7NRC: Yeast Gcn1

Name: PDB 7NRC: Structure of the yeast Gcn1 bound to a leading stalled 80S ribosome with Rbg2, Gir2, A- and P-tRNA and eIF5A
Published: 2021-05-05
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Structure of the yeast Gcn1 bound to a leading stalled 80S ribosome with Rbg2, Gir2, A- and P-tRNA and eIF5A. Determined by electron microscopy at 3.9 Å resolution. Released 5 May 2021.

Method: Electron microscopy
Resolution: 3.9 Å
Organism: Saccharomyces cerevisiae S288C
Chains: 86
Atoms: 213,576
Mol. weight: 3245.58 kDa
Released: 5 May 2021

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

Secondary structure: helices and β-sheets

7NRC contains 514 α-helices and 539 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: 67 helices, 0 β-strands

Element	Residues	Length
α-helix	917-919	3
α-helix	920-924	5
α-helix	925-926	2
α-helix	933-944	12
α-helix	950-963	14
α-helix	966-978	13
α-helix	979-983	5
α-helix	990-996	7
α-helix	1020-1043	24
α-helix	1056-1073	18
α-helix	1085-1103	19
α-helix	1125-1135	11
α-helix	1143-1153	11
α-helix	1165-1173	9
α-helix	1183-1196	14
α-helix	1204-1207	4
α-helix	1210-1215	6
α-helix	1223-1240	18
α-helix	1245-1254	10
α-helix	1261-1277	17
α-helix	1283-1298	16
α-helix	1303-1318	16
α-helix	1327-1333	7
α-helix	1342-1351	10
α-helix	1361-1372	12
α-helix	1380-1393	14
α-helix	1402-1416	15
α-helix	1421-1437	17
α-helix	1443-1452	10
α-helix	1460-1469	10
α-helix	1473-1484	12
α-helix	1488-1502	15
α-helix	1508-1517	10
α-helix	1526-1537	12
α-helix	1542-1553	12
α-helix	1561-1574	14
α-helix	1585-1596	12
α-helix	1603-1612	10
α-helix	1617-1635	19
α-helix	1642-1651	10
α-helix	1660-1670	11
α-helix	1675-1684	10
α-helix	1692-1703	12
α-helix	1709-1721	13
α-helix	1806-1812	7
α-helix	1821-1830	10
α-helix	1840-1851	12
α-helix	1859-1872	14
α-helix	1881-1895	15
α-helix	1900-1916	17
α-helix	2006-2012	7
α-helix	2021-2030	10
α-helix	2040-2051	12
α-helix	2059-2072	14
α-helix	2081-2095	15
α-helix	2102-2116	15
α-helix	2206-2213	8
α-helix	2221-2230	10
α-helix	2240-2251	12
α-helix	2259-2272	14
α-helix	2281-2295	15
α-helix	2300-2316	17
α-helix	2332-2341	10
α-helix	2351-2362	12
α-helix	2370-2383	14
α-helix	2392-2406	15
α-helix	2411-2427	17

Chain La: 4 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	12-20	9
α-helix	24-30	7
β-strand	32-34	3	102
β-strand	35	1	103
α-helix	37-42	6
β-strand	47-49	3	102
β-strand	55-58	4	103
β-strand	66-69	4	103
β-strand	70-72	3	104
β-strand	80-89	10	104
β-strand	93-99	7	104
β-strand	104-106	3	103
α-helix	113-122	10

Chain Lb: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	107
β-strand	21-29	9	107
β-strand	40-48	9	107
α-helix	49-52	4
α-helix	60-66	7
β-strand	69-76	8	107
α-helix	77-79	3
β-strand	80-86	7	107
α-helix	104-123	20
α-helix	128-131	4

Chain Lc: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	9-11	3
α-helix	42-47	6
α-helix	75-81	7
α-helix	84-92	9
β-strand	99	1	7
α-helix	100-101	2
β-strand	103	1	109
β-strand	124-127	4	109
α-helix	132-140	9
β-strand	144-147	4	109

Chain Ld: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	12-16	5
α-helix	37-57	21

Chain LD: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	6-10	5
α-helix	18-19	2
α-helix	29-31	3
α-helix	35-37	3
β-strand	40-50	11	111
α-helix	51	1
β-strand	57-64	8	111
β-strand	71-77	7	111
α-helix	78	1
β-strand	79	1	112
β-strand	80	1	113
β-strand	82	1	113
β-strand	83	1	37
β-strand	86-91	6	111
β-strand	112-114	3	114
β-strand	116	1	115
β-strand	126	1	115
β-strand	134-140	7	114
β-strand	145-150	6	114
β-strand	154-158	5	114
β-strand	165-166	2	114
β-strand	169	1	112
α-helix	174-176	3
α-helix	182-192	11
β-strand	224-225	2	116
β-strand	237-238	2	116

Chain Le: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	10-20	11
β-strand	22-25	4	122
α-helix	27-36	10
β-strand	41-44	4	122
α-helix	50-63	14
β-strand	66-69	4	122
α-helix	74-81	8
β-strand	89-94	6	122

Chain LE: 12 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	9-10	2
α-helix	40-41	2
β-strand	45-59	15	118
β-strand	71-80	10	118
α-helix	82-83	2
β-strand	84-95	12	119
β-strand	98-105	8	119
α-helix	112-118	7
α-helix	131-136	6
α-helix	145-153	9
β-strand	157-163	7	119
β-strand	178-182	5	119
α-helix	188-197	10
β-strand	201-203	3	119
α-helix	205-208	4
β-strand	214-221	8	118
α-helix	222-223	2
β-strand	226-227	2	120
α-helix	229-233	5
α-helix	235-238	4
β-strand	268-269	2	120
β-strand	273-286	14	118
β-strand	311	1	121
β-strand	315	1	121
β-strand	321-325	5	118
β-strand	335-340	6	118
β-strand	356-359	4	118
α-helix	373-380	8

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
18S rRNA (1771-mer)	S2	RNA	1800	Saccharomyces cerevisiae S288C
RNA (5'-r(papupgpapapa)-3')	Sl	RNA	6	Saccharomyces cerevisiae S288C
40S ribosomal protein S0-A	SP	protein	206	Saccharomyces cerevisiae S288C	P32905 (AlphaFold model)
40S ribosomal protein S1-A	SQ	protein	232	Saccharomyces cerevisiae S288C	P33442 (AlphaFold model)
40S ribosomal protein S15	SE	protein	117	Saccharomyces cerevisiae S288C	Q01855 (AlphaFold model)
40S ribosomal protein S2	SR	protein	216	Saccharomyces cerevisiae S288C	P25443 (AlphaFold model)
40S ribosomal protein S3	SA	protein	222	Saccharomyces cerevisiae S288C	P05750
40S ribosomal protein S4-A	SS	protein	258	Saccharomyces cerevisiae S288C	P0CX35
40S ribosomal protein S5	SB	protein	206	Saccharomyces cerevisiae S288C	P26783
40S ribosomal protein S6-A	ST	protein	228	Saccharomyces cerevisiae S288C	P0CX37
40S ribosomal protein S7-A	SU	protein	184	Saccharomyces cerevisiae S288C	P26786
40S ribosomal protein S8-A	SV	protein	198	Saccharomyces cerevisiae S288C	P0CX39

74 more molecules are not listed.

Sequence of entity 1 (S2), FASTA

>7NRC_1 18S rRNA (1771-MER) (chains S2)
UAUCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCU
AAGUAUAAGCAAUUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAU
UUGAUAGUUCCUUUACUACAUGGUAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCUUAA
AAUCUCGACCCUUUGGAAGAGAUGUAUUUAUUAGAUAAAAAAUCAAUGUCUUCGGACUCU
UUGAUGAUUCAUAAUAACUUUUCGAAUCGCAUGGCCUUGUGCUGGCGAUGGUUCAUUCAA
AUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUUUCAACGGGUAA
CGGGGAAUAAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGA
AGGCAGCAGGCGCGCAAAUUACCCAAUCCUAAUUCAGGGAGGUAGUGACAAUAAAUAACG
AUACAGGGCCCAUUCGGGUCUUGUAAUUGGAAUGAGUACAAUGUAAAUACCUUAACGAGG
AACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAU
AUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACUUUGGGCCCGGUUGGCCGGUCCG
AUUUUUUCGUGUACUGGAUUUCCAACGGGGCCUUUCCUUCUGGCUAACCUUGAGUCCUUG
UGGCUCUUGGCGAACCAGGACUUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUA
UUGCUCGAAUAUAUUAGCAUGGAAUAAUAGAAUAGGACGUUUGGUUCUAUUUUGUUGGUU
UCUAGGACCAUCGUAAUGAUUAAUAGGGACGGUCGGGGGCAUCAGUAUUCAAUUGUCAGA
GGUGAAAUUCUUGGAUUUAUUGAAGACUAACUACUGCGAAAGCAUUUGCCAAGGACGUUU
UCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUCAGAUACCGUCGUAGUCUUAA
CCAUAAACUAUGCCGACUAGGGAUCGGGUGGUGUUUUUUUAAUGACCCACUCGGCACCUU
ACGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAG
GAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGG
GAAACUCACCAGGUCCAGACACAAUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUUU
GUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAU
AACGAACGAGACCUUAACCUACUAAAUAGUGGUGCUAGCAUUUGCUGGUUAUCCACUUCU
UAGAGGGACUAUCGGUUUCAAGCCGAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCC
CUUAGACGUUCUGGGCCGCACGCGCGCUACACUGACGGAGCCAGCGAGUCUAACCUUGGC
CGAGAGGUCUUGGUAAUCUUGUGAAACUCCGUCGUGCUGGGGAUAGAGCAUUGUAAUUAU
UGCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUACGUCCC
UGCCCUUUGUACACACCGCCCGUCGCUAGUACCGAUUGAAUGGCUUAGUGAGGCCUCAGG
AUCUGCUUAGAGAAGGGGGCAACUCCAUCUCAGAGCGGAGAAUUUGGACAAACUUGGUCA
UUUAGAGGAACUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA

Sequence of entity 2 (Sl), FASTA

>7NRC_2 RNA (5'-R(P*AP*UP*GP*AP*AP*A)-3') (chains Sl)
AUGAAA

Sequence of entity 3 (SP), FASTA

>7NRC_3 40S ribosomal protein S0-A (chains SP)
SLPATFDLTPEDAQLLLAANTHLGARNVQVHQEPYVFNARPDGVHVINVGKTWEKLVLAA
RIIAAIPNPEDVVAISSRTFGQRAVLKFAAHTGATPIAGRFTPGSFTNYITRSFKEPRLV
IVTDPRSDAQAIKEASYVNIPVIALTDLDSPSEFVDVAIPCNNRGKHSIGLIWYLLAREV
LRLRGALVDRTQPWSIMPDLYFYRDP

Sequence of entity 4 (SQ), FASTA

>7NRC_4 40S ribosomal protein S1-A (chains SQ)
AVGKNKRLSKGKKGQKKRVVDPFTRKEWFDIKAPSTFENRNVGKTLVNKSTGLKSASDAL
KGRVVEVCLADLQGSEDHSFRKIKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTLI
EANVTVKTSDDYVLRIFAIAFTRKQANQVKRHSYAQSSHIRAIRKVISEILTKEVQGSTL
AQLTSKLIPEVINKEIENATKDIFPLQNIHVRKVKLLKQPKFDVGALMALHG

Sequence of entity 5 (SE), FASTA

>7NRC_5 40S ribosomal protein S15 (chains SE)
KTHSYRGVDLEKLLEMSTEDFVKLAPARVRRRFARGMTSKPAGFMKKLRAAKLAAPENEK
PAPVRTHMRNMIIVPEMIGSVVGIYNGKAFNQVEIRPEMLGHYLGEFSITYTPVRHG

Sequence of entity 6 (SR), FASTA

>7NRC_6 40S ribosomal protein S2 (chains SR)
GWVPVTKLGRLVKAGKITTIEEIFLHSLPVKEFQIIDTLLPGLQDEVMNIKPVQKQTRAG
QRTRFKAVVVVGDSNGHVGLGIKTAKEVAGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHS
LATKTTGKCGSVTVRLIPAPRGSGIVASPAVKKLLQLAGVEDVYTQSNGKTRTLENTLKA
AFVAIGNTYGFLTPNLWAEQPLPVSPLDIYSDEASA

Sequence of entity 7 (SA), FASTA

>7NRC_7 40S ribosomal protein S3 (chains SA)
LISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLGENG
RRINELTLLVQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAYGVV
RYVMESGAKGCEVVVSGKLRAARAKAMKFADGFLIHSGQPVNDFIDTATRHVLMRQGVLG
IKVKIMRDPAKSRTGPKALPDAVTIIEPKEEEPILAPSVKDY

Sequence of entity 8 (SS), FASTA

>7NRC_8 40S ribosomal protein S4-A (chains SS)
ARGPKKHLKRLAAPHHWLLDKLSGCYAPRPSAGPHKLRESLPLIVFLRNRLKYALNGREV
KAILMQRHVKVDGKVRTDTTYPAGFMDVITLDATNENFRLVYDVKGRFAVHRITDEEASY
KLGKVKKVQLGKKGVPYVVTHDGRTIRYPDPNIKVNDTVKIDLASGKITDFIKFDAGKLV
YVTGGRNLGRIGTIVHKERHDGGFDLVHIKDSLDNTFVTRLNNVFVIGEQGKPYISLPKG
KGIKLSIAEERDRRRAQQ

Sequence of entity 9 (SB), FASTA

>7NRC_9 40S ribosomal protein S5 (chains SB)
FTPVVLATPIPEEVQQAQTEIKLFNKWSFEEVEVKDASLVDYVQVRQPIFVAHTAGRYAN
KRFRKAQCPIIERLTNSLMMNGRNNGKKLKAVRIIKHTLDIINVLTDQNPIQVVVDAITN
TGPREDTTRVGGGGAARRQAVDVSPLRRVNQAIALLTIGAREAAFRNIKTIAETLAEELI
NAAKGSSTSYAIKKKDELERVAKSNR

Sequence of entity 10 (ST), FASTA

>7NRC_10 40S ribosomal protein S6-A (chains ST)
MKLNISYPVNGSQKTFEIDDEHRIRVFFDKRIGQEVDGEAVGDEFKGYVFKISGGNDKQG
FPMKQGVLLPTRIKLLLTKNVSCYRPRRDGERKRKSVRGAIVGPDLAVLALVIVKKGEQE
LEGLTDTTVPKRLGPKRANNIRKFFGLSKEDDVRDFVIRREVTKGEKTYTKAPKIQRLVT
PQRLQRKRHQRALKVRNAQAQREAAAEYAQLLAKRLSERKAEKAEIRK

Sequence of entity 11 (SU), FASTA

>7NRC_11 40S ribosomal protein S7-A (chains SU)
PQAKILSQAPTELELQVAQAFVELENSSPELKAELRPLQFKSIREIDVAGGKKALAIFVP
VPSLAGFHKVQTKLTRELEKKFQDRHVIFLAERRILPKPSRTSRQVQKRPRSRTLTAVHD
KILEDLVFPTEIVGKRVRYLVGGNKIQKVLLDSKDVQQIDYKLESFQAVYNKLTGKQIVF
EIPS

Sequence of entity 12 (SV), FASTA

>7NRC_12 40S ribosomal protein S8-A (chains SV)
GISRDSRHKRSATGAKRAQFRKKRKFELGRQPANTKIGAKRIHSVRTRGGNKKYRALRIE
TGNFSWASEGISKKTRIAGVVYHPSNNELVRTNTLTKAAIVQIDATPFRQWFEAHYGQTL
GKKKNVKEEETVAKSKNAERKWAARAASAKIESSVESQFSAGRLYACISSRPGQSGRCDG
YILEGEELAFYLRRLTAK

Primary citation

Structure of Gcn1 bound to stalled and colliding 80S ribosomes. Pochopien, A.A., Beckert, B., Kasvandik, S. et al. Proc Natl Acad Sci U S A (2021) 118. DOI 10.1073/pnas.2022756118 · PubMed

Other PDB entries of the same protein (UniProt P32905 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9PN5 1.75 Å, Composite map of hypomethylated 80S ribosome treated with hygromycin B
8CCS 1.97 Å, 80S S. cerevisiae ribosome with ligands in hybrid-1 pre-translocation (PRE-H1) complex
8CDR 2.04 Å, Translocation intermediate 2 (TI-2) of 80S S. cerevisiae ribosome with ligands and eEF2…
8CEH 2.05 Å, Translocation intermediate 4 (TI-4) of 80S S. cerevisiae ribosome with ligands and eEF2…
8EVT 2.2 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
8T2Y 2.2 Å, Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA,…
8CGN 2.28 Å, Non-rotated 80S S. cerevisiae ribosome with ligands
8ZHC 2.3 Å, pre-frameshift complex of yeast 80S ribosome with eRF1 and mRNA of WNV
8EVP 2.38 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
9DP7 2.38 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
7ZW0 2.4 Å, FAP-80S Complex - Rotated state
8BN3 2.4 Å, Yeast 80S, ES7s delta, eIF5A, Stm1 containing

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