7R72: Nucleolar complex protein 2

Name: PDB 7R72: State E1 nucleolar 60S ribosome biogenesis intermediate - Spb4 local model
Published: 2022-11-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

State E1 nucleolar 60S ribosome biogenesis intermediate - Spb4 local model. Determined by electron microscopy at 3.07 Å resolution. Released 9 Nov 2022.

Method: Electron microscopy
Resolution: 3.07 Å
Organism: Saccharomyces cerevisiae BY4741
Chains: 24
Atoms: 39,443
Mol. weight: 1017.95 kDa
Ligands: ZN
Released: 9 Nov 2022

Explore 7R72 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7R72 contains 126 α-helices and 132 β-strands across 21 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 8: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	6-14	9
α-helix	16-34	19
α-helix	42-49	8
α-helix	52-59	8

Chain b: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	490-510	21
β-strand	518	1	3
β-strand	526	1	6
α-helix	528-538	11

Chain c: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	11-20	10
β-strand	22-25	4	10
α-helix	27-36	10
β-strand	41-44	4	10
α-helix	50-63	14
β-strand	66-69	4	10
α-helix	74-81	8
β-strand	89-94	6	10

Chain d: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	12-15	4	11
α-helix	16-19	4
α-helix	28-43	16
β-strand	51	1	11
α-helix	53-59	7
β-strand	70-75	6	11
β-strand	93-95	3	11

Chain g: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	19-24	6	12
β-strand	30-35	6	12
α-helix	36-39	4
β-strand	43	1	13
α-helix	49	1
β-strand	50	1	13
α-helix	51	1
α-helix	59-64	6
α-helix	67-69	3
α-helix	82-110	29

Chain G: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	48-51	4
α-helix	54-61	8

Chain I: 17 helices, 0 β-strands

Element	Residues	Length
α-helix	131-149	19
α-helix	156-164	9
α-helix	171-188	18
α-helix	199-202	4
α-helix	210-235	26
α-helix	243-260	18
α-helix	269-280	12
α-helix	291-303	13
α-helix	309-324	16
α-helix	331-334	4
α-helix	335-339	5
α-helix	341-343	3
α-helix	363-365	3
α-helix	366-368	3
α-helix	371-420	50
α-helix	426-436	11
α-helix	437-439	3

Chain j: 0 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	16-18	3	14
β-strand	25-28	4	14
β-strand	33-34	2	14

13 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 rRNA	1	RNA	641	Saccharomyces cerevisiae BY4741
5.8S rRNA	2	RNA	72	Saccharomyces cerevisiae BY4741
Nucleolar complex protein 2	8	protein	710	Saccharomyces cerevisiae BY4741	P39744 (AlphaFold model)
60S ribosomal protein L3	B	protein	387	Saccharomyces cerevisiae BY4741	P14126 (AlphaFold model)
60S ribosomal protein L8-A	G	protein	256	Saccharomyces cerevisiae BY4741	P17076 (AlphaFold model)
Nucleolar complex-associated protein 3	I	protein	663	Saccharomyces cerevisiae BY4741	Q07896 (AlphaFold model)
60S ribosomal protein L17-A	P	protein	184	Saccharomyces cerevisiae BY4741	P05740
60S ribosomal protein L19-A	R	protein	189	Saccharomyces cerevisiae BY4741	P0CX82
60S ribosomal protein L22-A	U	protein	121	Saccharomyces cerevisiae BY4741	P05749
60S ribosomal protein L25	X	protein	142	Saccharomyces cerevisiae BY4741	P04456
60S ribosomal protein L27-A	Z	protein	136	Saccharomyces cerevisiae BY4741	P0C2H6
Nucleolar GTP-binding protein 1	b	protein	647	Saccharomyces cerevisiae BY4741	Q02892

12 more molecules are not listed.

Sequence of entity 1 (1), FASTA

>7R72_1 25S rRNA (chains 1)
AUGCCUGAAUAGGGUGAAGCCAGAGGAAACUCUGGUGGAGGCUCGCGAAUUUGGGUAUAG
UAGCAAAUAUUCAAAUGAGAACUUUGAAGACUGAAGUGGGGAAAGGUUCCACGUCAACAG
CAGUUGGACGUGGGUUAGUCGAUCCUAAGAGAUGGUUUCAAAGGCCUGAUUCAGGCCACC
AUCGAAAGGGAAUCCGGUUAAGAUUCCGGAACCUGGAUAUGGAUUCUUCACGGUAACGUA
ACUGAAUGUGGAGACGUCGGCGCGAGCCCUGGGAGGAGUUAUCUUUUCUUCUUAACAGCU
UAUCACCCCGGAAUUGGUUUAUCCGGAGAUGGGGUCUUAUGGCUGGAAGAGGCCAGCACC
UUUGCUGGCUCCGGUGCGCUUGUGACGGCCCGUGAAAAUCCACAGGAAGGAAUAGUUUUC
AUGCCAGGUCGUACUGUCUCCAAGGUGAACAGCCUCUAGUUGAUAGAAUCCGUAACUUCG
GGAUAAGGAUUGGCUCUAAGGGUCGGGUAGUGAGGGCCUUGGUCACGGCCUUGGCUUGCU
ACAAUUAACGAUCAACUUAGAACUGGUACGGACAAUAUCUAGCGAGGCUGUCUGAUCAGG
CAUUGCGUAAGCAGUAGAGUAGCCGUUACGAUCUGCUGAGA

Sequence of entity 2 (2), FASTA

>7R72_2 5.8S rRNA (chains 2)
GAACGCGCGAUACUCUUUGAACGCACAUUGCGCCCCUUGGUAUUCCAGGGGGCAUCUUUG
AAAGCGUAUUGC

Sequence of entity 3 (8), FASTA

>7R72_3 Nucleolar complex protein 2 (chains 8)
MGKVSKSTKKFQSKHLKHTLDQRRKEKIQKKRIQGRRGNKTDQEKADAAGTREQQQLKKS
AKEEVFKDMSVETFFEKGIEIPKENKKLKKKTTKEQSDEDSSSSEEEEDMGQSMAKLAEK
DPEFYKYLEENDKDLLDFAGTNPLDGIDSQDEGEDAERNSNIEEKSEQMELEKEKIELSL
KLVRKWKKQLHDSPSLKLLRNIISAFKVAVNLNKEENIEDYKYAITDEKAFHELMFMVLK
DVPQAIQKMAPYKIVKGARTLPNGGNVSRVSSIVKSHAGSLLILLNDITNTETAALVLHS
VNELMPYLLSYRRILKELIKSIVGVWSTTRELETQIASFAFLINTTKEFKKSMLETTLKT
TYSTFIKSCRKTNMRSMPLINFQKNSAAELFGIDEVLGYQVGFEYIRQLAIHLRNTMNAT
TKKSSKINSAEAYKIVYNWQFCHSLDFWSRVLSFACQPEKENGSESPLRQLIYPLVQVTL
GVIRLIPTPQFFPLRFYLIKSLIRLSQNSGVFIPIYPLLSEILTSTAFTKAPKKSPNLAA
FDFEHNIKCTQAYLNTKIYQEGLSEQFVDLLGDYFALYCKNIAFPELVTPVIISLRRYIK
TSTNVKLNKRLSTVVEKLNQNSTFIQEKRSDVEFGPTNKSEVSRFLNDVAWNKTPLGSYV
AVQREVKEEKARLMRESMEEQDKERETEEAKLLNSLESDDDNEDVEMSDA

Sequence of entity 4 (B), FASTA

>7R72_4 60S ribosomal protein L3 (chains B)
MSHRKYEAPRHGHLGFLPRKRAASIRARVKAFPKDDRSKPVALTSFLGYKAGMTTIVRDL
DRPGSKFHKREVVEAVTVVDTPPVVVVGVVGYVETPRGLRSLTTVWAEHLSDEVKRRFYK
NWYKSKKKAFTKYSAKYAQDGAGIERELARIKKYASVVRVLVHTQIRKTPLAQKKAHLAE
IQLNGGSISEKVDWAREHFEKTVAVDSVFEQNEMIDAIAVTKGHGFEGVTHRWGTKKLPR
KTHRGLRKVACIGAWHPAHVMWSVARAGQRGYHSRTSINHKIYRVGKGDDEANGATSFDR
TKKTITPMGGFVHYGEIKNDFIMVKGCIPGNRKRIVTLRKSLYTNTSRKALEEVSLKWID
TASKFGKGRFQTPAEKHAFMGTLKKDL

Sequence of entity 5 (G), FASTA

>7R72_5 60S ribosomal protein L8-A (chains G)
MAPGKKVAPAPFGAKSTKSNKTRNPLTHSTPKNFGIGQAVQPKRNLSRYVKWPEYVRVQR
QKKILSIRLKVPPTIAQFQYTLDRNTAAETFKLFNKYRPETAAEKKERLTKEAAAVAEGK
SKQDASPKPYAVKYGLNHVVALIENKKAKLVLIANDVDPIELVVFLPALCKKMGVPYAIV
KGKARLGTLVNQKTSAVAALTEVRAEDEAALAKLVSTIDANFADKYDEVKKHWGGGILGN
KAQAKMDKRAKNSDSA

Sequence of entity 6 (I), FASTA

>7R72_6 Nucleolar complex-associated protein 3 (chains I)
MAKRNRSQFRIQERTAKKRKHEDSLLEGNVFQNAPEDMDENTIYSAKGSSWDEEEQDYEM
VPRKNRSDTSNLVEGLPIKVNGKVERKLHKAQEKPKDDDEEDEDSNDSSEDDEGPNEEQE
AEAKEDEPDTEEKILQLKEDIADLVTKVMEEPEENTAALGRLCKMVESKNPNTCKFSMLA
LVPVFKSIIPGYRIRPLTETEKKEKVSKEVSKLRNFEQALVYNYKNYVGRLQSLSKTPSN
AAPIQVSLGILATQAAKELISTASHFNFRTDIFTLLLRRICKPRISTDPTSIQIIQTFET
LLNEDEEGSISFEILRIFNKILKTRNFNIEESVLNMLLSLDVLHDYDPNTKLKGNVSAPK
LKKKDRVHLSKKQRKARKEMQQIEEEMRNAEQAVSAEERERNQSEILKIVFTIYLNILKN
NAKTLIGSVLEGLTKFGNMANFDLLGDFLEVMKELISDTEFDNLSSAEVRKALLCIVSAF
SLISNTQYMKVNVDLSKFVDGLYALLPYICLDADIELSYRSLRLADPLNNEIIKPSVNVS
TKAELLLKALDHVFFRSKSGTKERATAFTKRLYMCISHTPEKTSIAILKFIDKLMNRYPE
ISGLYSSEDRIGNGHFIMEADNPSRSNPEAATLWDNALLEKHYCPVVTKGLRSLSSRSKE
CSK

Sequence of entity 7 (P), FASTA

>7R72_7 60S ribosomal protein L17-A (chains P)
MARYGATSTNPAKSASARGSYLRVSFKNTRETAQAINGWELTKAQKYLEQVLDHQRAIPF
RRFNSSIGRTAQGKEFGVTKARWPAKSVKFVQGLLQNAAANAEAKGLDATKLYVSHIQVN
QAPKQRRRTYRAHGRINKYESSPSHIELVVTEKEEAVAKAAEKKVVRLTSRQRGRIAAQK
RIAA

Sequence of entity 8 (R), FASTA

>7R72_8 60S ribosomal protein L19-A (chains R)
MANLRTQKRLAASVVGVGKRKVWLDPNETSEIAQANSRNAIRKLVKNGTIVKKAVTVHSK
SRTRAHAQSKREGRHSGYGKRKGTREARLPSQVVWIRRLRVLRRLLAKYRDAGKIDKHLY
HVLYKESKGNAFKHKRALVEHIIQAKADAQREKALNEEAEARRLKNRAARDRRAQRVAEK
RDALLKEDA

Sequence of entity 9 (U), FASTA

>7R72_9 60S ribosomal protein L22-A (chains U)
MAPNTSRKQKIAKTFTVDVSSPTENGVFDPASYAKYLIDHIKVEGAVGNLGNAVTVTEDG
TVVTVVSTAKFSGKYLKYLTKKYLKKNQLRDWIRFVSTKTNEYRLAFYQVTPEEDEEEDE
E

Sequence of entity 10 (X), FASTA

>7R72_10 60S ribosomal protein L25 (chains X)
MAPSAKATAAKKAVVKGTNGKKALKVRTSATFRLPKTLKLARAPKYASKAVPHYNRLDSY
KVIEQPITSETAMKKVEDGNILVFQVSMKANKYQIKKAVKELYEVDVLKVNTLVRPNGTK
KAYVRLTADYDALDIANRIGYI

Sequence of entity 11 (Z), FASTA

>7R72_11 60S ribosomal protein L27-A (chains Z)
MAKFLKAGKVAVVVRGRYAGKKVVIVKPHDEGSKSHPFGHALVAGIERYPLKVTKKHGAK
KVAKRTKIKPFIKVVNYNHLLPTRYTLDVEAFKSVVSTETFEQPSQREEAKKVVKKAFEE
RHQAGKNQWFFSKLRF

Sequence of entity 12 (b), FASTA

>7R72_12 Nucleolar GTP-binding protein 1 (chains b)
MQLSWKDIPTVAPANDLLDIVLNRTQRKTPTVIRPGFKITRIRAFYMRKVKYTGEGFVEK
FEDILKGFPNINDVHPFHRDLMDTLYEKNHYKISLAAISRAKSLVEQVARDYVRLLKFGQ
SLFQCKQLKRAALGRMATIVKKLRDPLAYLEQVRQHIGRLPSIDPNTRTLLICGYPNVGK
SSFLRCITKSDVDVQPYAFTTKSLYVGHFDYKYLRFQAIDTPGILDRPTEEMNNIEMQSI
YAIAHLRSCVLYFMDLSEQCGFTIEAQVKLFHSIKPLFANKSVMVVINKTDIIRPEDLDE
ERAQLLESVKEVPGVEIMTSSCQLEENVMEVRNKACEKLLASRIENKLKSQSRINNVLNK
IHVAQPQARDDVKRTPFIPESVKNLKKYDPEDPNRRKLARDIEAENGGAGVFNVNLKDKY
LLEDDEWKNDIMPEILDGKNVYDFLDPEIAAKLQALEEEEEKLENEGFYNSDDEEEIYDG
FEASEVDDIKEKAAWIRNRQKTMIAEARNRKSLKNKAIMPRSKLTKSFGKMEEHMSTLGH
DMSALQDKQNRAARKNRYVERGSDVVFGDQDALTASTENGVKLRQTDRLLDGVADGSMRS
KADRMAKMERRERNRHAKQGESDRHNAVSLSKHLFSGKRGVGKTDFR

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Primary citation

Sequence-specific remodeling of a topologically complex RNP substrate by Spb4. Cruz, V.E., Sekulski, K., Peddada, N. et al. Nat Struct Mol Biol (2022) 29:1228-1238. DOI 10.1038/s41594-022-00874-9 · PubMed

Other PDB entries of the same protein (UniProt P39744 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8V87 2.66 Å, 60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map)
7NAC 3.04 Å, State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model
7NAD 3.04 Å, State E2 nucleolar 60S ribosomal biogenesis intermediate - Spb4 local refinement model
7R7A 3.04 Å, State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model
7NAF 3.13 Å, State E2 nucleolar 60S ribosomal biogenesis intermediate - Spb1-MTD local model
7R6K 3.17 Å, State E2 nucleolar 60S ribosomal intermediate - Model for Noc2/Noc3 region
9QJC 3.2 Å, Yeast pre-60S Domain II intermediate
8E5T 4.0 Å, Yeast co-transcriptional Noc1-Noc2 RNP assembly checkpoint intermediate

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