7A01: Uncharacterized protein

The Halastavi arva virus intergenic region IRES promotes translation by the simplest possible initiation mechanism. Determined by electron microscopy at 3.6 Å resolution. Released 30 Dec 2020.

Method: Electron microscopy
Resolution: 3.6 Å
Organisms: Halastavi arva RNA virus, Oryctolagus cuniculus
Chains: 85
Atoms: 224,880
Mol. weight: 3332.09 kDa
Ligands: ZN
Released: 30 Dec 2020

Explore 7A01 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7A01 contains 459 α-helices and 527 β-strands across 80 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 02: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	11-15	5	107
β-strand	24-30	7	107
β-strand	35-40	6	107
β-strand	45-51	7	107
β-strand	55-61	7	107
α-helix	70-80	11
α-helix	82-88	7
α-helix	90-102	13
α-helix	106-137	32

Chain 12: 12 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	3-12	10
α-helix	18-27	10
α-helix	29-32	4
β-strand	36-39	4	115
α-helix	45-51	7
β-strand	59-66	8	115
α-helix	76-78	3
α-helix	98-109	12
β-strand	114-120	7	115
β-strand	128-135	8	115
α-helix	140-143	4
α-helix	146-148	3
α-helix	154-156	3
α-helix	159-162	4
α-helix	170-172	3
α-helix	190-193	4

Chain 13: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	14-23	10
β-strand	26-29	4	172
α-helix	32-39	8
β-strand	45-48	4	172
α-helix	54-67	14
β-strand	70-73	4	172
α-helix	78-85	8
β-strand	93-98	6	172

Chain 22: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	9	1	122
β-strand	10-13	4	123
α-helix	16-18	3
β-strand	22-29	8	123
β-strand	40-48	9	123
α-helix	49-52	4
α-helix	59-65	7
β-strand	69-76	8	123
α-helix	77-79	3
β-strand	80-81	2	123
β-strand	86	1	122
α-helix	104-122	19

Chain 32: 10 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	5-15	11
β-strand	22-24	3	130
α-helix	29-33	5
α-helix	38-47	10
β-strand	50-52	3	130
α-helix	53-57	5
α-helix	61-72	12
α-helix	78-80	3
α-helix	85-88	4
α-helix	91-112	22
α-helix	117-123	7
α-helix	135-180	46

Chain 42: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	32	1	138
β-strand	33-35	3	139
β-strand	52-54	3	140
α-helix	73-80	8
α-helix	120-123	4
α-helix	128-131	4
α-helix	148-151	4
β-strand	154-156	3	140
β-strand	170	1	138
α-helix	176-194	19
α-helix	204	1
β-strand	205-207	3	139
β-strand	214-215	2	139

Chain 52: 15 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	9-10	2
α-helix	14-16	3
α-helix	33-35	3
β-strand	42	1	141
β-strand	45-46	2	142
β-strand	49-59	11	143
β-strand	71-80	10	143
α-helix	82-83	2
β-strand	84-95	12	144
β-strand	98-106	9	144
α-helix	112-115	4
α-helix	116-118	3
α-helix	135-138	4
α-helix	140-155	16
β-strand	159-165	7	144
α-helix	168-170	3
α-helix	178-179	2
β-strand	180-184	5	144
β-strand	186	1	141
α-helix	190-199	10
β-strand	204-205	2	144
β-strand	217-222	6	142
β-strand	225	1	145
α-helix	238-241	4
β-strand	273	1	145
β-strand	276-282	7	142
β-strand	284-288	5	143
β-strand	292-293	2	146
β-strand	297-298	2	146
α-helix	316	1
β-strand	320	1	147
β-strand	324	1	147
β-strand	330-334	5	143
β-strand	346-348	3	142
α-helix	357-360	4
β-strand	365-368	4	143
α-helix	382-389	8

Chain 62: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	9-16	8	154
β-strand	28-33	6	154
α-helix	37-51	15
α-helix	56-58	3
β-strand	59-66	8	154
α-helix	68-69	2
β-strand	76-85	10	155
β-strand	90-99	10	155
α-helix	102-116	15
β-strand	124-131	8	155
α-helix	140-143	4
β-strand	168	1	114

72 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
Internal ribosome entry site	E1	RNA	153	Halastavi arva RNA virus
28S ribosomal RNA	e2	RNA	3825	Oryctolagus cuniculus
5.8S ribosomal RNA	h2	RNA	156	Oryctolagus cuniculus
5S ribosomal RNA	d2	RNA	120	Oryctolagus cuniculus
Uncharacterized protein	p2	protein	69	Oryctolagus cuniculus	G1U001 (AlphaFold model)
eL14	k2	protein	131	Oryctolagus cuniculus	G1T6D1 (AlphaFold model)
Ribosomal protein L24	l2	protein	63	Oryctolagus cuniculus	G1SE28 (AlphaFold model)
Uncharacterized protein	m2	protein	119	Oryctolagus cuniculus	G1SE76 (AlphaFold model)
Ribosomal protein L26	o2	protein	134	Oryctolagus cuniculus	G1SQH0
uL15	q2	protein	147	Oryctolagus cuniculus	G1SNY0
60S ribosomal protein L29	r2	protein	75	Oryctolagus cuniculus	G1SGR6
uL4	t2	protein	362	Oryctolagus cuniculus	G1SVW5

73 more molecules are not listed.

Sequence of entity 1 (E1), FASTA

>7A01_1 INTERNAL RIBOSOME ENTRY SITE (chains E1)
AAAACAUGUGAUCUUAUCACUUUUAUAGUUUAUGAAAUCUUUAUUAUUGUUAUUGCUAUG
UUUUAAAUUUCUUUUUCAAAAUUCAUCCUGUUCCAGCAAUGGUUUUAAAGGAACUUGUAU
AUGAAAACCGCCACUAUUACAUCAACAACAUCA

Sequence of entity 2 (e2), FASTA

>7A01_2 28S RIBOSOMAL RNA (chains e2)
CGCGACCUCAGAUCAGACGUGGCGACCCGCUGAAUUUAAGCAUAUUAGUCAGCGGAGGAG
AAGAAACUAACCAGGAUUCCCUCAGUAACGGCGAGUGAACAGGGAAGAGCCCAGCGCCGA
AUCCCCGCCCCGCGGCGGGGCGCGGGACAUGUGGCGUACGGAAGACCCGCUCCCCGGCGC
CGCUCGUGGGGGGCCCAAGUCCUUCUGAUCGAGGCCCAGCCCGUGGACGGUGUGAGGCCG
GUAGCGGCCCCCGGCGCGCCGGGCCCGGGUCUUCCCGGAGUCGGGUUGCUUGGGAAUGCA
GCCCAAAGCGGGUGGUAAACUCCAUCUAAGGCUAAAUACCGGCACGAGACCGAUAGUCAA
CAAGUACCGUAAGGGAAAGUUGAAAAGAACUUUGAAGAGAGAGUUCAAGAGGGCGUGAAA
CCGUUAAGAGGUAAACGGGUGGGGUCCGCGCAGUCCGCCCGGAGGAUUCAACCCGGCGGC
GGGUCCGGCCGUGUCGGCGGCCCGGCGGAUCUUUCCCGCCCCCCGUGGGGUCGGCGGGGG
ACCGUCCCCCGACCGGCGACCGGCCGCCGCCGGGCGCAUUUCCACCGCGGCGGUGCGCCG
CGACCGGCUCCGGGACGGCUGGGAAGGCCCGGCGGGGAAGGUGGCUCGGCCCGAGUGUUA
CAGCCCCCCCGGCAGCAGCACUCGCCGAAUCCCGGGGCCGAGGGAGCGAGACCCGUCGCC
GCGCUCUCCCCCCUCGGCGUCUCCUCGUGGGGGGGCCGGGCCACCCCUCCCACGGCGCGA
CCGCUCUCCCACCCCUCGUCGGGGGGCGGGGCGGACUGUCCCCAGUGCGCCCCGGGCGGG
UCGCGCCGUCGGGCCCGGGGGAGGUUCUCUCGGGGCCACGCGCGCGUCCCCCGAAGAGGG
GGACGGCGGAGCGAGCGCACGGGGUCGGCGGCGACGUCGGCUACCCACCCGACCCGUCUU
GAAACACGGACCAAGGAGUCUAACACGUGCGCGAGUCGGGGGCUCGCACGAAAGCCGCCG
UGGCGCAAUGAAGGUGAAGGCCGGCGCGCUCGCCGGCCGAGGUGGGAUCCCGAGGCCUCU
CCAGUCCGCCGAGGGCGCACCACCGGCCCGUCUCGCCCGCCGCGCCGGGGAGGUGGAGCA
CGAGCGCACGUGUUAGGACCCGAAAGAUGGUGAACUAUGCCUGGGCAGGGCGAAGCCAGA
GGAAACUCUGGUGGAGGUCCGUAGCGGUCCUGACGUGCAAAUCGGUCGUCCGACCUGGGU
AUAGGGGCGAAAGACUAAUCGAACCAUCUAGUAGCUGGUUCCCUCCGAAGUUUCCCUCAG
GAUAGCUGGCGCUCUCGCAGACCCGACGCACCCCCGCCACGCAGUUUUAUCCGGUAAAGC
GAAUGAUUAGAGGUCUUGGGGCCGAAACGAUCUCAACCUAUUCUCAAACUUUAAAUGGGU
AAGAAGCCCGGCUCGCUGGCGUGAGCCGGGCGUGGAAUGGAGUGCCUAGUGGGCCACUUU
UGGUAAGCAGAACUGGCGCUGCGGGAUGAACCGAACGCCGGGUUAAGGCGCCCGAUGCCG
ACGCUCAUCAGACCCCAGAAAAGGUGUUGGUUGAUAUAGACAGCAGGACGGUGGCCAUGG
AAGUCGGAAUCCGCUAAGGAGUGUGUAACAACUCACCUGCCGAAUCAACUAGCCCUGAAA
AUGGAUGGCGCUGGAGCGUCGGGCCCAUACCCGGCCGUCGCCGGCAGUCGAGAGUGGACG
GGAGCGGCGGGGGCGGCGCGCGCGCGCGCCCGCCCCCGGAGCCCCGCGGACGCUACGCCG
CGACGAGUAGGAGGGCCGCUGCGGUGAGCCUUGAAGCCUAGGGCGCGGGCCCGGGUGGAG
CCGCCGCAGGUGCAGAUCUUGGUGGUAGUAGCAAAUAUUCAAACGAGAACUUUGAAGGCC
GAAGUGGAGAAGGGUUCCAUGUGAACAGCAGUUGAACAUGGGUCAGUCGGUCCUGAGAGA
UGGGCGAGCGCCGUUCCGAAGGGACGGGCGAUGGCCUCCGUUGCCCUCGGCCGAUCGAAA
GGGAGUCGGGUUCAGAUCCCCGAAUCCGGAGUGGCGGAGAUGGGCGCCGCGAGGCGUCCA
GUGCGGUAACGCGACCGAUCCCGGAGAAGCCGGCGGGAGCCCCGGGGAGAGUUCUCUUUU
CUUUGUGAAGGGCAGGGCGCCCUGGAAUGGGUUCGCCCCGAGAGAGGGGCCCGUGCCUUG
GAAAGCGUCGCGGUUCCGGCGGCGUCCGGUGAGCUCUCGCUGGCCCUUGAAAAUCCGGGG
GAGAGGGUGUAAAUCUCGCGCCGGGCCGUACCCAUAUCCGCAGCAGGUCUCCAAGGUGAA
CAGCCUCUGGCAUGUUGGAACAAUGUAGGUAAGGGAAGUCGGCAAGCCGGAUCCGUAACU
UCGGGAUAAGGAUUGGCUCUAAGGGCUGCAGCCGACUUAGAACUGGUGCGGACCAGGGGA
AUCCGACUGUUUAAUUAAAACAAAGCAUCGCGAAGGCCCGCGGCGGGUGUUGACGCGAUG
UGAUUUCUGCCCAGUGCUCUGAAUGUCAAAGUGAAGAAAUUCAAUGAAGCGCGGGUAAAC
GGCGGGAGUAACUAUGACUCUCUUAAGGUAGCCAAAUGCCUCGUCAUCUAAUUAGUGACG
CGCAUGAAUGGAUGAACGAGAUUCCCACUGUCCCUACCUACUAUCCAGCGAAACCACAGC
CAAGGGAACGGGCUUGGCGGAAUCAGCGGGGAAAGAAGACCCUGUUGAGCUUGACUCUAG
UCUGGCACGGUGAAGAGACAUGAGAGGUGUAGAAUAAGUGGGAGGCCCCCGGCGCCCCCC
CGGUGUCCCCGCGAGGGGCCCGGGGCGGGGUCCGCCGGCCCUGCGGGCCGCCGGUGAAAU
ACCACUACUCUGAUCGUUUUUUCACUGACCCGGUGAGGCGGGGGGGCGAGCCCCGAGGGG
CUCUCGCUUCUGGCGCCAAGCGCCCGGCCGCGCGCCGGCCGGGCGCGACCCGCUCCGGGG
ACAGUGCCAGGUGGGGAGUUUGACUGGGGCGGUACACCUGUCAAACGGUAACGCAGGUGU
CCUAAGGCGAGCUCAGGGAGGACAGAAACCUCCCGUGGAGCAGAAGGGCAAAAGCUCGCU
UGAUCUUGAUUUUCAGUACGAAUACAGACCGUGAAAGCGGGGCCUCACGAUCCUUCUGAC
CUUUUGGGUUUUAAGCAGGAGGUGUCAGAAAAGUUACCACAGGGAUAACUGGCUUGUGGC
GGCCAAGCGUUCAUAGCGACGUCGCUUUUUGAUCCUUCGAUGUCGGCUCUUCCUAUCAUU
GUGAAGCAGAAUUCACCAAGCGUUGGAUUGUUCACCCACUAAUAGGGAACGUGAGCUGGG
UUUAGACCGUCGUGAGACAGGUUAGUUUUACCCUACUGAUGAUGUGUUGUUGCCAUGGUA
AUCCUGCUCAGUACGAGAGGAACCGCAGGUUCAGACAUUUGGUGUAUGUGCUUGGCUGAG
GAGCCAAUGGGGCGAAGCUACCAUCUGUGGGAUUAUGACUGAACGCCUCUAAGUCAGAAU
CCCGCCCAGGCGGAACGAUACGGCAGCGCCGCGGAGCCUCGGUUGGCCUCGGAUAGCCGG
UCCCCCGCCGGGACCGGGGUCCGGUGCGGAGUGCCCUUCGUCCUGGGAAACGGGGCGCGG
CCGGAGAGGCGGCCGCCCCCUCGCCCGUCACGCACCGGCCGUUCGUGGGGAACCUGGCGC
UAAACCAUUCGUAGACGACCUGCUUCUGGGUCGGGGUUUCGUACGUAGCAGAGCAGCUCC
CUCGCUGCGAUCUAUUGAAAGUCAGCCCUCGACACAAGGGUUUGU

Sequence of entity 3 (h2), FASTA

>7A01_3 5.8S RIBOSOMAL RNA (chains h2)
CGACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAG
AAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCG
GGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCGCU

Sequence of entity 4 (d2), FASTA

>7A01_4 5S RIBOSOMAL RNA (chains d2)
GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGG
GUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUU

Sequence of entity 5 (p2), FASTA

>7A01_5 Uncharacterized protein (chains p2)
PRKIEEIKDFLLTARRKDAKSVNIKKNKDNVKFKVRCSRYLYTLVITDKEKAEKLKQSLP
PGLAVKELK

Sequence of entity 6 (k2), FASTA

>7A01_6 eL14 (chains k2)
SGAKFRISLGLPVGAVINCADNTGAKNLYIISVKGIKGRLNRLPAAGVGDMVMATVKKGK
PELRKKVHPAVVIRQRKSYRRKDGVFLYFEDNAGVIVNNKGEMKGSAITGPVAKECADLW
PRIASNAGSIA

Sequence of entity 7 (l2), FASTA

>7A01_7 Ribosomal protein L24 (chains l2)
MKVELCSFSGYKIYPGHGRRYARTDGKVFQFLNAKCESAFLSKRNPRQINWTVLYRRKHK
KGQ

Sequence of entity 8 (m2), FASTA

>7A01_8 Uncharacterized protein (chains m2)
KKIRTSPTFRRPKTLRLRRQPKYPRKSAPRRNKLDHYAIIKFPLTTESAMKKIEDNNTLV
FIVDVKANKHQIKQAVKKLYDIDVAKVNTLIRPDGEKKAYVRLAPDYDALDVANKIGII

Sequence of entity 9 (o2), FASTA

>7A01_9 Ribosomal protein L26 (chains o2)
MKFNPFVTSDRSKNRKRHFNAPSHIRRKIMSSPLSKELRQKYNVRSMPIRKDDEVQVVRG
HYKGQQIGKVVQVYRKKYVIYIERVQREKANGTTVHVGIHPSKVVITRLKLDKDRKKILE
RKAKSRQVGKEKGK

Sequence of entity 10 (q2), FASTA

>7A01_10 uL15 (chains q2)
PSRLRKTRKLRGHVSHGHGRIGKHRKHPGGRGNAGGMHHHRINFDKYHPGYFGKVGMRHY
HLKRNQSFCPTVNLDKLWTLVSEQTRVNAAKNKTGAAPIIDVVRSGYYKVLGKGKLPKQP
VIVKAKFFSRRAEEKIKGVGGACVLVA

Sequence of entity 11 (r2), FASTA

>7A01_11 60S ribosomal protein L29 (chains r2)
AKSKNHTTHNQSRKWHRNGIKKPRSQRYESLKGVDPKFLRNMRFAKKHNKKGLKKMQANN
AKAMAARAEAIKALV

Sequence of entity 12 (t2), FASTA

>7A01_12 uL4 (chains t2)
ACARPLISVYSEKGESSGKNVTLPAVFKAPIRPDIVNFVHTNLRKNNRQPYAVSELAGHQ
TSAESWGTGRAVARIPRVRGGGTHRSGQGAFGNMCRGGRMFAPTKTWRRWHRRVNTTQKR
YAICSALAASALPALVMSKGHRIEEVPELPLVVEDKVEGYKKTKEAVLLLKKLKAWNDIK
KVYASQRMRAGKGKMRNRRRIQRRGPCVIYNEDNGIVKAFRNIPGITLLNVTKLNILKLA
PGGHVGRFCIWTESAFRKLDDLYGTWRKAASLKSNYNLPMHKMLNTDLSRILKSPEIQRA
LRAPRKKIHRRVLKKNPLKNLRIMLKLNPYAKTMRRNTILRQARNHKLRVERAAAALAAK
SD

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6

Primary citation

The Halastavi arva Virus Intergenic Region IRES Promotes Translation by the Simplest Possible Initiation Mechanism. Abaeva, I.S., Vicens, Q., Bochler, A. et al. Cell Rep (2020) 33:108476-108476. DOI 10.1016/j.celrep.2020.108476 · PubMed

Other PDB entries of the same protein (UniProt G1U001 (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
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…
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
8BPO 2.8 Å, Structure of rabbit 80S ribosome translating beta-tubulin in complex with…

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