed.

Sequence of entity 1 (A1), FASTA

>6SGC_1 18S ribosomal RNA (chains A1)
UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUA
AGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUU
UGGUCGCUCGCUCCUCUCCUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCG
ACGGGCGCUGACCCCCUUCGCGGGGGGGAUGCGUGCAUUUAUCAGAUCAAAACCAACCCG
GUCAGCCCCUCUCCGGCCCCGGCCGGGGGGCGGGCGCCGGCGGCUUUGGUGACUCUAGAU
AACCUCGGGCCGAUCGCACGCCCCCCGUGGCGGCGACGACCCAUUCGAACGUCUGCCCUA
UCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAGG
GUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCG
CGCAAAUUACCCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCU
UUCGAGGCCCUGUAAUUGGAAUGAGUCCACUUUAAAUCCUUUAACGAGGAUCCAUUGGAG
GGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGC
UGCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAGCGGGCGGGCGGUCCGCCGCGAGGCGA
GCCACCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAGUGU
CCCGCGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGAGCC
GCCUGGAUACCGCAGCUAGGAAUAAUGGAAUAGGACCGCGGUUCUAUUUUGUUGGUUUUC
GGAACUGAGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGU
GAAAUUCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUCA
UUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCA
UAAACGAUGCCGACCGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCUUCCG
GGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAA
UUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAA
CCUCACCCGGCCCGGACACGGACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCCGUG
GGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAAC
GAACGAGACUCUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAAC
UUCUUAGAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAUG
CCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCCU
ACGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCAA
UUAUUCCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAAG
UCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCC
UCGGAUCGGCCCCGCCGGGGUCGGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGUCGA
ACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAA
GGAUCAUUA

Sequence of entity 2 (B1), FASTA

>6SGC_2 uS2 (chains B1)
MSGALDVLQMKEEDVLKFLAAGTHLGGTNLDFQMEQYIYKRKSDGIYIINLKRTWEKLLL
AARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQTAFREPR
LLVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAR
EVLRMRGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQGEWTAPAPEFTA
TQPEVADWSEGVQVPSVPIQQFPTEDWSAQPATEDWSAAPTAQATEWVGTTTEWS

Sequence of entity 3 (C1), FASTA

>6SGC_3 40S ribosomal protein S3a (chains C1)
MAVGKNKRLTKGGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASD
GLKGRVFEVSLADLQNDEVAFRKFKLITEDVQGKNCLTNFHGMDLTRDKMCSMVKKWQTM
IEAHVDVKTTDGYLLRLFCVGFTKKRNNQIRKTSYAQHQQVRQIRKKMMEIMTREVQTND
LKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKPKFELGKLMELHGEGSSSGK
ATGDETGAKVERADGYEPPVQESV

Sequence of entity 4 (D1), FASTA

>6SGC_4 uS5 (chains D1)
MADDAGAAGGPGDPGGPGIGGRGGFRGGFGSGVRGRGRGRGRGRGRGRGARGGKAEDKEW
LPVTKLGRLVKDMKIKSLEEIYLFSLPIKESEIIDFFLGASLKDEVLKIMPVQKQTRAGQ
RTRFKAFVAIGDYNGHVGLGVKCSKEVATAIRGAIILAKLSIVPVRRGYWGNKIGKPHTV
PCKVTGRCGSVLVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNFAKAT
FDAISKTYSYLTPDLWKETVFTKSPYQEFTDHLVKTHTRVSVQRTQAPAVATT

Sequence of entity 5 (E1), FASTA

>6SGC_5 uS5 (chains E1)
MAVQISKKRKFVADGIFKAELNEFLTRELAEDGYSGVEVRVTPTRTEIIILATRTQNVLG
EKGRRIRELTAVVQKRFGFPEGSVELYAEKVATRGLCAIAQAESLRYKLLGGLAVRRACY
GVLRFIMESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPVNYYVDTAVRHVLLRQG
VLGIKVKIMLPWDPSGKIGPKKPLPDHVSIVEPKDEILPTTPISEQKGGKPEPPAMPQPV
PTA

Sequence of entity 6 (F1), FASTA

>6SGC_6 40S ribosomal protein S4 (chains F1)
MARGPKKHLKRVAAPKHWMLDKLTGVFAPRPSTGPHKLRECLPLIIFLRNRLKYALTGDE
VKKICMQRFIKIDGKVRTDITYPAGFMDVISIDKTGENFRLIYDTKGRFAVHRITPEEAK
YKLCKVRKIFVGTKGIPHLVTHDARTIRYPDPLIKVNDTIQIDLETGKITDFIKFDTGNL
CMVTGGANLGRIGVITNRERHPGSFDVVHVKDANGNSFATRLSNIFVIGKGNKPWISLPR
GKGIRLTIAEERDKRLAAKQSSG

Sequence of entity 7 (G1), FASTA

>6SGC_7 Ribosomal protein S5 (chains G1)
MTEWETAAPAVAETPDIKLFGKWSTDDVQINDISLQDYIAVKEKYAKYLPHSAGRYAAKR
FRKAQCPIVERLTNSMMMHGRNNGKKLMTVRIVKHAFEIIHLLTGENPLQVLVNAIINSG
PREDSTRIGRAGTVRRQAVDVSPLRRVNQAIWLLCTGAREAAFRNIKTIAECLADELINA
AKGSSNSYAIKKKDELERVAKSNR

Sequence of entity 8 (H1), FASTA

>6SGC_8 40S ribosomal protein S6 (chains H1)
MKLNISFPATGCQKLIEVDDERKLRTFYEKRMATEVAADALGEEWKGYVVRISGGNDKQG
FPMKQGVLTHGRVRLLLSKGHSCYRPRRTGERKRKSVRGCIVDANLSVLNLVIVKKGEKD
IPGLTDTTVPRRLGPKRASRIRKLFNLSKEDDVRQYVVRKPLNKEGKKPRTKAPKIQRLV
TPRVLQHKRRRIALKKQRTKKNKEEAAEYAKLLAKRMKEAKEKRQEQIAKRRRLSSLRAS
TSKSESSQK

Sequence of entity 9 (I1), FASTA

>6SGC_9 40S ribosomal protein S7 (chains I1)
MFSSSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAI
IIFVPVPQLKSFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSR
TLTAVHDAILEDLVFPSEIVGKRIRVKLDGSRLIKVHLDKAQQNNVEHKVETFSGVYKKL
TGKDVNFEFPEFQL

Sequence of entity 10 (J1), FASTA

>6SGC_10 40S ribosomal protein S8 (chains J1)
MGISRDNWHKRRKTGGKRKPYHKKRKYELGRPAANTKIGPRRIHTVRVRGGNKKYRALRL
DVGNFSWGSECCTRKTRIIDVVYNASNNELVRTKTLVKNCIVLIDSTPYRQWYESHYALP
LGRKKGAKLTPEEEEILNKKRSKKIQKKYDERKKNAKISSLLEEQFQQGKLLACIASRPG
QCGRADGYVLEGKELEFYLRKIKARKGK

Sequence of entity 11 (K1), FASTA

>6SGC_11 Ribosomal protein S9 (Predicted) (chains K1)
MPVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAAREL
LTLDEKDPRRLFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLA
KSIHHARVLIRQRHIRVRKQVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKK
GQGGAGAGDDEEED

Sequence of entity 12 (L1), FASTA

>6SGC_12 S10_plectin domain-ontaining protein (chains L1)
MLMPKKNRIAIYELLFKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSLKSRGYVKE
QFAWRHFYWYLTNEGIQYLRDYLHLPPEIVPATLRRSRPETGRPRPKGLEGERPARLTRG
EADRDTYRRSAVPPGADKKAEAGAGSATEFQFRGGFGRGRGQPPQ

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	275
ZN	Zinc ion	Zn	8
SPD	Spermidine	C7 H19 N3	2

Primary citation

Mechanism of ribosome stalling during translation of a poly(A) tail. Chandrasekaran, V., Juszkiewicz, S., Choi, J. et al. Nat Struct Mol Biol (2019) 26:1132-1140. DOI 10.1038/s41594-019-0331-x · PubMed

Other PDB entries of the same protein (UniProt G1SS70 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7O7Y 2.2 Å, Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a…
7OYD 2.3 Å, Cryo-EM structure of a rabbit 80S ribosome with zebrafish Dap1b
11IQ 2.4 Å, Rabbit 80S with eEF2,eIF5A and SERBP1
7O7Z 2.4 Å, Rabbit 80S ribosome stalled close to the mutated SARS-CoV-2 slippery site by a…
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…
7JQB 2.7 Å, SARS-CoV-2 Nsp1 and rabbit 40S ribosome complex
8VVQ 2.7 Å, Codon sampling state of elongation inhibitor-treated mammalian ribosomes obtained from…
7UCK 2.8 Å, 80S translation initiation complex with ac4c(-1) mRNA and Harringtonine
7ZJW 2.8 Å, Rabbit 80S ribosome as it decodes the Sec-UGA codon
9BDL 2.8 Å, 80S ribosome with angiogenin

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