6ZVK: Ribosomal protein L14

Name: PDB 6ZVK: The Halastavi arva virus (HalV) intergenic region IRES promotes translation by the simplest possible initiation mechanism
Published: 2020-12-23
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: translation

The Halastavi arva virus (HalV) intergenic region IRES promotes translation by the simplest possible initiation mechanism. Determined by electron microscopy at 3.49 Å resolution. Released 23 Dec 2020.

Method: Electron microscopy
Resolution: 3.49 Å
Organisms: Oryctolagus cuniculus, Halastavi arva RNA virus
Chains: 85
Atoms: 228,291
Mol. weight: 3371.25 kDa
Ligands: ZN
Released: 23 Dec 2020

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

Secondary structure: helices and β-sheets

6ZVK contains 459 α-helices and 569 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 12: 12 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	3-11	9
α-helix	20-32	13
β-strand	36-38	3	153
α-helix	45-50	6
β-strand	59-66	8	153
α-helix	76-78	3
α-helix	98-109	12
β-strand	114-122	9	153
β-strand	128-135	8	153
α-helix	140-143	4
α-helix	150-152	3
α-helix	154-156	3
α-helix	159-161	3
α-helix	166-169	4
α-helix	170-172	3
α-helix	190-193	4

Chain 13: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	15-24	10
β-strand	26-29	4	141
α-helix	32-39	8
β-strand	45-48	4	141
α-helix	54-67	14
β-strand	70-73	4	141
α-helix	78-85	8
β-strand	93-98	6	141

Chain 22: 6 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	9-13	5	157
β-strand	22-29	8	157
β-strand	40-45	6	157
α-helix	50-52	3
α-helix	59-65	7
β-strand	71-76	6	157
β-strand	80-86	7	157
α-helix	98-100	3
α-helix	104-122	19
α-helix	123-125	3
α-helix	133-134	2

Chain 32: 11 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	5-15	11
β-strand	22-24	3	56
α-helix	29-33	5
α-helix	38-46	9
β-strand	50-52	3	56
α-helix	53-57	5
α-helix	61-70	10
α-helix	85-88	4
α-helix	91-102	12
α-helix	104-110	7
α-helix	117-128	12
α-helix	136-154	19
α-helix	159-180	22

Chain 42: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	18-20	3
β-strand	33-36	4	162
β-strand	50-52	3	163
α-helix	74-77	4
α-helix	87-90	4
β-strand	93	1	164
β-strand	98	1	164
α-helix	116-118	3
α-helix	120-123	4
α-helix	126-131	6
α-helix	137-139	3
α-helix	148-151	4
β-strand	156-158	3	163
β-strand	166-168	3	162
α-helix	179-186	8
α-helix	188-191	4
β-strand	204-205	2	162
β-strand	216	1	162

Chain 52: 12 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	9-10	2
α-helix	14-16	3
β-strand	26	1	61
α-helix	32-35	4
α-helix	40-41	2
β-strand	42-43	2	62
β-strand	45-54	10	61
β-strand	57-58	2	63
β-strand	72-73	2	63
β-strand	76-80	5	61
β-strand	84-94	11	64
β-strand	99-106	8	64
α-helix	112-115	4
α-helix	140-156	17
β-strand	159-165	7	64
α-helix	178-179	2
β-strand	180-184	5	64
β-strand	185-186	2	62
α-helix	190-200	11
β-strand	204-205	2	64
β-strand	216-222	7	61
α-helix	223-224	2
β-strand	225-228	4	65
α-helix	231-235	5
α-helix	237-241	5
β-strand	271-273	3	65
β-strand	276-278	3	61
β-strand	282-287	6	61
β-strand	292-293	2	66
β-strand	297-298	2	66
β-strand	320	1	67
β-strand	324	1	67
β-strand	330-333	4	61
β-strand	343-349	7	61
β-strand	365	1	63
α-helix	382-389	8

Chain 62: 8 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	8-16	9	72
α-helix	17-18	2
β-strand	19	1	73
β-strand	22	1	73
α-helix	25-26	2
β-strand	27-34	8	72
α-helix	37-51	15
β-strand	59-66	8	72
α-helix	68-69	2
β-strand	76-85	10	74
β-strand	90-99	10	74
α-helix	102-117	16
β-strand	124	1	74
β-strand	129-132	4	74
α-helix	134-136	3
α-helix	140-143	4
β-strand	151-152	2	1
β-strand	168	1	35
α-helix	171-173	3

Chain 72: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	25-26	2
β-strand	39-41	3	81
α-helix	52-54	3
α-helix	55-57	3
β-strand	61-67	7	81
β-strand	71-79	9	81
β-strand	84-92	9	81
β-strand	97-98	2	81
α-helix	100-118	19
α-helix	131-134	4
β-strand	139-141	3	82
β-strand	149-150	2	72
α-helix	153-156	4

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
Ribosomal protein L14	Z2	protein	138	Oryctolagus cuniculus	G1SZ12 (AlphaFold model)
28S ribosomal RNA	e2	RNA	3920	Oryctolagus cuniculus
5S ribosomal RNA	d2	RNA	120	Oryctolagus cuniculus
5.8S ribosomal RNA	h2	RNA	156	Oryctolagus cuniculus
60S ribosomal protein EL38	p2	protein	69	Oryctolagus cuniculus	G1U001 (AlphaFold model)
60S ribosomal protein UL13	w2	protein	199	Oryctolagus cuniculus	G5B8P1 (AlphaFold model)
uL22	H2	protein	153	Oryctolagus cuniculus	G1SCJ6 (AlphaFold model)
60S ribosomal protein EL18	S2	protein	187	Oryctolagus cuniculus	Q07020
60S ribosomal protein EL19	32	protein	180	Oryctolagus cuniculus	Q3T0W9
uL3	52	protein	394	Oryctolagus cuniculus	G1TL06
60S ribosomal protein EL20	62	protein	175	Oryctolagus cuniculus	Q3T003
eL21	72	protein	159	Oryctolagus cuniculus	G1SHQ2

73 more molecules are not listed.

Sequence of entity 1 (Z2), FASTA

>6ZVK_1 Ribosomal protein L14 (chains Z2)
VFRRFVEVGRVAYVSFGPHAGKLVAIVDVIDQNRALVDGPCTRVRRQAMPFKCMQLTDFI
LKFPHSARQKYVRKAWEKADINTKWAATRWAKKIEARERKAKMTDFDRYKVMKAKKMRNR
IIKNEVKKLQRAALLKAS

Sequence of entity 2 (e2), FASTA

>6ZVK_2 28S RIBOSOMAL RNA (chains e2)
CGCGACCUCAGAUCAGACGUGGCGACCCGCUGAAUUUAAGCAUAUUAGUCAGCGGAGGAG
AAGAAACUAACCAGGAUUCCCUCAGUAACGGCGAGUGAACAGGGAAGAGCCCAGCGCCGA
AUCCCCGCCCCGCGGCGGGGCGCGGGACAUGUGGCGUACGGAAGACCCGCUCCCCGGCGC
CGCUCGUGGGGGGCCCAAGUCCUUCUGAUCGAGGCCCAGCCCGUGGACGGUGUGAGGCCG
GUAGCGGCCCCCGGCGCGCCGGGCCCGGGUCUUCCCGGAGUCGGGUUGCUUGGGAAUGCA
GCCCAAAGCGGGUGGUAAACUCCAUCUAAGGCUAAAUACCGGCACGAGACCGAUAGUCAA
CAAGUACCGUAAGGGAAAGUUGAAAAGAACUUUGAAGAGAGAGUUCAAGAGGGCGUGAAA
CCGUUAAGAGGUAAACGGGUGGGGUCCGCGCAGUCCGCCCGGAGGAUUCAACCCGGCGGC
GGGUCCGGCCGUGUCGGCGGCCCGGCGGAUCUUUCCCGCCCCCCGUGGGGUCGGCGGGGG
ACCGUCCCCCGACCGGCGACCGGCCGCCGCCGGGCGCAUUUCCACCGCGGCGGUGCGCCG
CGACCGGCUCCGGGACGGCUGGGAAGGCCCGGCGGGGAAGGUGGCUCGGGGGGCCCCGCG
GGACCGAAACCCCCCCCGAGUGUUACAGCCCCCCCGGCAGCAGCACUCGCCGAAUCCCGG
GGCCGAGGGAGCGAGACCCGUCGCCGCGCUCUCCCCCCUCCCGGCGCCCACCCGGGGCGC
GCCGGCGUCUCCUCGUGGGGGGGCCGGGCCACCCCUCCCACGGCGCGACCGCUCUCCCAC
CCCUCGUCGGGGGGCGGGGCGGACUGUCCCCAGUGCGCCCCGGGCGGGUCGCGCCGUCGG
GCCCGGGGGAGGUUCUCUCGGGGCCACGCGCGCGUCCCCCGAAGAGGGGGACGGCGGAGC
GAGCGCACGGGGUCGGCGGCGACGUCGGCUACCCACCCGACCCGUCUUGAAACACGGACC
AAGGAGUCUAACACGUGCGCGAGUCGGGGGCUCGCACGAAAGCCGCCGUGGCGCAAUGAA
GGUGAAGGCCGGCGCGCUCGCCGGCCGAGGUGGGAUCCCGAGGCCUCUCCAGUCCGCCGA
GGGCGCACCACCGGCCCGUCUCGCCCGCCGCGCCGGGGAGGUGGAGCACGAGCGCACGUG
UUAGGACCCGAAAGAUGGUGAACUAUGCCUGGGCAGGGCGAAGCCAGAGGAAACUCUGGU
GGAGGUCCGUAGCGGUCCUGACGUGCAAAUCGGUCGUCCGACCUGGGUAUAGGGGCGAAA
GACUAAUCGAACCAUCUAGUAGCUGGUUCCCUCCGAAGUUUCCCUCAGGAUAGCUGGCGC
UCUCGCAGACCCGACGCACCCCCGCCACGCAGUUUUAUCCGGUAAAGCGAAUGAUUAGAG
GUCUUGGGGCCGAAACGAUCUCAACCUAUUCUCAAACUUUAAAUGGGUAAGAAGCCCGGC
UCGCUGGCGUGAGCCGGGCGUGGAAUGGAGUGCCUAGUGGGCCACUUUUGGUAAGCAGAA
CUGGCGCUGCGGGAUGAACCGAACGCCGGGUUAAGGCGCCCGAUGCCGACGCUCAUCAGA
CCCCAGAAAAGGUGUUGGUUGAUAUAGACAGCAGGACGGUGGCCAUGGAAGUCGGAAUCC
GCUAAGGAGUGUGUAACAACUCACCUGCCGAAUCAACUAGCCCUGAAAAUGGAUGGCGCU
GGAGCGUCGGGCCCAUACCCGGCCGUCGCCGGCAGUCGAGAGUGGACGGGAGCGGCGGGG
GCGGCGCGCGCGCGCGCCCGCCCCCGGAGCCCCGCGGACGCUACGCCGCGACGAGUAGGA
GGGCCGCUGCGGUGAGCCUUGAAGCCUAGGGCGCGGGCCCGGGUGGAGCCGCCGCAGGUG
CAGAUCUUGGUGGUAGUAGCAAAUAUUCAAACGAGAACUUUGAAGGCCGAAGUGGAGAAG
GGUUCCAUGUGAACAGCAGUUGAACAUGGGUCAGUCGGUCCUGAGAGAUGGGCGAGCGCC
GUUCCGAAGGGACGGGCGAUGGCCUCCGUUGCCCUCGGCCGAUCGAAAGGGAGUCGGGUU
CAGAUCCCCGAAUCCGGAGUGGCGGAGAUGGGCGCCGCGAGGCGUCCAGUGCGGUAACGC
GACCGAUCCCGGAGAAGCCGGCGGGAGCCCCGGGGAGAGUUCUCUUUUCUUUGUGAAGGG
CAGGGCGCCCUGGAAUGGGUUCGCCCCGAGAGAGGGGCCCGUGCCUUGGAAAGCGUCGCG
GUUCCGGCGGCGUCCGGUGAGCUCUCGCUGGCCCUUGAAAAUCCGGGGGAGAGGGUGUAA
AUCUCGCGCCGGGCCGUACCCAUAUCCGCAGCAGGUCUCCAAGGUGAACAGCCUCUGGCA
UGUUGGAACAAUGUAGGUAAGGGAAGUCGGCAAGCCGGAUCCGUAACUUCGGGAUAAGGA
UUGGCUCUAAGGGCUGGGUCGGUCGUCGGCCGGCGCCUAGCAGCCGACUUAGAACUGGUG
CGGACCAGGGGAAUCCGACUGUUUAAUUAAAACAAAGCAUCGCGAAGGCCCGCGGCGGGU
GUUGACGCGAUGUGAUUUCUGCCCAGUGCUCUGAAUGUCAAAGUGAAGAAAUUCAAUGAA
GCGCGGGUAAACGGCGGGAGUAACUAUGACUCUCUUAAGGUAGCCAAAUGCCUCGUCAUC
UAAUUAGUGACGCGCAUGAAUGGAUGAACGAGAUUCCCACUGUCCCUACCUACUAUCCAG
CGAAACCACAGCCAAGGGAACGGGCUUGGCGGAAUCAGCGGGGAAAGAAGACCCUGUUGA
GCUUGACUCUAGUCUGGCACGGUGAAGAGACAUGAGAGGUGUAGAAUAAGUGGGAGGCCC
CCGGCGCCCCCCCGGUGUCCCCGCGAGGGGCCCGGGGCGGGGUCCGCCGGCCCUGCGGGC
CGCCGGUGAAAUACCACUACUCUGAUCGUUUUUUCACUGACCCGGUGAGGCGGGGGGGCG
AGCCCCGAGGGGCUCUCGCUUCUGGCGCCAAGCGCCCGGCCGCGCGCCGGCCGGGCGCGA
CCCGCUCCGGGGACAGUGCCAGGUGGGGAGUUUGACUGGGGCGGUACACCUGUCAAACGG
UAACGCAGGUGUCCUAAGGCGAGCUCAGGGAGGACAGAAACCUCCCGUGGAGCAGAAGGG
CAAAAGCUCGCUUGAUCUUGAUUUUCAGUACGAAUACAGACCGUGAAAGCGGGGCCUCAC
GAUCCUUCUGACCUUUUGGGUUUUAAGCAGGAGGUGUCAGAAAAGUUACCACAGGGAUAA
CUGGCUUGUGGCGGCCAAGCGUUCAUAGCGACGUCGCUUUUUGAUCCUUCGAUGUCGGCU
CUUCCUAUCAUUGUGAAGCAGAAUUCACCAAGCGUUGGAUUGUUCACCCACUAAUAGGGA
ACGUGAGCUGGGUUUAGACCGUCGUGAGACAGGUUAGUUUUACCCUACUGAUGAUGUGUU
GUUGCCAUGGUAAUCCUGCUCAGUACGAGAGGAACCGCAGGUUCAGACAUUUGGUGUAUG
UGCUUGGCUGAGGAGCCAAUGGGGCGAAGCUACCAUCUGUGGGAUUAUGACUGAACGCCU
CUAAGUCAGAAUCCCGCCCAGGCGGAACGAUACGGCAGCGCCGCGGAGCCUCGGUUGGCC
UCGGAUAGCCGGUCCCCCGCCUGUCCCCGCCGGCGCCGCGCGCCGGGACCGGGGUCCGGU
GCGGAGUGCCCUUCGUCCUGGGAAACGGGGCGCGGCCGGAGAGGCGGCCGCCCCCUCGCC
CGUCACGCACCGGCCGUUCGUGGGGAACCUGGCGCUAAACCAUUCGUAGACGACCUGCUU
CUGGGUCGGGGUUUCGUACGUAGCAGAGCAGCUCCCUCGCUGCGAUCUAUUGAAAGUCAG
CCCUCGACACAAGGGUUUGU

Sequence of entity 3 (d2), FASTA

>6ZVK_3 5S RIBOSOMAL RNA (chains d2)
GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGG
GUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUU

Sequence of entity 4 (h2), FASTA

>6ZVK_4 5.8S RIBOSOMAL RNA (chains h2)
CGACUCUUAGCGGUGGAUCACUCGGCUCGUGCGUCGAUGAAGAACGCAGCUAGCUGCGAG
AAUUAAUGUGAAUUGCAGGACACAUUGAUCAUCGACACUUCGAACGCACUUGCGGCCCCG
GGUUCCUCCCGGGGCUACGCCUGUCUGAGCGUCGCU

Sequence of entity 5 (p2), FASTA

>6ZVK_5 60S RIBOSOMAL PROTEIN EL38 (chains p2)
PRKIEEIKDFLLTARRKDAKSVNIKKNKDNVKFKVRCSRYLYTLVITDKEKAEKLKQSLP
PGLAVKELK

Sequence of entity 6 (w2), FASTA

>6ZVK_6 60S RIBOSOMAL PROTEIN UL13 (chains w2)
QVLVLDGRGHLLGRLAAIVAKQVLLGRKVVVVRCEGINISGNFYRNKLKYLAFLRKRMNT
NPSRGPYHFRAPSRIFWRTVRGMLPHKTKRGQAALDRLKVFDGIPPPYDKKKRMVVPAAL
KVVRLKPTRKFAYLGRLAHEVGWKYQAVTATLEEKRKEKAKIHYRKKKQLMRLRKQAEKN
VEKKISKFTDVLKTHGLLV

Sequence of entity 7 (H2), FASTA

>6ZVK_7 uL22 (chains H2)
VRYSLDPENPTKSCKSRGSNLRVHFKNTRETAQAIKGMHIRKATKYLKDVTLKKQCVPFR
RYNGGVGRCAQAKQWGWTQGRWPKKSAEFLLHMLKNAESNAELKGLDVDSLVIEHIQVNK
APKMRRRTYRAHGRINPYMSSPCHIEMILTEKE

Sequence of entity 8 (S2), FASTA

>6ZVK_8 60S RIBOSOMAL PROTEIN EL18 (chains S2)
GVDIRHNKDRKVRRKEPKSQDIYLRLLVKLYRFLARRTNSTFNQVVLKRLFMSRTNRPPL
SLSRMIRKMKLPGRENKTAVVVGTITDDVRVQEVPKLKVCALRVTSRARSRILRAGGKIL
TFDQLALDSPKGCGTVLLSGPRKGREVYRHFGKAPGTPHSHTKPYVRSKGRKFERARGRR
ASRGYKN

Sequence of entity 9 (32), FASTA

>6ZVK_9 60S RIBOSOMAL PROTEIN EL19 (chains 32)
SMLRLQKRLASSVLRCGKKKVWLDPNETNEIANANSRQQIRKLIKDGLIIRKPVTVHSRA
RCRKNTLARRKGRHMGIGKRKGTANARMPEKVTWMRRMRILRRLLRRYRESKKIDRHMYH
SLYLKVKGNVFKNKRILMEHIHKLKADKARKKLLADQAEARRSKTKEARKRREERLQAKK

Sequence of entity 10 (52), FASTA

>6ZVK_10 uL3 (chains 52)
SHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDPSKPVHLTAFLGYKAGMTHIVREVD
RPGSKVNKKEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYKN
WHKSKKKAFTKYCKKWQDDAGKRQLDKDFSSMKKYCQVIRVLAHTQMRLLPLRQKKAHLM
EIQVNGGTVAEKLDWARERLEQQVPVSQVFGQDEMIDVIGVTKGKGYKGVTSRWHTKKLP
RKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEINKKIYKIGQGYLIKDGKLIKN
NASTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRALE
KIDLKFIDTTSKFGHGRFQTVEEKKAFMGPLKKD

Sequence of entity 11 (62), FASTA

>6ZVK_11 60S RIBOSOMAL PROTEIN EL20 (chains 62)
KASGTLREYKVVGRCLPTPKCHTPPLYRMRIFAPNHVVAKSRFWYFVSQLKKMKKSSGEI
VYCGQVFEKSPLRVKNFGIWLRYDSRSGTHNMYREYRDLTTAGAVTQCYRDMGARHRARA
HSIQIMKVEEIAASKCRRPAVKQFHDSKIKFPLPHRVLRRQHKPRFTTKRPNTFF

Sequence of entity 12 (72), FASTA

>6ZVK_12 eL21 (chains 72)
TNTKGKRRGTRYMFSRPFRKHGVVPLATYMRIYKKGDIVDIKGMGTVQKGMPHKCYHGKT
GRVYNVTQHAVGIVVNKQVKGKILAKRINVRIEHIKHSKSRDSFLKRVKENDQKKKEAKE
KGTWVQLKRQPAPPREAHFVRTNGKEPELLEPIPYEFMA

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 G1SZ12 (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…
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

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