8E5T: Ribosome biogenesis protein MAK21

Yeast co-transcriptional Noc1-Noc2 RNP assembly checkpoint intermediate. Determined by electron microscopy at 4.0 Å resolution. Released 12 Apr 2023.

Method
Electron microscopy
Resolution
4.0 Å
Organism
Saccharomyces cerevisiae BY4741
Chains
28
Atoms
55,125
Mol. weight
2176.77 kDa
Ligands
MG, ZN
Released
12 Apr 2023

Explore 8E5T in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8E5T contains 279 α-helices and 150 β-strands across 25 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: 33 helices, 1 β-strand

ElementResiduesLengthSheet
α-helix226-2283
α-helix239-25315
α-helix257-26610
α-helix268-28013
α-helix283-29614
α-helix302-31211
α-helix317-33014
α-helix331-3355
α-helix344-3463
α-helix356-38328
α-helix388-40417
α-helix409-41810
α-helix419-4213
α-helix425-44117
α-helix443-4453
α-helix446-45712
α-helix464-47512
α-helix484-50219
α-helix551-56717
α-helix575-58915
α-helix594-61118
α-helix616-62510
α-helix629-6335
α-helix637-65014
α-helix655-66915
α-helix675-69117
α-helix693-6997
α-helix746-7505
β-strand75211
α-helix755-76612
α-helix773-7753
α-helix782-7898
α-helix848-8503
α-helix851-86010
Chain 6: 30 helices, 7 β-strands
ElementResiduesLengthSheet
β-strand176-17722
α-helix1781
α-helix180-19011
α-helix196-21116
β-strand223-22422
α-helix228-24922
β-strand253-25533
β-strand258-26033
α-helix265-27511
α-helix278-2869
α-helix291-30212
α-helix305-3084
α-helix315-32814
α-helix332-34918
α-helix354-36613
α-helix369-3724
α-helix377-39317
α-helix395-42127
α-helix433-4364
α-helix439-45517
α-helix458-4614
α-helix467-4715
α-helix472-48312
α-helix489-4913
α-helix492-50918
β-strand51211
α-helix516-5227
α-helix531-5322
β-strand53414
α-helix539-5413
β-strand55614
α-helix557-57721
α-helix584-60118
α-helix605-62925
α-helix639-6424
α-helix651-6533
α-helix655-69137
Chain b: 6 helices, 9 β-strands
ElementResiduesLengthSheet
β-strand33-36429
α-helix43-5513
α-helix62-654
α-helix73-819
β-strand85-92829
β-strand96-102729
β-strand109-1181029
α-helix133-1353
β-strand136-139429
α-helix147-16014
β-strand176-181629
β-strand185-192829
β-strand213-2271529
β-strand235-238429
α-helix245-26218
Chain C: 22 helices, 8 β-strands
ElementResiduesLengthSheet
β-strand5-955
α-helix141
β-strand15-2175
α-helix22-232
α-helix32-4312
α-helix115-12814
α-helix132-1387
β-strand150-15235
α-helix154-1585
α-helix162-17211
α-helix175-18410
β-strand186-18726
α-helix191-1944
β-strand199-20026
β-strand206-20945
α-helix215-2206
β-strand226-22945
α-helix235-2384
α-helix240-2423
β-strand248-25145
α-helix252-26211
α-helix276-2794
α-helix286-2916
α-helix294-2985
α-helix300-3023
α-helix307-3093
α-helix321-3277
α-helix330-3378
α-helix339-3413
α-helix342-3454
Chain D: 6 helices, 5 β-strands
ElementResiduesLengthSheet
α-helix3-1210
β-strand18-2037
β-strand26-2837
β-strand50-5678
β-strand59-6578
α-helix67-693
α-helix73-753
β-strand78-8148
α-helix82-832
α-helix86-9611
α-helix102-12524
Chain e: 4 helices, 3 β-strands
ElementResiduesLengthSheet
α-helix55-573
α-helix58-603
β-strand72-76530
α-helix79-835
β-strand92-96530
α-helix102-11514
β-strand119130
Chain E: 6 helices, 7 β-strands
ElementResiduesLengthSheet
α-helix17-215
β-strand38-4259
β-strand50110
β-strand51-5779
β-strand63-6649
α-helix69-724
β-strand77-7939
β-strand84-9079
α-helix103-1064
α-helix136-15116
α-helix155-1606
β-strand162110
α-helix165-1662
Chain f: 4 helices, 6 β-strands
ElementResiduesLengthSheet
β-strand8-16931
β-strand27-31531
α-helix38-414
α-helix42-443
β-strand48-51431
β-strand67-75931
β-strand80-85631
β-strand97-101531
α-helix1031
α-helix1051

17 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Ribosome biogenesis protein MAK215protein1025Saccharomyces cerevisiae BY4741Q12176 (AlphaFold model)
NOC2 isoform 16protein710Saccharomyces cerevisiae BY4741P39744 (AlphaFold model)
60S ribosomal protein L4-ACprotein362Saccharomyces cerevisiae BY4741P10664 (AlphaFold model)
Protein MAK16Dprotein306Saccharomyces cerevisiae BY4741P10962 (AlphaFold model)
60S ribosomal protein L6-AEprotein176Saccharomyces cerevisiae BY4741Q02326
60S ribosomal protein L7-AFprotein244Saccharomyces cerevisiae BY4741P05737
60S ribosomal protein L8-AGprotein256Saccharomyces cerevisiae BY4741P17076
Proteasome-interacting protein CIC1Kprotein376Saccharomyces cerevisiae BY4741P38779
60S ribosomal protein L13-ALprotein199Saccharomyces cerevisiae BY4741Q12690
60S ribosomal protein L14-AMprotein138Saccharomyces cerevisiae BY4741P36105
60S ribosomal protein L15-ANprotein204Saccharomyces cerevisiae BY4741P05748
60S ribosomal protein L18-AQprotein186Saccharomyces cerevisiae BY4741P0CX49

16 more molecules are not listed.

Sequence of entity 1 (5), FASTA
>8E5T_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
>8E5T_2 NOC2 isoform 1 (chains 6)
MGKVSKSTKKFQSKHLKHTLDQRRKEKIQKKRIQGRRGNKTDQEKADAAGTREQQQLKKS
AKEEVFKDMSVETFFEKGIEIPKENKKLKKKTTKEQSDEDSSSSEEEEDMGQSMAKLAEK
DPEFYKYLEENDKDLLDFAGTNPLDGIDSQDEGEDAERNSNIEEKSEQMELEKEKIELSL
KLVRKWKKQLHDSPSLKLLRNIISAFKVAVNLNKEENIEDYKYAITDEKAFHELMFMVLK
DVPQAIQKMAPYKIVKGARTLPNGGNVSRVSSIVKSHAGSLLILLNDITNTETAALVLHS
VNELMPYLLSYRRILKELIKSIVGVWSTTRELETQIASFAFLINTTKEFKKSMLETTLKT
TYSTFIKSCRKTNMRSMPLINFQKNSAAELFGIDEVLGYQVGFEYIRQLAIHLRNTMNAT
TKKSSKINSAEAYKIVYNWQFCHSLDFWSRVLSFACQPEKENGSESPLRQLIYPLVQVTL
GVIRLIPTPQFFPLRFYLIKSLIRLSQNSGVFIPIYPLLSEILTSTAFTKAPKKSPNLAA
FDFEHNIKCTQAYLNTKIYQEGLSEQFVDLLGDYFALYCKNIAFPELVTPVIISLRRYIK
TSTNVKLNKRLSTVVEKLNQNSTFIQEKRSDVEFGPTNKSEVSRFLNDVAWNKTPLGSYV
AVQREVKEEKARLMRESMEEQDKERETEEAKLLNSLESDDDNEDVEMSDA
Sequence of entity 3 (C), FASTA
>8E5T_3 60S ribosomal protein L4-A (chains C)
MSRPQVTVHSLTGEATANALPLPAVFSAPIRPDIVHTVFTSVNKNKRQAYAVSEKAGHQT
SAESWGTGRAVARIPRVGGGGTGRSGQGAFGNMCRGGRMFAPTKTWRKWNVKVNHNEKRY
ATASAIAATAVASLVLARGHRVEKIPEIPLVVSTDLESIQKTKEAVAALKAVGAHSDLLK
VLKSKKLRAGKGKYRNRRWTQRRGPLVVYAEDNGIVKALRNVPGVETANVASLNLLQLAP
GAHLGRFVIWTEAAFTKLDQVWGSETVASSKVGYTLPSHIISTSDVTRIINSSEIQSAIR
PAGQATQKRTHVLKKNPLKNKQVLLRLNPYAKVFAAEKLGSKKAEKTGTKPAAVFTETLK
HD
Sequence of entity 4 (D), FASTA
>8E5T_4 Protein MAK16 (chains D)
MSDEIVWQVINQSFCSHRIKAPNGQNFCRNEYNVTGLCTRQSCPLANSKYATVKCDNGKL
YLYMKTPERAHTPAKLWERIKLSKNYTKALQQIDEHLLHWSKFFRHKCKQRFTKLTQVMI
TERRLALREEERHYVGVAPKVKRREQNRERKALVAAKIEKAIEKELMDRLKSGAYGDKPL
NVDEKVWKKIMGQMEEENSQDEEEDWDEEEESDDGEVEYVADDGEGEYVDVDDLEKWLAD
SDREASSASESESDSESESDSDSDEENKNSAKRRKKGTSAKTKRPKVEIEYEEEHEVQNA
EQEVAQ
Sequence of entity 5 (E), FASTA
>8E5T_5 60S ribosomal protein L6-A (chains E)
MSAQKAPKWYPSEDVAALKKTRKAARPQKLRASLVPGTVLILLAGRFRGKRVVYLKHLED
NTLLISGPFKVNGVPLRRVNARYVIATSTKVSVEGVNVEKFNVEYFAKEKLTKKEKKEAN
LFPEQQNKEIKAERVEDQKVVDKALIAEIKKTPLLKQYLSASFSLKNGDKPHMLKF
Sequence of entity 6 (F), FASTA
>8E5T_6 60S ribosomal protein L7-A (chains F)
MAAEKILTPESQLKKSKAQQKTAEQVAAERAARKAANKEKRAIILERNAAYQKEYETAER
NIIQAKRDAKAAGSYYVEAQHKLVFVVRIKGINKIPPKPRKVLQLLRLTRINSGTFVKVT
KATLELLKLIEPYVAYGYPSYSTIRQLVYKRGFGKINKQRVPLSDNAIIEANLGKYGILS
IDDLIHEIITVGPHFKQANNFLWPFKLSNPSGGWGVPRKFKHFIQGGSFGNREEFINKLV
KSMN
Sequence of entity 7 (G), FASTA
>8E5T_7 60S ribosomal protein L8-A (chains G)
MAPGKKVAPAPFGAKSTKSNKTRNPLTHSTPKNFGIGQAVQPKRNLSRYVKWPEYVRVQR
QKKILSIRLKVPPTIAQFQYTLDRNTAAETFKLFNKYRPETAAEKKERLTKEAAAVAEGK
SKQDASPKPYAVKYGLNHVVALIENKKAKLVLIANDVDPIELVVFLPALCKKMGVPYAIV
KGKARLGTLVNQKTSAVAALTEVRAEDEAALAKLVSTIDANFADKYDEVKKHWGGGILGN
KAQAKMDKRAKNSDSA
Sequence of entity 8 (K), FASTA
>8E5T_8 Proteasome-interacting protein CIC1 (chains K)
MAKKSNSKKSTPVSTPSKEKKKVIEKKSSTAIPRERVIKAVNELIKFTSKPQDENNEEGN
NGKKNLLEDDEEELKKDLQLIVVNNKSFTGTSKSFKLKLLNVKHSFYKPWKEASATAVKD
FKVLLILKDSDIKKVSEDDLFDQLDSEGIKVDEIICGKDLKTVYKAYEARNAFISQFSLI
LADDSIVTSLPKLMGGKAYNKVETTPISIRTHANKEFSLTTLTNNIKKVYMNQLPVKLPR
GTTLNVHLGNLEWLRPEEFVDNVELISEQLIKAYQIRSIFIKTNRSPVLPLYYNQDVLDE
LEAKKDKIEETHEDDMVTIDGVQVHLSTFNKGLMEIANPSELGSIFSKQINNAKKRSSSE
LEKESSESEAVKKAKS
Sequence of entity 9 (L), FASTA
>8E5T_9 60S ribosomal protein L13-A (chains L)
MAISKNLPILKNHFRKHWQERVKVHFDQAGKKVSRRNARATRAAKIAPRPLDLLRPVVRA
PTVKYNRKVRAGRGFTLAEVKAAGLTAAYARTIGIAVDHRRQNRNQEIFDANVQRLKEYQ
SKIIVFPRNGKAPEAEQVLSAAATFPIAQPATDVEARAVQDNGESAFRTLRLARSEKKFR
GIREKRAREKAEAEAEKKK
Sequence of entity 10 (M), FASTA
>8E5T_10 60S ribosomal protein L14-A (chains M)
MSTDSIVKASNWRLVEVGRVVLIKKGQSAGKLAAIVEIIDQKKVLIDGPKAGVPRQAINL
GQVVLTPLTFALPRGARTATVSKKWAAAAVCEKWAASSWAKKIAQRERRAALTDFERFQV
MVLRKQKRYTVKKALAKA
Sequence of entity 11 (N), FASTA
>8E5T_11 60S ribosomal protein L15-A (chains N)
MGAYKYLEELQRKKQSDVLRFLQRVRVWEYRQKNVIHRAARPTRPDKARRLGYKAKQGFV
IYRVRVRRGNRKRPVPKGATYGKPTNQGVNELKYQRSLRATAEERVGRRAANLRVLNSYW
VNQDSTYKYFEVILVDPQHKAIRRDARYNWICDPVHKHREARGLTATGKKSRGINKGHKF
NNTKAGRRKTWKRQNTLSLWRYRK
Sequence of entity 12 (Q), FASTA
>8E5T_12 60S ribosomal protein L18-A (chains Q)
MGIDHTSKQHKRSGHRTAPKSDNVYLKLLVKLYTFLARRTDAPFNKVVLKALFLSKINRP
PVSVSRIARALKQEGAANKTVVVVGTVTDDARIFEFPKTTVAALRFTAGARAKIVKAGGE
CITLDQLAVRAPKGQNTLILRGPRNSREAVRHFGMGPHKGKAPRILSTGRKFERARGRRR
SKGFKV

Ligands and cofactors

IDNameFormulaCopies
MGMagnesium ionMg33
ZNZinc ionZn1

Primary citation

A co-transcriptional ribosome assembly checkpoint controls nascent large ribosomal subunit maturation. Sanghai, Z.A., Piwowarczyk, R., Broeck, A.V. et al. Nat Struct Mol Biol (2023) 30:594-599. DOI 10.1038/s41594-023-00947-3 · PubMed

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

Browse structure collections

About this viewer

MolViewer shows 8E5T directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.