7R7C: 60S ribosome subunit biogenesis protein NIP7

Name: PDB 7R7C: State E2 nucleolar 60S ribosomal biogenesis intermediate - L1 stalk local model
Published: 2022-11-09
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ribosome

State E2 nucleolar 60S ribosomal biogenesis intermediate - L1 stalk local model. Determined by electron microscopy at 3.71 Å resolution. Released 9 Nov 2022.

Method: Electron microscopy
Resolution: 3.71 Å
Organism: Saccharomyces cerevisiae BY4741
Chains: 11
Atoms: 14,950
Mol. weight: 282.83 kDa
Released: 9 Nov 2022

Explore 7R7C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7R7C contains 62 α-helices and 67 β-strands across 10 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 7: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-29	5
β-strand	30	1	6
α-helix	47-57	11
β-strand	88-90	3	15
α-helix	91	1
β-strand	99	1	2
α-helix	100-101	2
α-helix	105-115	11
α-helix	126-146	21

Chain a: 10 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	6-18	13
α-helix	19-23	5
β-strand	31-38	8	19
β-strand	50-54	5	20
β-strand	66-68	3	21
α-helix	71-78	8
β-strand	84	1	21
α-helix	89-92	4
α-helix	97-107	11
β-strand	110-113	4	21
α-helix	114-117	4
α-helix	120-123	4
α-helix	127-130	4
β-strand	136-138	3	21
α-helix	144-152	9
β-strand	154-158	5	20
β-strand	164-171	8	19
α-helix	176-193	18
β-strand	201-208	8	19
β-strand	214-215	2	19

Chain A: 3 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	44-55	12
β-strand	118	1	16
β-strand	130	1	17
β-strand	133	1	18
α-helix	134-135	2
α-helix	162-163	2
β-strand	170	1	18
β-strand	175-178	4	15
β-strand	189-197	9	15
β-strand	210-214	5	15
β-strand	218	1	16

Chain b: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	39-50	12
α-helix	104-116	13
α-helix	122-141	20

Chain J: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	246-264	19
α-helix	270-271	2
β-strand	278	1	17
α-helix	282-313	32
α-helix	315-338	24

Chain l: 11 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	1
β-strand	5	1	2
α-helix	6-17	12
β-strand	35-40	6	1
β-strand	43-48	6	1
α-helix	49-54	6
α-helix	55-57	3
α-helix	60-62	3
β-strand	65-66	2	3
β-strand	68-73	6	1
β-strand	79-81	3	1
α-helix	83-85	3
α-helix	86-89	4
β-strand	96-99	4	4
α-helix	101-103	3
α-helix	104-108	5
β-strand	113-114	2	4
β-strand	118	1	4
α-helix	125-126	2
β-strand	130-135	6	4
β-strand	140-146	7	4
β-strand	161-168	8	4
α-helix	169-171	3
α-helix	172-175	4

Chain m: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	162-164	3
β-strand	170-173	4	5
β-strand	179-181	3	5
α-helix	185-187	3
α-helix	188-196	9
β-strand	205	1	6
β-strand	206	1	7
β-strand	213	1	7
α-helix	214	1

Chain q: 18 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	199-212	14
α-helix	225-238	14
α-helix	243-251	9
α-helix	255-263	9
β-strand	271-275	5	8
α-helix	282-292	11
β-strand	294-298	5	8
β-strand	306-312	7	8
α-helix	320-323	4
β-strand	327-329	3	8
α-helix	335-341	7
β-strand	350-351	2	3
α-helix	358-367	10
β-strand	373-375	3	3
α-helix	380-393	14
β-strand	398-400	3	3
α-helix	405-407	3
α-helix	408-411	4
β-strand	415	1	9
β-strand	417-420	4	3
α-helix	436-439	4
α-helix	444-446	3
α-helix	448-461	14
β-strand	463	1	9
β-strand	472-475	4	3
β-strand	476	1	10
α-helix	482-494	13
β-strand	499	1	11
α-helix	510	1
β-strand	511	1	10
α-helix	512-513	2
α-helix	523-527	5
β-strand	529	1	10
β-strand	543	1	10
β-strand	546-547	2	3
β-strand	548	1	11

2 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	226	Saccharomyces cerevisiae BY4741
60S ribosome subunit biogenesis protein NIP7	l	protein	181	Saccharomyces cerevisiae BY4741	Q08962 (AlphaFold model)
Ribosome biogenesis protein ERB1	m	protein	63	Saccharomyces cerevisiae BY4741	Q04660 (AlphaFold model)
25S rRNA (cytosine(2870)-C(5))-methyltransferase	q	protein	618	Saccharomyces cerevisiae BY4741	P40991 (AlphaFold model)
Ribosome biogenesis protein NSA2 homolog	r	protein	104	Saccharomyces cerevisiae BY4741	P40078 (AlphaFold model)
27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase	w	protein	12	Saccharomyces cerevisiae BY4741	P25582
60S ribosomal subunit assembly/export protein LOC1	7	protein	204	Saccharomyces cerevisiae BY4741	P43586
Ribosome biogenesis protein BRX1	A	protein	291	Saccharomyces cerevisiae BY4741	Q08235
rRNA-processing protein EBP2	J	protein	96	Saccharomyces cerevisiae BY4741	P36049
Nucleolar GTP-binding protein 1	b	protein	54	Saccharomyces cerevisiae BY4741	Q02892
60S ribosomal protein L1-A	a	protein	217	Saccharomyces cerevisiae BY4741	P0CX43

Sequence of entity 1 (1), FASTA

>7R7C_1 25S rRNA (chains 1)
GCGGUCGAUCGUUUCCCUCAGGAUAUUUUUGGUAAGCAGAACUACCCUGUUGAGCUUGAC
UCUAGUUUGACAUUGUGAAGAGACAUAGAGGGUGUAGAAUAAGUGGGAGCUUCGGCGCCA
GUGAAAUACCACUACCUUUAUAGUUUCUUUACUAUUGUCAGGUGGGGAGUAAAGUUACCA
CAGGGAUAAUUGUGGCAGUCUUGCUGACCGUCGUGAGACAGGUUAG

Sequence of entity 2 (l), FASTA

>7R7C_2 60S ribosome subunit biogenesis protein NIP7 (chains l)
MRQLTEEETKVVFEKLAGYIGRNISFLVDNKELPHVFRLQKDRVYYVPDHVAKLATSVAR
PNLMSLGICLGKFTKTGKFRLHITSLTVLAKHAKYKIWIKPNGEMPFLYGNHVLKAHVGK
MSDDIPEHAGVIVFAMNDVPLGFGVSAKSTSESRNMQPTGIVAFRQADIGEYLRDEDTLF
T

Sequence of entity 3 (m), FASTA

>7R7C_3 Ribosome biogenesis protein ERB1 (chains m)
TQNTIGNIPLSAYDEMPHIGYDINGKRIMRPAKGSALDQLLDSIELPEGWTGLLDKNSGS
SLN

Sequence of entity 4 (q), FASTA

>7R7C_4 25S rRNA (cytosine(2870)-C(5))-methyltransferase (chains q)
MGSRRHKNKQAAPPTLEEFQARKEKKANRKLEKGKRPSTTQGDEVSDRKKKKSKPFKKSR
KEEEEVVEEDKDLPEVDLEELSKARKSLFDDEEDDDEAGLVDEELKDEFDLEQEYDYDED
EDNDAHPIFSDDDDEADLEELNAQNMEALSKKLDEEEAEEAEEAEMELVEAENMQPRADI
LPTEEQEEMMAQETPNLTSTRTRMIEIVKVLENFKTLGAEGRSRGEYVDRLLKDICEYFG
YTPFLAEKLFNLFSPAEAMEFFEANEIARPITIRTNTLKTRRRDLAQTLVNRGVNLQPIG
SWTKVGLQIFDSQVPIGATPEYLAGHYILQAASSFLPVIALDPHENERILDMAAAPGGKT
TYISAMMKNTGCVFANDANKSRTKSLIANIHRLGCTNTIVCNYDAREFPKVIGGFDRILL
DAPCSGTGVIGKDQSVKVSRTEKDFIQIPHLQKQLLLSAIDSVDCNSKHGGVIVYSTCSV
AVEEDEAVIDYALRKRPNVKLVDTGLAIGKEAFTSYRGKKFHPSVKLARRYYPHTYNVDG
FFVAKFQKIGPSSFDDNQASAKEKETAARKEALEEGIIHSDFATFEDEEDDKYIEKSVKN
NLLKKGVNPKAKRPSNEK

Sequence of entity 5 (r), FASTA

>7R7C_5 Ribosome biogenesis protein NSA2 homolog (chains r)
RMITKHTFVGEGFTRRPVKMERIIRPSALRQKKANVTHPELGVTVFLPILAVKKNPQSPM
YTQLGVLTKGTIIEVNVSELVWGKYAQVTNEPDRDGCVNAVLLD

Sequence of entity 6 (w), FASTA

>7R7C_6 27S pre-rRNA (guanosine(2922)-2'-O)-methyltransferase (chains w)
QRALRRIAKKHH

Sequence of entity 7 (7), FASTA

>7R7C_7 60S ribosomal subunit assembly/export protein LOC1 (chains 7)
MAPKKPSKRQNLRREVAPEVFQDSQARNQLANVPHLTEKSAQRKPSKTKVKKEQSLARLY
GAKKDKKGKYSEKDLNIPTLNRAIVPGVKIRRGKKGKKFIADNDTLTLNRLITTIGDKYD
DIAESKLEKARRLEEIRELKRKEIERKEALKQDKLEEKKDEIKKKSSVARTIRRKNKRDM
LKSEAKASESKTEGRKVKKVSFAQ

Sequence of entity 8 (A), FASTA

>7R7C_8 Ribosome biogenesis protein BRX1 (chains A)
MSSIYKALAGKSKDNKSEKKQGNVKQFMNKQRTLLISSRGVNYRHRHLIQDLSGLLPHSR
KEPKLDTKKDLQQLNEIAELYNCNNVLFFEARKHQDLYLWLSKPPNGPTIKFYIQNLHTM
DELNFTGNCLKGSRPVLSFDQRFESSPHYQLIKELLVHNFGVPPNARKSKPFIDHVMSFS
IVDDKIWVRTYEISHSTKNKEEYEDGEEDISLVEIGPRFVMTVILILEGSFGGPKIYENK
QYVSPNVVRAQIKQQAAEEAKSRAEAAVERKIKRRENVLAADPLSNDALFK

Sequence of entity 9 (J), FASTA

>7R7C_9 rRNA-processing protein EBP2 (chains J)
AFYKQSLDAVLVARDELKRLKVPFKRPLDYFAEMVKSDEHMDKIKGKLIEEASDKKAREE
ARRQRQLKKFGKQVQNATLQKRQLEKRETLEKIKSL

Sequence of entity 10 (b), FASTA

>7R7C_10 Nucleolar GTP-binding protein 1 (chains b)
KITRIRAFYMRKVKSLVEQVARDYVRLLKFGQSLFQCKQLKRAALGRMATIVKK

Sequence of entity 11 (a), FASTA

>7R7C_11 60S ribosomal protein L1-A (chains a)
MSKITSSQVREHVKELLKYSNETKKRNFLETVELQVGLKNYDPQRDKRFSGSLKLPNCPR
PNMSICIFGDAFDVDRAKSCGVDAMSVDDLKKLNKNKKLIKKLSKKYNAFIASEVLIKQV
PRLLGPQLSKAGKFPTPVSHNDDLYGKVTDVRSTIKFQLKKVLCLAVAVGNVEMEEDVLV
QQILMSVNFFVSLLKKNWQNVGSLVVKSSMGPAFRLY

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 Q08962 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8V83 2.53 Å, 60S ribosome biogenesis intermediate (Dbp10 pre-catalytic structure - Overall map)
8V87 2.66 Å, 60S ribosome biogenesis intermediate (Dbp10 post-catalytic structure - Overall map)
8V84 2.7 Å, 60S ribosome biogenesis intermediate (Dbp10 catalytic structure - Overall map)
7NAC 3.04 Å, State E2 nucleolar 60S ribosomal biogenesis intermediate - Composite model
7R7A 3.04 Å, State E1 nucleolar 60S ribosome biogenesis intermediate - Composite model
7R6K 3.17 Å, State E2 nucleolar 60S ribosomal intermediate - Model for Noc2/Noc3 region
6ELZ 3.3 Å, State E (TAP-Flag-Ytm1 E80A) - Visualizing the assembly pathway of nucleolar pre-60S…
6EM5 4.3 Å, State D architectural model (Nsa1-TAP Flag-Ytm1) - Visualizing the assembly pathway of…
7OHR 4.72 Å, Nog1-TAP associated immature ribosomal particle population E from S. cerevisiae

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