8CBJ: 40S ribosomal protein S27-A

Name: PDB 8CBJ: Cryo-EM structure of Otu2-bound cytoplasmic pre-40S ribosome biogenesis complex
Published: 2023-05-24
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Cryo-EM structure of Otu2-bound cytoplasmic pre-40S ribosome biogenesis complex. Determined by electron microscopy at 3.8 Å resolution. Released 24 May 2023.

Method: Electron microscopy
Resolution: 3.8 Å
Organisms: Saccharomyces cerevisiae W303, Saccharomyces cerevisiae
Chains: 39
Atoms: 87,884
Mol. weight: 1604.18 kDa
Ligands: ZN, MG
Released: 24 May 2023

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

Secondary structure: helices and β-sheets

8CBJ contains 276 α-helices and 296 β-strands across 38 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: 16 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	9-14	6	50
α-helix	16-21	6
α-helix	24-28	5
β-strand	31-36	6	50
α-helix	38-42	5
α-helix	47-59	13
β-strand	62-64	3	50
α-helix	66-68	3
α-helix	69-82	14
α-helix	90-106	17
α-helix	119-121	3
α-helix	123-125	3
β-strand	239-240	2	51
α-helix	251-258	8
α-helix	261-263	3
β-strand	265-268	4	50
α-helix	272-280	9
β-strand	285-286	2	50
α-helix	292	1
β-strand	293	1	50
α-helix	294	1
β-strand	296-304	9	51
β-strand	310-312	3	51
α-helix	318-320	3
β-strand	332-340	9	51
β-strand	346-347	2	51
α-helix	398-423	26

Chain A: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	5-7	3
α-helix	11-19	9
β-strand	24	1	52
α-helix	34-36	3
β-strand	37-41	5	52
β-strand	45-48	4	52
α-helix	50-66	17
β-strand	73-76	4	53
α-helix	80-93	14
β-strand	96-98	3	53
α-helix	102-103	2
β-strand	120-123	4	53
α-helix	130-136	7
β-strand	143-147	5	53
β-strand	159-161	3	53
α-helix	167-185	19
α-helix	194-195	2
α-helix	199-201	3

Chain b: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	32-36	5	1
β-strand	44-47	4	1
β-strand	54-55	2	2
β-strand	62-65	4	2
α-helix	71	1
β-strand	72-73	2	2
α-helix	74	1
β-strand	78-81	4	1

Chain B: 8 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	23-26	4
β-strand	28-29	2	55
β-strand	31-33	3	56
β-strand	47-48	2	55
α-helix	54-62	9
β-strand	65-69	5	56
α-helix	70-74	5
β-strand	82-91	10	56
β-strand	95-105	11	56
α-helix	107-113	7
β-strand	118	1	57
β-strand	121-128	8	56
β-strand	134-141	8	56
β-strand	154	1	57
α-helix	158-177	20
α-helix	181-188	8
α-helix	192-200	9
β-strand	211-219	9	56
α-helix	226-232	7

Chain c: 0 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	8-11	4	4
β-strand	15-19	5	5
β-strand	25-31	7	5
β-strand	39-45	7	5
β-strand	53-56	4	4

Chain C: 10 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	40-46	7
α-helix	54-59	6
α-helix	61-63	3
α-helix	66-72	7
β-strand	77-89	13	58
β-strand	94-105	12	58
β-strand	110-118	9	58
α-helix	121-134	14
β-strand	136-138	3	58
β-strand	141-142	2	59
β-strand	153-154	2	59
β-strand	158-162	5	60
β-strand	165-171	7	60
β-strand	178-179	2	60
α-helix	182-189	8
β-strand	195	1	59
β-strand	196-201	6	60
α-helix	207-219	13
α-helix	227-229	3
α-helix	234-238	5
α-helix	239-242	4

Chain d: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	21	1	9
β-strand	26	1	9
β-strand	30	1	10
α-helix	33-35	3
β-strand	39	1	10
α-helix	40-50	11

Chain D: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-28	22
β-strand	34-41	8	61
β-strand	46-52	7	61
α-helix	61-63	3
α-helix	64-76	13
β-strand	84-88	5	61
α-helix	98-111	14
α-helix	117-127	11
β-strand	133-140	8	62
β-strand	148-155	8	62
α-helix	162-167	6
β-strand	169-176	8	62
β-strand	181-189	9	62
α-helix	192-194	3
β-strand	221-224	4	21

30 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
40S ribosomal protein S27-A	b	protein	82	Saccharomyces cerevisiae W303	P35997 (AlphaFold model)
40S ribosomal protein S28-A	c	protein	67	Saccharomyces cerevisiae W303	Q3E7X9 (AlphaFold model)
RPS29A isoform 1	d	protein	56	Saccharomyces cerevisiae W303	P41057 (AlphaFold model)
40S ribosomal protein S30-A	e	protein	63	Saccharomyces cerevisiae W303	P0CX33 (AlphaFold model)
Guanine nucleotide-binding protein subunit beta-like protein	g	protein	319	Saccharomyces cerevisiae W303	P38011
Pre-rRNA-processing protein PNO1	h	protein	274	Saccharomyces cerevisiae W303	Q99216
ENP1 isoform 1	i	protein	483	Saccharomyces cerevisiae W303	P38333
LTV1 isoform 1	j	protein	463	Saccharomyces cerevisiae W303	P34078
TSR1 isoform 1	k	protein	788	Saccharomyces cerevisiae W303	Q07381
non-specific serine/threonine protein kinase	l	protein	425	Saccharomyces cerevisiae W303	P40160
40S ribosomal protein S0-A	A	protein	252	Saccharomyces cerevisiae W303	P32905
40S ribosomal protein S1-A	B	protein	255	Saccharomyces cerevisiae W303	P33442

27 more molecules are not listed.

Sequence of entity 1 (b), FASTA

>8CBJ_1 40S ribosomal protein S27-A (chains b)
MVLVQDLLHPTAASEARKHKLKTLVQGPRSYFLDVKCPGCLNITTVFSHAQTAVTCESCS
TILCTPTGGKAKLSEGTSFRRK

Sequence of entity 2 (c), FASTA

>8CBJ_2 40S ribosomal protein S28-A (chains c)
MDNKTPVTLAKVIKVLGRTGSRGGVTQVRVEFLEDTSRTIVRNVKGPVRENDILVLMESE
REARRLR

Sequence of entity 3 (d), FASTA

>8CBJ_3 RPS29A isoform 1 (chains d)
MAHENVWFSHPRRYGKGSRQCRVCSSHTGLIRKYGLNICRQCFREKANDIGFNKFR

Sequence of entity 4 (e), FASTA

>8CBJ_4 40S ribosomal protein S30-A (chains e)
MAKVHGSLARAGKVKSQTPKVEKTEKPKKPKGRAYKRLLYTRRFVNVTLVNGKRRMNPGP
SVQ

Sequence of entity 5 (g), FASTA

>8CBJ_5 Guanine nucleotide-binding protein subunit beta-like protein (chains g)
MASNEVLVLRGTLEGHNGWVTSLATSAGQPNLLLSASRDKTLISWKLTGDDQKFGVPVRS
FKGHSHIVQDCTLTADGAYALSASWDKTLRLWDVATGETYQRFVGHKSDVMSVDIDKKAS
MIISGSRDKTIKVWTIKGQCLATLLGHNDWVSQVRVVPNEKADDDSVTIISAGNDKMVKA
WNLNQFQIEADFIGHNSNINTLTASPDGTLIASAGKDGEIMLWNLAAKKAMYTLSAQDEV
FSLAFSPNRYWLAAATATGIKVFSLDPQYLVDDLRPEFAGYSKAAEPHAVSLAWSADGQT
LFAGYTDNVIRVWQVMTAN

Sequence of entity 6 (h), FASTA

>8CBJ_6 Pre-rRNA-processing protein PNO1 (chains h)
MVAPTALKKATVTPVSGQDGGSSRIIGINNTESIDEDDDDDVLLDDSDNNTAKEEVEGEE
GSRKTHESKTVVVDDQGKPRFTSASKTQGNKIKFESRKIMVPPHRMTPLRNSWTKIYPPL
VEHLKLQVRMNLKTKSVELRTNPKFTTDPGALQKGADFIKAFTLGFDLDDSIALLRLDDL
YIETFEVKDVKTLTGDHLSRAIGRIAGKDGKTKFAIENATRTRIVLADSKIHILGGFTHI
RMARESVVSLILGSPPGKVYGNLRTVASRLKERY

Sequence of entity 7 (i), FASTA

>8CBJ_7 ENP1 isoform 1 (chains i)
MARASSTKARKQRHDPLLKDLDAAQGTLKKINKKKLAQNDAANHDAANEEDGYIDSKASR
KILQLAKEQQDEIEGEELAESERNKQFEARFTTMSYDDEDEDEDEDEEAFGEDISDFEPE
GDYKEEEEIVEIDEEDAAMFEQYFKKSDDFNSLSGSYNLADKIMASIREKESQVEDMQDD
EPLANEQNTSRGNISSGLKSGEGVALPEKVIKAYTTVGSILKTWTHGKLPKLFKVIPSLR
NWQDVIYVTNPEEWSPHVVYEATKLFVSNLTAKESQKFINLILLERFRDNIETSEDHSLN
YHIYRAVKKSLYKPSAFFKGFLFPLVETGCNVREATIAGSVLAKVSVPALHSSAALSYLL
RLPFSPPTTVFIKILLDKKYALPYQTVDDCVYYFMRFRILDDGSNGEDATRVLPVIWHKA
FLTFAQRYKNDITQDQRDFLLETVRQRGHKDIGPEIRRELLAGASREFVDPQEANDDLMI
DVN

Sequence of entity 8 (j), FASTA

>8CBJ_8 LTV1 isoform 1 (chains j)
MSKKFSSKNSQRYVVVHRPHDDPSFYDTDASAHVLVPVSNPNKTSPEADLRKKDVSSTKP
KGRRAHVGEAALYGINFDDSEYDYTQHLKPIGLDPENSIFIASKGNEQKVEKKNIEDLFI
EPKYRRDEIEKDDALPVFQRGMAKPEYLLHQQDTTDEIRGFKPDMNPALREVLEALEDEA
YVVNDDVVVEDISKKTQLQGDNYGEEEKEDDIFAQLLGSGEAKDEDEFEDEFDEWDIDNV
ENFEDENYVKEMAQFDNIENLEDLENIDYQADVRRFQKDNSILEKHNSDDEFSNAGLDSV
NPSEEEDVLGELPSIQDKSKTGKKKRKSRQKKGAMSDVSGFSMSSSAIARTETMTVLDDQ
YDQIINGYENYEEELEEDEEQNYQPFDMSAERSDFESMLDDFLDNYELESGGRKLAKKDK
EIERLKEAADEVSKGKLSQRRNRERQEKKKLEKVTNTLSSLKF

Sequence of entity 9 (k), FASTA

>8CBJ_9 TSR1 isoform 1 (chains k)
MAGHSHRSSLKNGHKSYKSKHASKGALKRLYKGKVEKEPVGTGKPDKQVSKLQRKNKAKQ
LRAQRILDSIENRKLFEGKNGAAKIITIVPLVNDLDPLDILYKLLKCADDEGIMVQEVDS
KRIFNVHIKKFKSNLKIIIPDMTNFLNILDCAKVADFVVFGLSGVQEVDEEFGEQIIRAL
ELQGIASYIGVISNLSAVHEKEKFQLDVKQSLESYFKHFFPSEERVYNLEKNSDALNVLR
TLCQRLPRSINWRDNRGYVVADFVDFVETSPDSGDLVIEGTVRGIGFNANRLVHIPDFGD
FQLNKIEKISESSQKRKIIKEKATDSLSLELDLQTVFESNMNRDTLDEYAPEGTEDWSDY
DEDFEYDGLTTARYDDHGFLPGREQTSKKAAVPKGTSDYQAKWYLDDVIDANEEEEAEQT
NGKDETMMEIDDEMMVEQDNEEVAGDEEYDIEDNEGFEELSPEEEERQLREFRDMEKEDR
EFPDEIELEPSESAIERLKRYRGLKNLYNCDWQVDEKDPSSPAEWKRLLRIGNYKNTKNR
IIKETKNEAQAIAGDRIRMFIRFPKFLLEKIQDPKQLLFAVYGLLLHEHKNAVVNFSLQR
WEQYDKPVPSQEPIVVQYGVRRYTIQPLFSQGSNSPNNVHKYERFLHPDTVSVATCIAPV
DFTQSPAIFFKPSPTDAKNIELIGHGTFLNADHSRILAKRAILTGHPFRFHKTVVTVRYM
FFRPEDVEWFKSIPLFTKSGRSGFIKESLGTHGYFKATFDGKLSAQDVVAMSLYKRMWPM
PSLPWNGM

Sequence of entity 10 (l), FASTA

>8CBJ_10 non-specific serine/threonine protein kinase (chains l)
MKLDTSHMRYLTTDDFRVLQAVEQGSRSHEVVPTPLIHQISGMRSQSGTNRAISDLAKLS
LISKMRNVKYDGYRLTYNGIDYLALKTMLNRDTVYSVGNTIGVGKESDIYKVSDKNGNPR
VMKIHRLGRTSFHSVRNNRDYLKKSNQGANWMHLSRLAANKEYQFMSMLYSKGFKVPEPF
DNSRHIVVMELIEGYPMRRLRKHKNIPKLYSDLMCFIVDLANSGLIHCDFNEFNIMIKDK
LEDENDCGFVVIDFPQCISIQHQDADYYFQRDVDCIRRFFKKKLKYEPKPDSSMLDTEGF
GDGYKYAYPDFKRDVKRTDNLDELVQASGFSKKHPGDRGLETAVESMRNAVYNSDDDMSN
DEAEEENGEGDYSEEDEYYDSELDNESSEDDSEDAQEEENERIIEALSSGVENLKMDKLG
NYILE

Sequence of entity 11 (A), FASTA

>8CBJ_11 40S ribosomal protein S0-A (chains A)
MSLPATFDLTPEDAQLLLAANTHLGARNVQVHQEPYVFNARPDGVHVINVGKTWEKLVLA
ARIIAAIPNPEDVVAISSRTFGQRAVLKFAAHTGATPIAGRFTPGSFTNYITRSFKEPRL
VIVTDPRSDAQAIKEASYVNIPVIALTDLDSPSEFVDVAIPCNNRGKHSIGLIWYLLARE
VLRLRGALVDRTQPWSIMPDLYFYRFPEEVEQQVAEEATTEEAGEEEAKEEVTEEQAEAT
EWAEENADNVEW

Sequence of entity 12 (B), FASTA

>8CBJ_12 40S ribosomal protein S1-A (chains B)
MAVGKNKRLSKGKKGQKKRVVDPFTRKEWFDIKAPSTFENRNVGKTLVNKSTGLKSASDA
LKGRVVEVCLADLQGSEDHSFRKIKLRVDEVQGKNLLTNFHGMDFTTDKLRSMVRKWQTL
IEANVTVKTSDDYVLRIFAIAFTRKQANQVKRHSYAQSSHIRAIRKVISEILTKEVQGST
LAQLTSKLIPEVINKEIENATKDIFPLQNIHVRKVKLLKQPKFDVGALMALHGEGSGEEK
GKKVTGFKDEVLETV

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
MG	Magnesium ion	Mg	46

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 P35997 (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…
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,…
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
8EVP 2.38 Å, Hypopseudouridylated yeast 80S bound with Taura syndrome virus (TSV) internal ribosome…
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

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