9QJC: Yeast pre-60S Domain II intermediate

Name: PDB 9QJC: Yeast pre-60S Domain II intermediate
Published: 2026-01-28
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

Yeast pre-60S Domain II intermediate. Determined by electron microscopy at 3.2 Å resolution. Released 28 Jan 2026.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Saccharomyces cerevisiae
Chains: 16
Atoms: 34,817
Mol. weight: 1686.4 kDa
Released: 28 Jan 2026

Explore 9QJC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9QJC contains 177 α-helices and 89 β-strands across 14 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 5: 34 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	223-225	3
α-helix	226-229	4
α-helix	236-238	3
α-helix	239-265	27
α-helix	268-280	13
α-helix	283-294	12
α-helix	302-312	11
α-helix	317-330	14
α-helix	331-335	5
α-helix	344-346	3
α-helix	356-383	28
α-helix	388-404	17
α-helix	409-417	9
α-helix	418-421	4
α-helix	425-441	17
α-helix	443-445	3
α-helix	446-458	13
α-helix	464-475	12
α-helix	484-502	19
α-helix	551-567	17
α-helix	576-588	13
α-helix	594-611	18
α-helix	616-625	10
α-helix	629-631	3
α-helix	638-650	13
α-helix	655-669	15
α-helix	675-688	14
α-helix	693-696	4
α-helix	697-700	4
α-helix	747-750	4
β-strand	752	1	1
α-helix	755-766	12
β-strand	777	1	2
β-strand	779	1	2
α-helix	782-789	8
α-helix	848-850	3
α-helix	851-859	9

Chain 6: 32 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	176-177	2	3
α-helix	180-192	13
α-helix	196-210	15
α-helix	211-213	3
β-strand	223-224	2	3
α-helix	228-249	22
β-strand	253-255	3	4
β-strand	258-260	3	4
α-helix	261-263	3
α-helix	265-286	22
α-helix	291-303	13
α-helix	305-308	4
α-helix	312-328	17
α-helix	332-348	17
α-helix	350-363	14
β-strand	369-370	2	5
α-helix	371-372	2
α-helix	377-388	12
α-helix	395-421	27
α-helix	429-435	7
α-helix	439-455	17
α-helix	458-461	4
α-helix	467-471	5
α-helix	472-483	12
α-helix	489-491	3
α-helix	492-509	18
β-strand	512	1	1
α-helix	516-520	5
α-helix	526-529	4
α-helix	531-532	2
α-helix	538-541	4
α-helix	551-553	3
α-helix	557-576	20
α-helix	584-599	16
α-helix	605-628	24
α-helix	639-643	5
α-helix	651-653	3
α-helix	655-689	35

Chain B: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	291-295	5	28
α-helix	303-311	9
β-strand	319-324	6	28
β-strand	329-337	9	28
α-helix	341-349	9
α-helix	367-369	3
β-strand	370-371	2	29
β-strand	374-375	2	29
β-strand	377-380	4	28
α-helix	384-402	19

Chain C: 23 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	6
β-strand	15-21	7	6
α-helix	22-23	2
α-helix	24-27	4
α-helix	29-30	2
α-helix	32-43	12
α-helix	115-128	14
α-helix	132-138	7
β-strand	151-152	2	6
α-helix	154-158	5
α-helix	162-172	11
α-helix	175-183	9
β-strand	186-187	2	7
α-helix	191-194	4
β-strand	199-200	2	7
β-strand	206-209	4	6
α-helix	215-218	4
α-helix	219-221	3
β-strand	226-229	4	6
α-helix	230-232	3
α-helix	235-238	4
α-helix	240-242	3
β-strand	248-251	4	6
α-helix	252-262	11
α-helix	286-290	5
α-helix	293-296	4
α-helix	300-302	3
α-helix	307-309	3
α-helix	321-327	7
α-helix	331-337	7
α-helix	339-341	3

Chain D: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-8	6
α-helix	9-13	5
β-strand	18-20	3	8
β-strand	26-28	3	8
β-strand	37	1	8
β-strand	50	1	9
β-strand	53-55	3	10
β-strand	60-64	5	10
β-strand	65	1	9
α-helix	67-69	3
α-helix	73-75	3
β-strand	78-81	4	10
α-helix	82-83	2
α-helix	86-96	11
α-helix	104-124	21

Chain e: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	55-57	3
α-helix	58-60	3
β-strand	72-76	5	26
α-helix	79-82	4
α-helix	83-85	3
β-strand	92-96	5	26
α-helix	102-115	14
β-strand	119	1	26
β-strand	127-128	2	5

Chain E: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	10-11	2
α-helix	17-21	5
β-strand	38	1	11
β-strand	39-42	4	12
β-strand	51-57	7	12
β-strand	62-66	5	12
β-strand	77-80	4	12
β-strand	84-85	2	12
β-strand	90	1	11
α-helix	98-100	3
α-helix	103-106	4
α-helix	137-149	13
α-helix	155-160	6

Chain f: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	8-16	9	27
β-strand	27-32	6	27
α-helix	38-41	4
β-strand	48-51	4	27
β-strand	67-75	9	27
β-strand	80-85	6	27
β-strand	97-101	5	27
α-helix	103	1
α-helix	105	1

6 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
Ribosome biogenesis protein MAK21	5	protein	1025	Saccharomyces cerevisiae	Q12176 (AlphaFold model)
Nucleolar complex protein 2	6	protein	710	Saccharomyces cerevisiae	P39744 (AlphaFold model)
60S ribosomal protein L4-A	C	protein	362	Saccharomyces cerevisiae	P10664 (AlphaFold model)
Protein MAK16	D	protein	306	Saccharomyces cerevisiae	P10962 (AlphaFold model)
60S ribosomal protein L6-A	E	protein	176	Saccharomyces cerevisiae	Q02326
60S ribosomal protein L7-A	F	protein	244	Saccharomyces cerevisiae	P05737
60S ribosomal protein L14-A	M	protein	138	Saccharomyces cerevisiae	P36105
60S ribosomal protein L16-A	O	protein	199	Saccharomyces cerevisiae	P26784
60S ribosomal protein L18-A	Q	protein	186	Saccharomyces cerevisiae	P0CX49
60S ribosomal protein L20-A	S	protein	172	Saccharomyces cerevisiae	P0CX23
60S ribosomal protein L32	e	protein	130	Saccharomyces cerevisiae	P38061
60S ribosomal protein L33-A	f	protein	107	Saccharomyces cerevisiae	P05744

4 more molecules are not listed.

Sequence of entity 1 (5), FASTA

>9QJC_1 Ribosome biogenesis protein MAK21 (chains 5)
MSENNGNPLDLSSLRNKISSKLRDNNSKKAKKTHKGKDVKASSNSKKVNEDIRREALALG
ASEEDLKLIQGLSDDDDAKSEQEFDAVADEDADDKGFKNDLQNFMKNVGFDQHKLEDVDD
DDIEEESTSSKESKIPAQEKEHAQSNIASSTIEKTSQESIDNGSEQEENTVEEANLSSDQ
EPESESAEKEKKEEKDGGLITQTTIISSDKLIIPYDKPWYEIPLDPQVGQNDDVEELSKE
QIEKLFERGKQTLEADNQTYYEEFTKDSSQAKFMSQILSDGTLNDKISAVTLLIQDSPLH
NTKSLETLVSYCGKKSRNSALQSLNALKDLFLNGLLPNRKLRYFKNQPGLSMMLNKKTLA
IFYFEDYLKKLFFRVLEVLEVLSHDPIIHVRLQILNHVFDLLTNQPEQEFNLLRLGVNKI
GDIDSKVSSKASYLLLKLEQAHPNMKSIVIDAIVDIALRPNADYHTTYYSVITLNQTILK
RSEDSVANKLVKTYFTLFEKFLINTDKDNTNGVVKSNSKSYEEKRKKNFKKGKHGGKSVK
IEKTENEVLDEKNSKLFSALLTGINRAFPFAQIPASVYEVHMETLFKITHSSNFNTSIQA
LVLINQVTVKAKLNSDRYYRTLYESLFDPRLVNSSKQGIYLNLLYKSLKQDALNVERVEA
FVKRILQVCSHWLNVGTITGFFFLLIQLAKTVPQIKNLLTNTPVDYEYESDAEEEQGDKD
IKRKEYDGRKRDPKFANAEKSSLWEINNFINHFHPTVKTYANAYVTGETEQIAKPDLGLF
TLSHFLDRFVYRSAKQTNTARGTSIMQPLFSGSRVNDSVLVKASDIMHDQGPVNTEDWLT
KKVEDIKPEDKFFYQYFTTKKTADGKGKKSNKASNFDSDDEMDENEIWSALVKSRPDVED
DSDDSELDFAEDDFSDSTSDDEPKLDAIDDEDAKSEGSQESDQEEGLDEDIFYSFDGEQD
NSDKKRSFAESSEEDESSEEEKEEEENKEVSAKRAKKKQRKNMLKSLPVFASADDYAQYL
DQDSD

Sequence of entity 2 (6), FASTA

>9QJC_2 Nucleolar complex protein 2 (chains 6)
MGKVSKSTKKFQSKHLKHTLDQRRKEKIQKKRIQGRRGNKTDQEKADAAGTREQQQLKKS
AKEEVFKDMSVETFFEKGIEIPKENKKLKKKTTKEQSDEDSSSSEEEEDMGQSMAKLAEK
DPEFYKYLEENDKDLLDFAGTNPLDGIDSQDEGEDAERNSNIEEKSEQMELEKEKIELSL
KLVRKWKKQLHDSPSLKLLRNIISAFKVAVNLNKEENIEDYKYAITDEKAFHELMFMVLK
DVPQAIQKMAPYKIVKGARTLPNGGNVSRVSSIVKSHAGSLLILLNDITNTETAALVLHS
VNELMPYLLSYRRILKELIKSIVGVWSTTRELETQIASFAFLINTTKEFKKSMLETTLKT
TYSTFIKSCRKTNMRSMPLINFQKNSAAELFGIDEVLGYQVGFEYIRQLAIHLRNTMNAT
TKKSSKINSAEAYKIVYNWQFCHSLDFWSRVLSFACQPEKENGSESPLRQLIYPLVQVTL
GVIRLIPTPQFFPLRFYLIKSLIRLSQNSGVFIPIYPLLSEILTSTAFTKAPKKSPNLAA
FDFEHNIKCTQAYLNTKIYQEGLSEQFVDLLGDYFALYCKNIAFPELVTPVIISLRRYIK
TSTNVKLNKRLSTVVEKLNQNSTFIQEKRSDVEFGPTNKSEVSRFLNDVAWNKTPLGSYV
AVQREVKEEKARLMRESMEEQDKERETEEAKLLNSLESDDDNEDVEMSDA

Sequence of entity 3 (C), FASTA

>9QJC_3 60S ribosomal protein L4-A (chains C)
MSRPQVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQT
SAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEKRY
ATASAIAATAVASLVLARGHRVEKIPEIPLVVSTDLESIQKTKEAVAALKAVGAHSDLLK
VLKSKKLRAGKGKYRNRRWTQRRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAP
GAHLGRFVIWTEAAFTKLDQVWGSETVASSKVGYTLPSHIISTSDVTRIINSSEIQSAIR
PAGQATQKRTHVLKKNPLKNKQVLLRLNPYAKVFAAEKLGSKKAEKTGTKPAAVFTETLK
HD

Sequence of entity 4 (D), FASTA

>9QJC_4 Protein MAK16 (chains D)
MSDEIVWQVINQSFCSHRIKAPNGQNFCRNEYNVTGLCTRQSCPLANSKYATVKCDNGKL
YLYMKTPERAHTPAKLWERIKLSKNYTKALQQIDEHLLHWSKFFRHKCKQRFTKLTQVMI
TERRLALREEERHYVGVAPKVKRREQNRERKALVAAKIEKAIEKELMDRLKSGAYGDKPL
NVDEKVWKKIMGQMEEENSQDEEEDWDEEEESDDGEVEYVADDGEGEYVDVDDLEKWLAD
SDREASSASESESDSESESDSDSDEENKNSAKRRKKGTSAKTKRPKVEIEYEEEHEVQNA
EQEVAQ

Sequence of entity 5 (E), FASTA

>9QJC_5 60S ribosomal protein L6-A (chains E)
MSAQKAPKWYPSEDVAALKKTRKAARPQKLRASLVPGTVLILLAGRFRGKRVVYLKHLED
NTLLISGPFKVNGVPLRRVNARYVIATSTKVSVEGVNVEKFNVEYFAKEKLTKKEKKEAN
LFPEQQNKEIKAERVEDQKVVDKALIAEIKKTPLLKQYLSASFSLKNGDKPHMLKF

Sequence of entity 6 (F), FASTA

>9QJC_6 60S ribosomal protein L7-A (chains F)
MAAEKILTPESQLKKSKAQQKTAEQVAAERAARKAANKEKRAIILERNAAYQKEYETAER
NIIQAKRDAKAAGSYYVEAQHKLVFVVRIKGINKIPPKPRKVLQLLRLTRINSGTFVKVT
KATLELLKLIEPYVAYGYPSYSTIRQLVYKRGFGKINKQRVPLSDNAIIEANLGKYGILS
IDDLIHEIITVGPHFKQANNFLWPFKLSNPSGGWGVPRKFKHFIQGGSFGNREEFINKLV
KSMN

Sequence of entity 7 (M), FASTA

>9QJC_7 60S ribosomal protein L14-A (chains M)
MSTDSIVKASNWRLVEVGRVVLIKKGQSAGKLAAIVEIIDQKKVLIDGPKAGVPRQAINL
GQVVLTPLTFALPRGARTATVSKKWAAAAVCEKWAASSWAKKIAQRERRAALTDFERFQV
MVLRKQKRYTVKKALAKA

Sequence of entity 8 (O), FASTA

>9QJC_8 60S ribosomal protein L16-A (chains O)
MSVEPVVVIDGKGHLVGRLASVVAKQLLNGQKIVVVRAEELNISGEFFRNKLKYHDFLRK
ATAFNKTRGPFHFRAPSRIFYKALRGMVSHKTARGKAALERLKVFEGIPPPYDKKKRVVV
PQALRVLRLKPGRKYTTLGKLSTSVGWKYEDVVAKLEAKRKVSSAEYYAKKRAFTKKVAS
ANATAAESDVAKQLAALGY

Sequence of entity 9 (Q), FASTA

>9QJC_9 60S ribosomal protein L18-A (chains Q)
MGIDHTSKQHKRSGHRTAPKSDNVYLKLLVKLYTFLARRTDAPFNKVVLKALFLSKINRP
PVSVSRIARALKQEGAANKTVVVVGTVTDDARIFEFPKTTVAALRFTAGARAKIVKAGGE
CITLDQLAVRAPKGQNTLILRGPRNSREAVRHFGMGPHKGKAPRILSTGRKFERARGRRR
SKGFKV

Sequence of entity 10 (S), FASTA

>9QJC_10 60S ribosomal protein L20-A (chains S)
MAHFKEYQVIGRRLPTESVPEPKLFRMRIFASNEVIAKSRYWYFLQKLHKVKKASGEIVS
INQINEAHPTKVKNFGVWVRYDSRSGTHNMYKEIRDVSRVAAVETLYQDMAARHRARFRS
IHILKVAEIEKTADVKRQYVKQFLTKDLKFPLPHRVQKSTKTFSYKRPSTFY

Sequence of entity 11 (e), FASTA

>9QJC_11 60S ribosomal protein L32 (chains e)
MASLPHPKIVKKHTKKFKRHHSDRYHRVAENWRKQKGIDSVVRRRFRGNISQPKIGYGSN
KKTKFLSPSGHKTFLVANVKDLETLTMHTKTYAAEIAHNISAKNRVVILARAKALGIKVT
NPKGRLALEA

Sequence of entity 12 (f), FASTA

>9QJC_12 60S ribosomal protein L33-A (chains f)
MAESHRLYVKGKHLSYQRSKRVNNPNVSLIKIEGVATPQDAQFYLGKRIAYVYRASKEVR
GSKIRVMWGKVTRTHGNSGVVRATFRNNLPAKTFGASVRIFLYPSNI

Primary citation

A comprehensive view on r-protein binding and rRNA domain structuring during early eukaryotic ribosome formation. Gerhalter, M., Prattes, M., Grundmann, L.E. et al. Nucleic Acids Res (2026) 54. DOI 10.1093/nar/gkag036 · PubMed

Other PDB entries of the same protein (UniProt Q12176 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8E5T 4.0 Å, Yeast co-transcriptional Noc1-Noc2 RNP assembly checkpoint intermediate

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