8CAH: PDB entry 8CAH

Name: PDB 8CAH: Cryo-EM structure of native Otu2-bound ubiquitinated 43S pre-initiation complex
Published: 2023-05-24
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Cryo-EM structure of native Otu2-bound ubiquitinated 43S pre-initiation complex. Determined by electron microscopy at 3.0 Å resolution. Released 24 May 2023.

Method: Electron microscopy
Resolution: 3.0 Å
Organism: Saccharomyces cerevisiae W303
Chains: 48
Atoms: 95,563
Mol. weight: 1743.3 kDa
Ligands: ADP, SF4, ZN, MG
Released: 24 May 2023

Explore 8CAH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8CAH contains 338 α-helices and 398 β-strands across 47 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: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	105
β-strand	8	1	105
α-helix	13-15	3
β-strand	16	1	106
β-strand	23	1	106
β-strand	32-39	8	107
β-strand	45-55	11	107
α-helix	57-61	5
α-helix	65-75	11

Chain A: 11 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	7-28	22
β-strand	34-42	9	12
β-strand	45-52	8	12
α-helix	55-59	5
α-helix	61-63	3
α-helix	64-77	14
α-helix	79-80	2
β-strand	84-90	7	12
α-helix	91	1
α-helix	98-111	14
β-strand	114	1	13
α-helix	115-128	14
β-strand	133-139	7	14
β-strand	141	1	15
β-strand	147	1	15
β-strand	152-155	4	14
α-helix	163-167	5
β-strand	168-176	9	14
β-strand	181-189	9	14
α-helix	192-194	3
β-strand	207-208	2	16
α-helix	209-211	3
β-strand	221-224	4	17

Chain b: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-20	15
β-strand	24-27	4	108
α-helix	32-43	12
β-strand	50-54	5	108
β-strand	60-64	5	108
β-strand	72-74	3	109
β-strand	80-81	2	109
α-helix	83-93	11
β-strand	101-106	6	109
β-strand	109-112	4	109
α-helix	113-119	7
β-strand	123-129	7	109

Chain B: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	31-34	4
β-strand	59	1	19
β-strand	62	1	19
α-helix	83-85	3
α-helix	89-95	7
α-helix	107-124	18
α-helix	129-139	11
β-strand	144-149	6	20
β-strand	156-161	6	20
α-helix	164-182	19
α-helix	190-203	14
α-helix	209-223	15

Chain c: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	12-22	11
α-helix	23-25	3
α-helix	27-34	8
α-helix	36-39	4
β-strand	49-57	9	112
α-helix	59	1
β-strand	60	1	113
α-helix	61	1
β-strand	68	1	113
β-strand	71-76	6	112
β-strand	82-86	5	112
α-helix	92-95	4
β-strand	101-106	6	112
β-strand	122-127	6	112
β-strand	130-131	2	112
α-helix	132-136	5

Chain C: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	5-18	14
β-strand	20-22	3	36
α-helix	39-50	12
β-strand	55-58	4	36
β-strand	65-68	4	36
α-helix	70-80	11
α-helix	82-83	2

Chain d: 8 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	8-15	8	116
β-strand	20-27	8	116
α-helix	37-48	12
α-helix	52-54	3
β-strand	55-62	8	116
α-helix	63	1
β-strand	69-76	8	116
α-helix	79-85	7
α-helix	88-94	7
α-helix	99-101	3
α-helix	105-115	11
α-helix	123-132	10

Chain D: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	28-36	9
β-strand	41-43	3	39
α-helix	45-51	7
β-strand	59-63	5	39
α-helix	70-78	9
β-strand	89-91	3	39
α-helix	94-100	7
β-strand	121-123	3	39
α-helix	131-141	11

39 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
Eukaryotic translation initiation factor 3 subunit I	l	protein	347	Saccharomyces cerevisiae W303	P40217 (AlphaFold model)
Eukaryotic translation initiation factor 3 subunit G	r	protein	274	Saccharomyces cerevisiae W303	Q04067 (AlphaFold model)
Eukaryotic translation initiation factor 3 subunit A	o	protein	964	Saccharomyces cerevisiae W303	P38249 (AlphaFold model)
Eukaryotic translation initiation factor 3 subunit B	p	protein	763	Saccharomyces cerevisiae W303	P06103 (AlphaFold model)
Eukaryotic translation initiation factor 3 subunit C	q	protein	812	Saccharomyces cerevisiae W303	P32497
Eukaryotic translation initiation factor 4C	i	protein	153	Saccharomyces cerevisiae W303	P38912
SUI1 isoform 1	m	protein	108	Saccharomyces cerevisiae W303	P32911
RNA recognition motif (unknown)	j	protein	77	Saccharomyces cerevisiae W303
18S ribosomal RNA	2	RNA	1800	Saccharomyces cerevisiae W303
40S ribosomal protein S0-A	P	protein	252	Saccharomyces cerevisiae W303	P32905
40S ribosomal protein S1-A	Q	protein	255	Saccharomyces cerevisiae W303	P33442
40S ribosomal protein S2	R	protein	254	Saccharomyces cerevisiae W303	P25443

35 more molecules are not listed.

Sequence of entity 1 (l), FASTA

>8CAH_1 Eukaryotic translation initiation factor 3 subunit I (chains l)
MKAIKLTGHERPLTQVKYNKEGDLLFSCSKDSSASVWYSLNGERLGTLDGHTGTIWSIDV
DCFTKYCVTGSADYSIKLWDVSNGQCVATWKSPVPVKRVEFSPCGNYFLAILDNVMKNPG
SINIYEIERDSATHELTKVSEEPIHKIITHEGLDAATVAGWSTKGKYIIAGHKDGKISKY
DVSNNYEYVDSIDLHEKSISDMQFSPDLTYFITSSRDTNSFLVDVSTLQVLKKYETDCPL
NTAVITPLKEFIILGGGQEAKDVTTTSANEGKFEARFYHKIFEEEIGRVQGHFGPLNTVA
ISPQGTSYASGGEDGFIRLHHFEKSYFDFKYDVEKAAEAKEHMQEAN

Sequence of entity 2 (r), FASTA

>8CAH_2 Eukaryotic translation initiation factor 3 subunit G (chains r)
MSEVAPEEIIENADGSRSIITYKIEDGVKYKITQKVKEVKVLEKVHKSVAERKNWHKYGS
EKGSPAGPSAVTARLGEEVELRLSRNWKQAEEERIQKEKASLTKTGLQCRLCGNDHMTMN
CPFKTILSELSALEDPATNEGGVEAASEEKAGQVGGAGSIPGQYVPPSRRAGARDPSSDA
YRDSRERDDMCTLKIMQVNENADENSLREELLFPFAPIPRVSVVRNKETGKSRGLAFVTF
SSEEVAEQALRFLDGRGYMNLILRVEWSKPKVKE

Sequence of entity 3 (o), FASTA

>8CAH_3 Eukaryotic translation initiation factor 3 subunit A (chains o)
MAPPPFRPENAIKRADELISVGEKQAALQSLHDFITARRIRWATPSTVEPVVFKFLEIGV
ELKKGKLLKDGLHQYKKLIQGSTEGLVSVGAVARKFIDLVESKIASEQTRADELQKQEID
DDLEGGVTPENLLISVYESDQSVAGFNDEAITSWLRFTWESYRAVLDLLRNNALLEITYS
GVVKKTMHFCLKYQRKNEFKRLAEMLRQHLDAANYQQSKSGNNLVDLSDADTLQRYLDQR
FQQVDVSVKLELWHEAYRSIEDVFHLMKISKRAPKPSTLANYYENLVKVFFVSGDPLLHT
TAWKKFYKLYSTNPRATEEEFKTYSSTIFLSAISTQLDEIPSIGYDPHLRMYRLLNLDAK
PTRKEMLQSIIEDESIYGKVDEELKELYDIIEVNFDVDTVKQQLENLLVKLSSKTYFSQY
IAPLRDVIMRRVFVAASQKFTTVSQSELYKLATLPAPLDLSAWDIEKSLLQAAVEDYVSI
TIDHESAKVTFAKDPFDIFASTASKEVSEEENTEPEVQEEKEETDEALGPQETEDGEEKE
EESDPVIIRNSYIHNKLLELSNVLHDVDSFNNASYMEKVRIARETLIKKNKDDLEKISKI
VDERVKRSQEQKQKHMEHAALHAEQDAEVRQQRILEEKAAIEAKLEEEAHRRLIEKKKRE
FEAIKEREITKMITEVNAKGHVYIDPNEAKSLDLDTIKQVIIAEVSKNKSELESRMEYAM
KKLDHTERALRKVELPLLQKEVDKLQETDTANYEAMKKKIVDAAKAEYEARMADRKNLVM
VYDDYLKFKEHVSGTKESELAAIRNQKKAELEAAKKARIEEVRKRRYEEAIARRKEEIAN
AERQKRAQELAEATRKQREIEEAAAKKSTPYSFRAGNREPPSTPSTLPKATVSPDKAKLD
MIAQKQREMEEAIEQRLAGRTAGGSSPATPATPATPATPTPSSGPKKMTMAEKLRAKRLA
KGGR

Sequence of entity 4 (p), FASTA

>8CAH_4 Eukaryotic translation initiation factor 3 subunit B (chains p)
MKNFLPRTLKNIYELYFNNISVHSIVSRNTQLKRSKIIQMTTETFEDIKLEDIPVDDIDF
SDLEEQYKVTEEFNFDQYIVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEAT
GKTKGFLFVECGSMNDAKKIIKSFHGKRLDLKHRLFLYTMKDVERYNSDDFDTEFREPDM
PTFVPSSSLKSWLMDDKVRDQFVLQDDVKTSVFWNSMFNEEDSLVESRENWSTNYVRFSP
KGTYLFSYHQQGVTAWGGPNFDRLRRFYHPDVRNSSVSPNEKYLVTFSTEPIIVEEDNEF
SPFTKKNEGHQLCIWDIASGLLMATFPVIKSPYLKWPLVRWSYNDKYCARMVGDSLIVHD
ATKNFMPLEAKALKPSGIRDFSFAPEGVKLQPFRNGDEPSVLLAYWTPETNNSACTATIA
EVPRGRVLKTVNLVQVSNVTLHWQNQAEFLCFNVERHTKSGKTQFSNLQICRLTERDIPV
EKVELKDSVFEFGWEPHGNRFVTISVHEVADMNYAIPANTIRFYAPETKEKTDVIKRWSL
VKEIPKTFANTVSWSPAGRFVVVGALVGPNMRRSDLQFYDMDYPGEKNINDNNDVSASLK
DVAHPTYSAATNITWDPSGRYVTAWSSSLKHKVEHGYKIFNIAGNLVKEDIIAGFKNFAW
RPRPASILSNAERKKVRKNLREWSAQFEEQDAMEADTAMRDLILHQRELLKQWTEYREKI
GQEMEKSMNFKIFDVQPEDASDDFTTIEEIVEEVLEETKEKVE

Sequence of entity 5 (q), FASTA

>8CAH_5 Eukaryotic translation initiation factor 3 subunit C (chains q)
MSRFFSSNYEYDVASSSSEEDLLSSSEEDLLSSSSSESELDQESDDSFFNESESESEADV
DSDDSDAKPYGPDWFKKSEFRKQGGGSNKFLKSSNYDSSDEESDEEDGKKVVKSAKEKLL
DEMQDVYNKISQAENSDDWLTISNEFDLISRLLVRAQQQNWGTPNIFIKVVAQVEDAVNN
TQQADLKNKAVARAYNTTKQRVKKVSRENEDSMAKFRNDPESFDKEPTADLDISANGFTI
SSSQGNDQAVQEDFFTRLQTIIDSRGKKTVNQQSLISTLEELLTVAEKPYEFIMAYLTLI
PSRFDASANLSYQPIDQWKSSFNDISKLLSILDQTIDTYQVNEFADPIDFIEDEPKEDSD
GVKRILGSIFSFVERLDDEFMKSLLNIDPHSSDYLIRLRDEQSIYNLILRTQLYFEATLK
DEHDLERALTRPFVKRLDHIYYKSENLIKIMETAAWNIIPAQFKSKFTSKDQLDSADYVD
NLIDGLSTILSKQNNIAVQKRAILYNIYYTALNKDFQTAKDMLLTSQVQTNINQFDSSLQ
ILFNRVVVQLGLSAFKLCLIEECHQILNDLLSSSHLREILGQQSLHRISLNSSNNASADE
RARQCLPYHQHINLDLIDVVFLTCSLLIEIPRMTAFYSGIKVKRIPYSPKSIRRSLEHYD
KLSFQGPPETLRDYVLFAAKSMQKGNWRDSVKYLREIKSWALLPNMETVLNSLTERVQVE
SLKTYFFSFKRFYSSFSVAKLAELFDLPENKVVEVLQSVIAELEIPAKLNDEKTIFVVEK
GDEITKLEEAMVKLNKEYKIAKERLNPPSNRR

Sequence of entity 6 (i), FASTA

>8CAH_6 Eukaryotic translation initiation factor 4C (chains i)
MGKKNTKGGKKGRRGKNDSDGPKRELIYKEEGQEYAQITKMLGNGRVEASCFDGNKRMAH
IRGKLRKKVWMGQGDIILVSLRDFQDDQCDVVHKYNLDEARTLKNQGELPENAKINETDN
FGFESDEDVNFEFGNADEDDEEGEDEELDIDDI

Sequence of entity 7 (m), FASTA

>8CAH_7 SUI1 isoform 1 (chains m)
MSIENLKSFDPFADTGDDETATSNYIHIRIQQRNGRKTLTTVQGVPEEYDLKRILKVLKK
DFACNGNIVKDPEMGEIIQLQGDQRAKVCEFMISQLGLQKKNIKIHGF

Sequence of entity 8 (j), FASTA

>8CAH_8 RNA recognition motif (unknown) (chains j)
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXX

Sequence of entity 9 (2), FASTA

>8CAH_9 18S ribosomal RNA (chains 2)
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 10 (P), FASTA

>8CAH_10 40S ribosomal protein S0-A (chains P)
MSLPATFDLTPEDAQLLLAANTHLGARNVQVHQEPYVFNARPDGVHVINVGKTWEKLVLA
ARIIAAIPNPEDVVAISSRTFGQRAVLKFAAHTGATPIAGRFTPGSFTNYITRSFKEPRL
VIVTDPRSDAQAIKEASYVNIPVIALTDLDSPSEFVDVAIPCNNRGKHSIGLIWYLLARE
VLRLRGALVDRTQPWSIMPDLYFYRDPEEVEQQVAEEATTEEAGEEEAKEEVTEEQAEAT
EWAEENADNVEW

Sequence of entity 11 (Q), FASTA

>8CAH_11 40S ribosomal protein S1-A (chains Q)
MAVGKNKRLSKGKKGQKKRVVDPFTRKEWFDIKAPSTFENRNVGKTLVNKSTGLKSASDA
LKGRVVEVCLADLQGSEDHSFRKIKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTL
IEANVTVKTSDDYVLRIFAIAFTRKQANQVKRHSYAQSSHIRAIRKVISEILTKEVQGST
LAQLTSKLIPEVINKEIENATKDIFPLQNIHVRKVKLLKQPKFDVGALMALHGEGSGEEK
GKKVTGFKDEVLETV

Sequence of entity 12 (R), FASTA

>8CAH_12 40S ribosomal protein S2 (chains R)
MSAPEAQQQKRGGFGGRNRGRPNRRGPRNTEEKGWVPVTKLGRLVKAGKITTIEEIFLHS
LPVKEFQIIDTLLPGLQDEVMNIKPVQKQTRAGQRTRFKAVVVVGDSNGHVGLGIKTAKE
VAGAIRAGIIIAKLSVIPIRRGYWGTNLGQPHSLATKTTGKCGSVTVRLIPAPRGSGIVA
SPAVKKLLQLAGVEDVYTQSNGKTRTLENTLKAAFVAIGNTYGFLTPNLWAEQPLPVSPL
DIYSDEASAQKKRF

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
SF4	Iron/sulfur cluster	Fe4 S4	2
ZN	Zinc ion	Zn	2
MG	Magnesium ion	Mg	80

Primary citation

Molecular basis for recognition and deubiquitination of 40S ribosomes by Otu2. Ikeuchi, K., Ivic, N., Buschauer, R. et al. Nat Commun (2023) 14:2730-2730. DOI 10.1038/s41467-023-38161-w · PubMed

Other PDB entries of the same protein (UniProt P40217 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3ZWL 2.2 Å, Structure of eukaryotic translation initiation factor eIF3i complex with eIF3b…
8CAS 3.3 Å, Cryo-EM structure of native Otu2-bound ubiquitinated 48S initiation complex (partial)
6FYX 3.5 Å, Structure of a partial yeast 48S preinitiation complex with eIF5 N-terminal domain…
3JAP 4.9 Å, Structure of a partial yeast 48S preinitiation complex in closed conformation
6GSM 5.15 Å, Structure of a partial yeast 48S preinitiation complex in open conformation.
6ZCE 5.3 Å, Structure of a yeast ABCE1-bound 43S pre-initiation complex
6GSN 5.75 Å, Structure of a partial yeast 48S preinitiation complex in closed conformation
9CPA 6.0 Å, Structure of a Mammalian DHX29-bound 43S Pre-initiation Complex
6ZU9 6.2 Å, Structure of a yeast ABCE1-bound 48S initiation complex
5A5U 9.0 Å, Structure of mammalian eIF3 in the context of the 43S preinitiation complex

Browse structure collections

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