6WOO: UL2

Name: PDB 6WOO: CryoEM structure of yeast 80S ribosome with Met-tRNAiMet, eIF5B, and GDP
Published: 2020-09-23
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

CryoEM structure of yeast 80S ribosome with Met-tRNAiMet, eIF5B, and GDP. Determined by electron microscopy at 2.9 Å resolution. Released 23 Sept 2020.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Saccharomyces cerevisiae
Chains: 84
Atoms: 211,119
Mol. weight: 3121.3 kDa
Ligands: ZN, GDP, U6A, MET
Released: 23 Sept 2020

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

Secondary structure: helices and β-sheets

6WOO contains 502 α-helices and 576 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 1: 19 helices, 42 β-strands

Element	Residues	Length	Sheet
β-strand	407-409	3	34
β-strand	410-411	2	35
α-helix	421-425	5
β-strand	444-447	4	34
α-helix	449-455	7
α-helix	458-462	5
β-strand	472-475	4	34
β-strand	497-500	4	35
α-helix	503-505	3
α-helix	511-518	8
β-strand	525-529	5	35
β-strand	531	1	36
α-helix	546-551	6
α-helix	555-573	19
β-strand	580	1	37
α-helix	592	1
β-strand	593	1	37
β-strand	594-596	3	35
β-strand	598	1	36
α-helix	605-617	13
β-strand	632-638	7	38
β-strand	646-651	6	38
β-strand	655-656	2	39
β-strand	661-663	3	40
β-strand	672-674	3	40
β-strand	675-679	5	38
β-strand	699-700	2	39
β-strand	704-709	6	38
β-strand	720	1	38
β-strand	722-723	2	40
β-strand	755-759	5	41
α-helix	762-773	12
β-strand	779-781	3	41
β-strand	784	1	41
β-strand	787	1	42
α-helix	789-792	4
α-helix	793-798	6
β-strand	807-811	5	41
α-helix	814	1
β-strand	815	1	42
α-helix	816	1
α-helix	817-825	9
β-strand	829-833	5	41
α-helix	842-857	16
β-strand	867	1	43
β-strand	870-875	6	44
β-strand	880-884	5	44
β-strand	888	1	43
β-strand	890-892	3	45
β-strand	897-900	4	43
β-strand	911-913	3	43
β-strand	917-922	6	44
β-strand	925-927	3	44
β-strand	929-931	3	45
β-strand	939-943	5	44
β-strand	953	1	46
β-strand	957	1	46
α-helix	962-963	2
β-strand	964-965	2	43
α-helix	969-975	7
α-helix	993-999	7

Chain a: 5 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	7-11	5
α-helix	42-46	5
β-strand	72-73	2	20
α-helix	78-81	4
α-helix	84-91	8
β-strand	99-100	2	105
β-strand	102-103	2	21
β-strand	111-112	2	20
β-strand	125-126	2	21
β-strand	129-130	2	20
α-helix	132-141	10
β-strand	145-146	2	21

Chain A: 11 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
α-helix	6-9	4
α-helix	29-31	3
α-helix	34-38	5
β-strand	40-51	12	25
β-strand	54-62	9	25
β-strand	73-75	3	25
α-helix	78	1
β-strand	79	1	26
β-strand	83	1	27
α-helix	86	1
β-strand	87-91	5	25
β-strand	101-103	3	25
α-helix	104-106	3
β-strand	112-114	3	25
β-strand	116	1	28
β-strand	126	1	28
β-strand	134-135	2	25
β-strand	145-149	5	25
β-strand	155-159	5	25
β-strand	163-166	4	25
α-helix	168	1
β-strand	169	1	26
α-helix	183-189	7
α-helix	198-200	3
α-helix	201-203	3
β-strand	224-225	2	29
β-strand	237-238	2	29

Chain aa: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	18-19	2
β-strand	20-22	3	151
β-strand	29-31	3	151
β-strand	36-43	8	152
α-helix	50-55	6
β-strand	57	1	82
β-strand	66-73	8	152
α-helix	75-79	5

Chain AA: 8 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	11-17	7
α-helix	40-41	2
α-helix	50-66	17
α-helix	70-72	3
β-strand	73-76	4	150
α-helix	80-82	3
α-helix	83-92	10
β-strand	97-98	2	150
β-strand	120-123	4	150
α-helix	130-137	8
β-strand	143-145	3	150
β-strand	157-159	3	150
α-helix	168-183	16

Chain b: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	12-19	8
α-helix	37-57	21

Chain B: 13 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	9-10	2
α-helix	40-41	2
β-strand	43	1	47
β-strand	46-58	13	48
β-strand	63	1	49
β-strand	65	1	49
β-strand	72-80	9	48
β-strand	84-86	3	50
β-strand	88-96	9	50
β-strand	98-106	9	50
α-helix	112-115	4
α-helix	116-118	3
α-helix	122-124	3
α-helix	134-137	4
α-helix	142-153	12
β-strand	157-163	7	50
β-strand	178-182	5	50
β-strand	183	1	47
α-helix	188-197	10
β-strand	202-203	2	50
α-helix	205-208	4
β-strand	214-220	7	48
α-helix	229-232	4
α-helix	236-239	4
β-strand	274-276	3	48
β-strand	280-284	5	48
α-helix	307	1
β-strand	311	1	51
β-strand	315	1	51
β-strand	321-325	5	48
β-strand	335-340	6	48
β-strand	356-359	4	48
α-helix	373-379	7

Chain bb: 1 helix, 7 β-strands

Element	Residues	Length	Sheet
α-helix	12-15	4
β-strand	32-34	3	156
β-strand	36	1	157
β-strand	45-47	3	156
β-strand	55	1	158
β-strand	62	1	158
β-strand	78	1	157
β-strand	81	1	156

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
25S ribosomal RNA	5	RNA	3271	Saccharomyces cerevisiae
5S ribosomal RNA	7	RNA	121	Saccharomyces cerevisiae
5.8S ribosomal rRNA	8	RNA	157	Saccharomyces cerevisiae
uL2	A	protein	249	Saccharomyces cerevisiae	P0CX45 (AlphaFold model)
uL3	B	protein	384	Saccharomyces cerevisiae	P14126 (AlphaFold model)
uL4	C	protein	359	Saccharomyces cerevisiae	P10664 (AlphaFold model)
uL18	D	protein	295	Saccharomyces cerevisiae	P26321 (AlphaFold model)
eL6	E	protein	175	Saccharomyces cerevisiae	Q02326
uL30	F	protein	222	Saccharomyces cerevisiae	P05737
eL8	G	protein	233	Saccharomyces cerevisiae	P17076
uL6	H	protein	191	Saccharomyces cerevisiae	P51401
uL16	I	protein	216	Saccharomyces cerevisiae	P41805

72 more molecules are not listed.

Sequence of entity 1 (5), FASTA

>6WOO_1 25S ribosomal RNA (chains 5)
GUUUGACCUCAAAUCAGGUAGGAGUACCCGCUGAACUUAAGCAUAUCAAUAAGCGGAGGA
AAAGAAACCAACCGGGAUUGCCUUAGUAACGGCGAGUGAAGCGGCAAAAGCUCAAAUUUG
AAAUCUGGUACCUUCGGUGCCCGAGUUGUAAUUUGGAGAGGGCAACUUUGGGGCCGUUCC
UUGUCUAUGUUCCUUGGAACAGGACGUCAUAGAGGGUGAGAAUCCCGUGUGGCGAGGAGU
GCGGUUCUUUGUAAAGUGCCUUCGAAGAGUCGAGUUGUUUGGGAAUGCAGCUCUAAGUGG
GUGGUAAAUUCCAUCUAAAGCUAAAUAUUGGCGAGAGACCGAUAGCGAACAAGUACAGUG
AUGGAAAGAUGAAAAGAACUUUGAAAAGAGAGUGAAAAAGUACGUGAAAUUGUUGAAAGG
GAAGGGCAUUUGAUCAGACGCCAGCAUCAGUUUUGGUGGCAGGAUAAAUCCAUAGGAAUG
UAGCUUGCCUCGGUAAGUAUUAUAGCCUGUGGGAAUACUGCCAGCUGGGACUGAGGACUG
CGACGUAAGUCAAGGAUGCUGGCAUAAUGGUUAUAUGCCGCCCGUCUUGAAACACGGACC
AAGGAGUCUAACGUCUAUGCGAGUGUUUGGGUGUAAAACCCAUACGCGUAAUGAAAGUGA
ACGUAGGUUGGGGCCUCGCAAGAGGUGCACAAUCGACCGAUCCUGAUGUCUUCGGAUGGA
UUUGAGUAAGAGCAUAGCUGUUGGGACCCGAAAGAUGGUGAACUAUGCCUGAAUAGGGUG
AAGCCAGAGGAAACUCUGGUGGAGGCUCGUAGCGGUUCUGACGUGCAAAUCGAUCGUCGA
AUUUGGGUAUAGGGGCGAAAGACUAAUCGAACCAUCUAGUAGCUGGUUCCUGCCGAAGUU
UCCCUCAGGAUAGCAGAAGCUCGUAUCAGUUUUAUGAGGUAAAGCGAAUGAUUAGAGGUU
CCGGGGUCGAAAUGACCUUGACCUAUUCUCAAACUUUAAAUAUGUAAGAAGUCCUUGUUA
CUUAAUUGAACGUGGACAUUUGAAUGAAGAGCUUUUAGUGGGCCAUUUUUGGUAAGCAGA
ACUGGCGAUGCGGGAUGAACCGAACGUAGAGUUAAGGUGCCGGAAUACACGCUCAUCAGA
CACCACAAAAGGUGUUAGUUCAUCUAGACAGCCGGACGGUGGCCAUGGAAGUCGGAAUCC
GCUAAGGAGUGUGUAACAACUCACCGGCCGAAUGAACUAGCCCUGAAAAUGGAUGGCGCU
CAAGCGUGUUACCUAUACUCUACCGUCAGGGUUGAUAUGAUGCCCUGACGAGUAGGCAGG
CGUGGAGGUCAGUGACGAAGCCUAGACCGUAAGGUCGGGUCGAACGGCCUCUAGUGCAGA
UCUUGGUGGUAGUAGCAAAUAUUCAAAUGAGAACUUUGAAGACUGAAGUGGGGAAAGGUU
CCACGUCAACAGCAGUUGGACGUGGGUUAGUCGAUCCUAAGAGAUGGGGAAGCUCCGUUU
CAAAGGCCUGAUUUUAUGCAGGCCACCAUCGAAAGGGAAUCCGGUUAAGAUUCCGGAACC
UGGAUAUGGAUUCUUCACGGUAACGUAACUGAAUGUGGAGACGUCGGCGCGAGCCCUGGG
AGGAGUUAUCUUUUCUUCUUAACAGCUUAUCACCCCGGAAUUGGUUUAUCCGGAGAUGGG
GUCUUAUGGCUGGAAGAGGCCAGCACCUUUGCUGGCUCCGGUGCGCUUGUGACGGCCCGU
GAAAAUCCACAGGAAGGAAUAGUUUUCAUGCCAGGUCGUACUGAUAACCGCAGCAGGUCU
CCAAGGUGAACAGCCUCUAGUUGAUAGAAUAAUGUAGAUAAGGGAAGUCGGCAAAAUAGA
UCCGUAACUUCGGGAUAAGGAUUGGCUCUAAGGGUCGGGUAGUGAGGGCCUUGGUCAGAC
GCAGCGUUGUAGACGGCCUUGGUAGGUCUCUUGUAGAUGCUACAAUUACGAUCAACUUAG
AACUGGUACGGACAAGGGGAAUCUGACUGUCUAAUUAAAACAUAGCAUUGCGAUGGUCAG
AAAGUGAUGUUGACGCAAUGUGAUUUCUGCCCAGUGCUCUGAAUGUCAAAGUGAAGAAAU
UCAACCAAGCGCGGGUAAACGGCGGGAGUAACUAUGACUCUCUUAAGGUAGCCAAAUGCC
UCGUCAUCUAAUUAGUGACGCGCAUGAAUGGAUUAACGAGAUUCCCACUGUCCCUAUCUA
CUAUCUAGCGAAACCACAGCCAAGGGAACGGGCUUGGCAGAAUCAGCGGGGAAAGAAGAC
CCUGUUGAGCUUGACUCUAGUUUGACAUUGUGAAGAGACAUAGAGGGUGUAGAAUAAGUG
GGAGCUUCGGCGCCAGUGAAAUACCACUACCUUUAUAGUUUCUUUACUUAUUCAAUGAAG
CGGAGCUGGAAUUCAUUUUCCACGUUCUAGCAUUCAAGGUCCCAUUCGGGGCUGAUCCGG
GUUGAAGACAUUGUCAGGUGGGGAGUUUGGCUGGGGCGGCACAUCUGUUAAACGAUAACG
CAGAUGUCCUAAGGGGGGCUCAUGGAGAACAGAAAUCUCCAGUAGAACAAAAGGGUAAAA
GCCCCCUUGAUUUUGAUUUUCAGUGUGAAUACAAACCAUGAAAGUGUGGCCUAUCGAUCC
UUUAGUCCCUCGGAAUUUGAGGCUAGAGGUGCCAGAAAAGUUACCACAGGGAUAACUGGC
UUGUGGCAGUCAAGCGUUCAUAGCGACAUUGCUUUUUGAUUCUUCGAUGUCGGCUCUUCC
UAUCAUACCGAAGCAGAAUUCGGUAAGCGUUGGAUUGUUCACCCACUAAUAGGGAACGUG
AGCUGGGUUUAGACCGUCGUGAGACAGGUUAGUUUUACCCUACUGAUGAAUGUUACCGCA
AUAGUAAUUGAACUUAGUACGAGAGGAACAGUUCAUUCGGAUAAUUGGUUUUUGCGGCUG
UCUGAUCAGGCAUUGCCGCGAAGCUACCAUCCGCUGGAUUAUGGCUGAACGCCUCUAAGU
CAGAAUCCAUGCUAGAACGCGGUGAUUUCUUUGCUCCACACAAUAUAGAUGGAUACGAAU
AAGGCGUCCUUGUGGCGUCGCUGAACCAUAGCAGGCUAGCAACGGUGCACUUGGCGGAAA
GGCCUUGGGUGCUUGCUGGCGAAUUGCAAUGUCAUUUUGCGUGGGGAUAAAUCAUUUGUA
UACGACUUAGAUGUACAACGGGGUAUUGUAAGCAGUAGAGUAGCCUUGUUGUUACGAUCU
GCUGAGAUUAAGCCUUUGUUGUCUGAUUUGU

Sequence of entity 2 (7), FASTA

>6WOO_2 5S ribosomal RNA (chains 7)
GGUUGCGGCCAUAUCUACCAGAAAGCACCGUUUCCCGUCCGAUCAACUGUAGUUAAGCUG
GUAAGAGCCUGACCGAGUAGUGUAGUGGGUGACCAUACGCGAAACUCAGGUGCUGCAAUC
U

Sequence of entity 3 (8), FASTA

>6WOO_3 5.8S ribosomal rRNA (chains 8)
AAACUUUCAACAACGGAUCUCUUGGUUCUCGCAUCGAUGAAGAACGCAGCGAAAUGCGAU
ACGUAAUGUGAAUUGCAGAAUUCCGUGAAUCAUCGAAUCUUUGAACGCACAUUGCGCCCC
UUGGUAUUCCAGGGGGCAUGCCUGUUUGAGCGUCAUU

Sequence of entity 4 (A), FASTA

>6WOO_4 uL2 (chains A)
GRVIRNQRKGAGSIFTSHTRLRQGAAKLRTLDYAERHGYIRGIVKQIVHDSGRGAPLAKV
VFRDPYKYRLREEIFIANEGVHTGQFIYAGKKASLNVGNVLPLGSVPEGTIVSNVEEKPG
DRGALARASGNYVIIIGHNPDENKTRVRLPSGAKKVISSDARGVIGVIAGGGRVDKPLLK
AGRAFHKYRLKRNSWPKTRGVAMNPVDHPHGGGNHQHIGKASTISRGAVSGQKAGLIAAR
RTGLLRGSQ

Sequence of entity 5 (B), FASTA

>6WOO_5 uL3 (chains B)
SHRKYEAPRHGHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKAGMTTIVRDLD
RPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRSLTTVWAEHLSDEVKRRFYKN
WYKSKKKAFTKYSAKYAQDGAGIERELARIKKYASVVRVLVHTQIRKTPLAQKKAHLAEI
QLNGGSISEKVDWAREHFEKTVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPRK
THRGLRKVACIGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEANGATSFDRT
KKTITPMGGFVHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKALEEVSLKWIDT
ASKFGKGRFQTPAEKHAFMGTLKK

Sequence of entity 6 (C), FASTA

>6WOO_6 uL4 (chains C)
RPQVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQTSA
ESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEKRYAT
ASAIAATAVASLVLARGHRVEKIPEIPLVVSTDLESIQKTKEAVAALKAVGAHSDLLKVL
KSKKLRAGKGKYRNRRWTQRRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAPGA
HLGRFVIWTEAAFTKLDQVWGSETVASSKVGYTLPSHIISTSDVTRIINSSEIQSAIRPA
GQATQKRTHVLKKNPLKNKQVLLRLNPYAKVFAAEKLGSKKAEKTGTKPAAVFTETLKH

Sequence of entity 7 (D), FASTA

>6WOO_7 uL18 (chains D)
FQKDAKSSAYSSRFQTPFRRRREGKTDYYQRKRLVTQHKAKYNTPKYRLVVRFTNKDIIC
QIISSTITGDVVLAAAYSHELPRYGITHGLTNWAAAYATGLLIARRTLQKLGLDETYKGV
EEVEGEYELTEAVEDGPRPFKVFLDIGLQRTTTGARVFGALKGASDGGLYVPHSENRFPG
WDFETEEIDPELLRSYIFGGHVSQYMEELADDDEERFSELFKGYLADDIDADSLEDIYTS
AHEAIRADPAFKPTEKKFTKEQYAAESKKYRQTKLSKEERAARVAAKIAALAGQQ

Sequence of entity 8 (E), FASTA

>6WOO_8 eL6 (chains E)
SAQKAPKWYPSEDVAALKKTRKAARPQKLRASLVPGTVLILLAGRFRGKRVVYLKHLEDN
TLLISGPFKVNGVPLRRVNARYVIATSTKVSVEGVNVEKFNVEYFAKEKLTKKEKKEANL
FPEQQNKEIKAERVEDQKVVDKALIAEIKKTPLLKQYLSASFSLKNGDKPHMLKF

Sequence of entity 9 (F), FASTA

>6WOO_9 uL30 (chains F)
AEQVAAERAARKAANKEKRAIILERNAAYQKEYETAERNIIQAKRDAKAAGSYYVEAQHK
LVFVVRIKGINKIPPKPRKVLQLLRLTRINSGTFVKVTKATLELLKLIEPYVAYGYPSYS
TIRQLVYKRGFGKINKQRVPLSDNAIIEANLGKYGILSIDDLIHEIITVGPHFKQANNFL
WPFKLSNPSGGWGVPRKFKHFIQGGSFGNREEFINKLVKSMN

Sequence of entity 10 (G), FASTA

>6WOO_10 eL8 (chains G)
NPLTHSTPKNFGIGQAVQPKRNLSRYVKWPEYVRVQRQKKILSIRLKVPPTIAQFQYTLD
RNTAAETFKLFNKYRPETAAEKKERLTKEAAAVAEGKSKQDASPKPYAVKYGLNHVVALI
ENKKAKLVLIANDVDPIELVVFLPALCKKMGVPYAIVKGKARLGTLVNQKTSAVAALTEV
RAEDEAALAKLVSTIDANFADKYDEVKKHWGGGILGNKAQAKMDKRAKNSDSA

Sequence of entity 11 (H), FASTA

>6WOO_11 uL6 (chains H)
MKYIQTEQQIEIPEGVTVSIKSRIVKVVGPRGTLTKNLKHIDVTFTKVNNQLIKVAVHNG
DRKHVAALRTVKSLVDNMITGVTKGYKYKMRYVYAHFPINVNIVEKDGAKFIEVRNFLGD
KKIRNVPVRDGVTIEFSTNVKDEIVLSGNSVEDVSQNAADLQQICRVRNKDIRKFLDGIY
VSHKGFIVEDE

Sequence of entity 12 (I), FASTA

>6WOO_12 uL16 (chains I)
RRPARCYRYQKNKPYPKSRYNRAVPDSKIRIYDLGKKKATVDEFPLCVHLVSNELEQLSS
EALEAARICANKYMTTVSGRDAFHLRVRVHPFHVLRINKMLSCAGADRLQQGMRGAWGKP
HGLAARVDIGQIIFSVRTKDSNKDVVVEGLRRARYKFPGQQKIILSKKWGFTNLDRPEYL
KKREAGEVKDDGAFVKFLSKKGSLENNIREFPEYFA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	6
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
U6A	N-carboxy-L-threonine	C5 H9 N O5	1
MET	Methionine	C5 H11 N O2 S	1

Primary citation

Structural basis for the transition from translation initiation to elongation by an 80S-eIF5B complex. Wang, J., Wang, J., Shin, B.S. et al. Nat Commun (2020) 11:5003-5003. DOI 10.1038/s41467-020-18829-3 · PubMed

Other PDB entries of the same protein (UniProt P0CX45 (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…
8P8N 2.15 Å, Mouse RPL39 integrated into the yeast 60S ribosomal subunit
8PFR 2.15 Å, Mouse RPL39L integrated into the yeast 60S ribosomal subunit
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,…
8P8U 2.23 Å, Yeast 60S ribosomal subunit
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
7UOO 2.34 Å, Nucleoplasmic pre-60S intermediate of the Nog2 containing pre-rotation state

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