7NRD: Yeast Gcn1

Name: PDB 7NRD: Structure of the yeast Gcn1 bound to a colliding stalled 80S ribosome with MBF1, A/P-tRNA and P/E-tRNA
Published: 2021-04-14
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Structure of the yeast Gcn1 bound to a colliding stalled 80S ribosome with MBF1, A/P-tRNA and P/E-tRNA. Determined by electron microscopy at 4.36 Å resolution. Released 14 Apr 2021.

Method: Electron microscopy
Resolution: 4.36 Å
Organisms: Saccharomyces cerevisiae S288C, Saccharomyces cerevisiae S288c
Chains: 82
Atoms: 204,032
Mol. weight: 3082.67 kDa
Released: 14 Apr 2021

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

Secondary structure: helices and β-sheets

7NRD contains 418 α-helices and 491 β-strands across 75 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 La: 6 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	12-20	9
α-helix	24-30	7
β-strand	33-34	2	67
β-strand	35	1	68
α-helix	36	1
α-helix	37-43	7
β-strand	47-48	2	67
β-strand	55-58	4	68
α-helix	61-63	3
β-strand	66-69	4	68
β-strand	70-72	3	69
β-strand	80-89	10	69
β-strand	93-99	7	69
β-strand	104-106	3	68
α-helix	113-122	10

Chain Lb: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	71
β-strand	21-29	9	71
β-strand	40-48	9	71
α-helix	49-52	4
α-helix	60-65	6
β-strand	69-76	8	71
β-strand	80-86	7	71
α-helix	104-123	20

Chain Lc: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	42-47	6
β-strand	53	1	36
α-helix	58-59	2
β-strand	72-74	3	74
α-helix	75-81	7
α-helix	84-92	9
β-strand	99-100	2	154
β-strand	101-103	3	75
β-strand	111-113	3	74
β-strand	124-127	4	75
β-strand	129	1	74
α-helix	132-141	10
β-strand	144-147	4	75

Chain Ld: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	12-17	6
α-helix	37-57	21

Chain LD: 7 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	6-10	5
α-helix	29-31	3
α-helix	35-37	3
β-strand	41-49	9	82
α-helix	50-51	2
β-strand	52	1	83
β-strand	54	1	83
β-strand	58-63	6	82
β-strand	73-77	5	82
β-strand	79	1	84
β-strand	83	1	31
β-strand	86-90	5	82
β-strand	101	1	82
β-strand	113-114	2	85
β-strand	134	1	85
β-strand	135-140	6	86
β-strand	145-150	6	86
β-strand	154-159	6	86
β-strand	165-166	2	85
β-strand	169	1	84
α-helix	174-176	3
α-helix	182-190	9
α-helix	201-203	3
β-strand	224-225	2	87
β-strand	237-238	2	87

Chain Le: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	10-20	11
β-strand	22-25	4	94
α-helix	27-36	10
β-strand	41-45	5	94
α-helix	50-63	14
β-strand	66-70	5	94
α-helix	74-80	7
β-strand	89-94	6	94

Chain LE: 14 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	14-16	3
α-helix	27-28	2
α-helix	33-35	3
β-strand	45-59	15	91
β-strand	71-80	10	91
α-helix	82-83	2
β-strand	84-95	12	92
β-strand	98-105	8	92
α-helix	112-118	7
α-helix	122-124	3
α-helix	131-136	6
α-helix	145-153	9
β-strand	157-163	7	92
β-strand	178-182	5	92
α-helix	188-197	10
β-strand	201-203	3	92
α-helix	205-208	4
β-strand	214-227	14	91
α-helix	229-233	5
β-strand	268-286	19	91
α-helix	307	1
β-strand	311	1	93
β-strand	315	1	93
β-strand	321-325	5	91
β-strand	334-339	6	91
α-helix	352-355	4
β-strand	356-359	4	91
α-helix	373-380	8

Chain Lf: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	9-15	7	103
α-helix	18-20	3
α-helix	25-27	3
α-helix	28-44	17
β-strand	49-50	2	103
α-helix	53-59	7
β-strand	70-79	10	103
β-strand	89-95	7	103
α-helix	104-106	3
β-strand	107-108	2	103

67 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
TPA_inf: Saccharomyces cerevisiae S288C chromosome XII, complete sequence	S2	RNA	1800	Saccharomyces cerevisiae S288C
40S ribosomal protein S3	SA	protein	223	Saccharomyces cerevisiae S288c	P05750 (AlphaFold model)
40S ribosomal protein S5	SB	protein	206	Saccharomyces cerevisiae S288c	P26783 (AlphaFold model)
40S ribosomal protein S10-A	SC	protein	92	Saccharomyces cerevisiae S288c	Q08745 (AlphaFold model)
40S ribosomal protein S12	SD	protein	124	Saccharomyces cerevisiae S288c	P48589 (AlphaFold model)
40S ribosomal protein S15	SE	protein	119	Saccharomyces cerevisiae S288c	Q01855
40S ribosomal protein S16-A	SF	protein	141	Saccharomyces cerevisiae S288c	P0CX51
40S ribosomal protein S17-B	SG	protein	125	Saccharomyces cerevisiae S288c	P14127
40S ribosomal protein S18-A	SH	protein	145	Saccharomyces cerevisiae S288c	P0CX55
40S ribosomal protein S19-A	SI	protein	143	Saccharomyces cerevisiae S288c	P07280
40S ribosomal protein S20	SJ	protein	101	Saccharomyces cerevisiae S288c	P38701
40S ribosomal protein S25-A	SK	protein	69	Saccharomyces cerevisiae S288c	Q3E792

70 more molecules are not listed.

Sequence of entity 1 (S2), FASTA

>7NRD_1 TPA_inf: Saccharomyces cerevisiae S288C chromosome XII, complete sequence (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 (SA), FASTA

>7NRD_2 40S ribosomal protein S3 (chains SA)
ALISKKRKLVADGVFYAELNEFFTRELAEEGYSGVEVRVTPTKTEVIIRATRTQDVLGEN
GRRINELTLLVQKRFKYAPGTIVLYAERVQDRGLSAVAQAESMKFKLLNGLAIRRAAYGV
VRYVMESGAKGCEVVVSGKLRAARAKAMKFADGFLIHSGQPVNDFIDTATRHVLMRQGVL
GIKVKIMRDPAKSRTGPKALPDAVTIIEPKEEEPILAPSVKDY

Sequence of entity 3 (SB), FASTA

>7NRD_3 40S ribosomal protein S5 (chains SB)
FTPVVLATPIPEEVQQAQTEIKLFNKWSFEEVEVKDASLVDYVQVRQPIFVAHTAGRYAN
KRFRKAQCPIIERLTNSLMMNGRNNGKKLKAVRIIKHTLDIINVLTDQNPIQVVVDAITN
TGPREDTTRVGGGGAARRQAVDVSPLRRVNQAIALLTIGAREAAFRNIKTIAETLAEELI
NAAKGSSTSYAIKKKDELERVAKSNR

Sequence of entity 4 (SC), FASTA

>7NRD_4 40S ribosomal protein S10-A (chains SC)
MLMPKEDRNKIHQYLFQEGVVVAKKDFNQAKHEEIDTKNLYVIKALQSLTSKGYVKTQFS
WQYYYYTLTEEGVEYLREYLNLPEHIVPGTYI

Sequence of entity 5 (SD), FASTA

>7NRD_5 40S ribosomal protein S12 (chains SD)
AEVTIEDALKVVLRTALVHDGLARGLRESTKALTRGEALLVVLVSSVTEANIIKLVEGLA
NDPENKVPLIKVADAKQLGEWAGLGKIDREGNARKVVGASVVVVKNWGAETDELSMIMEH
FSQQ

Sequence of entity 6 (SE), FASTA

>7NRD_6 40S ribosomal protein S15 (chains SE)
THSYRGVDLEKLLEMSTEDFVKLAPARVRRRFARGMTSKPAGFMKKLRAAKLAAPENEKP
APVRTHMRNMIIVPEMIGSVVGIYNGKAFNQVEIRPEMLGHYLGEFSITYTPVRHGRAG

Sequence of entity 7 (SF), FASTA

>7NRD_7 40S ribosomal protein S16-A (chains SF)
AVPSVQTFGKKKSATAVAHVKAGKGLIKVNGSPITLVEPEILRFKVYEPLLLVGLDKFSN
IDIRVRVTGGGHVSQVYAIRQAIAKGLVAYHQKYVDEQSKNELKKAFTSYDRTLLIADSR
RPEPKKFGGKGARSRFQKSYR

Sequence of entity 8 (SG), FASTA

>7NRD_8 40S ribosomal protein S17-B (chains SG)
GRVRTKTVKRASKALIERYYPKLTLDFQTNKRLCDEIATIQSKRLRNKIAGYTTHLMKRI
QKGPVRGISFKLQEEERERKDQYVPEVSALDLSRSNGVLNVDNQTSDLVKSLGLKLPLSV
INVSA

Sequence of entity 9 (SH), FASTA

>7NRD_9 40S ribosomal protein S18-A (chains SH)
SLVVQEQGSFQHILRLLNTNVDGNIKIVYALTTIKGVGRRYSNLVCKKADVDLHKRAGEL
TQEELERIVQIMQNPTHYKIPAWFLNRQNDITDGKDYHTLANNVESKLRDDLERLKKIRA
HRGIRHFWGLRVRGQHTKTTGRRRA

Sequence of entity 10 (SI), FASTA

>7NRD_10 40S ribosomal protein S19-A (chains SI)
PGVSVRDVAAQDFINAYASFLQRQGKLEVPGYVDIVKTSSGNEMPPQDAEGWFYKRAASV
ARHIYMRKQVGVGKLNKLYGGAKSRGVRPYKHIDASGSINRKVLQALEKIGIVEISPKGG
RRISENGQRDLDRIAAQTLEEDE

Sequence of entity 11 (SJ), FASTA

>7NRD_11 40S ribosomal protein S20 (chains SJ)
IIKIRITLTSTKVKQLENVSSNIVKNAEQHNLVKKGPVRLPTKVLKISTRKTPNGEGSKT
WETYEMRIHKRYIDLEAPVQIVKRITQITIEPGVDVEVVVA

Sequence of entity 12 (SK), FASTA

>7NRD_12 40S ribosomal protein S25-A (chains SK)
QHAVILDQEKYDRILKEVPTYRYVSVSVLVDRLKIGGSLARIALRHLEKEGIIKPISKHS
KQAIYTRAT

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 P05750 (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…
8T2Y 2.2 Å, Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA,…
8ZHC 2.3 Å, pre-frameshift complex of yeast 80S ribosome with eRF1 and mRNA of WNV
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
8T2Z 2.4 Å, Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, and A-site tRNA,…
8T2X 2.46 Å, Hypomethylated yeast 80S bound with cycloheximide, P-site tRNA, A-site tRNA, messenger…
9DOV 2.49 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
7ZUX 2.5 Å, Collided ribosome in a disome unit from S. cerevisiae

Browse structure collections

About this viewer

MolViewer shows 7NRD directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.