6N8N | pdb_00006n8n

Cryo-EM structure of Lsg1-engaged (LE) pre-60S ribosomal subunit

PDB DOI: https://doi.org/10.2210/pdb6N8N/pdb
EM Map EMD-0373: EMDB EMDataResource
NAKB: 6N8N

Classification: RIBOSOME
Organism(s): Saccharomyces cerevisiae S288C
Mutation(s): No

Deposited: 2018-11-29 Released: 2019-03-13
Deposition Author(s): Zhou, Y., Musalgaonkar, S., Johnson, A.W., Taylor, D.W.
Funding Organization(s): Cancer Prevention and Research Institute of Texas (CPRIT), Robert A. Welch Foundation, Army Research Office, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Tightly-orchestrated rearrangements govern catalytic center assembly of the ribosome.

Zhou, Y., Musalgaonkar, S., Johnson, A.W., Taylor, D.W.

(2019) Nat Commun 10: 958-958

PubMed: 30814529 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-019-08880-0
Primary Citation Related Structures:
6N8J, 6N8K, 6N8L, 6N8M, 6N8N, 6N8O

PubMed Abstract:
The catalytic activity of the ribosome is mediated by RNA, yet proteins are essential for the function of the peptidyl transferase center (PTC). In eukaryotes, final assembly of the PTC occurs in the cytoplasm by insertion of the ribosomal protein Rpl10 (uL16). We determine structures of six intermediates in late nuclear and cytoplasmic maturation of the large subunit that reveal a tightly-choreographed sequence of protein and RNA rearrangements controlling the insertion of Rpl10. We also determine the structure of the biogenesis factor Yvh1 and show how it promotes assembly of the P stalk, a critical element for recruitment of GTPases that drive translation. Together, our structures provide a blueprint for final assembly of a functional ribosome.

Organizational Affiliation

Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA.

Macromolecule Content

Total Structure Weight: 2,136.13 kDa
Atom Count: 131,813
Modeled Residue Count: 10,869
Deposited Residue Count: 12,161
Unique protein chains: 45
Unique nucleic acid chains: 3

Macromolecules

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein phosphatase YVH1	D [auth Y]	364	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.1.3.48
UniProt
Find proteins for Q02256 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02256 Go to UniProtKB: Q02256
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q02256
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation initiation factor 6	E [auth X]	245	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q12522 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12522 Go to UniProtKB: Q12522
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UniProt Group	Q12522
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Large subunit GTPase 1	F [auth W]	640	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.6.1
UniProt
Find proteins for P53145 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53145 Go to UniProtKB: P53145
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UniProt Group	P53145
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal export protein NMD3	G [auth V]	518	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P38861 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38861 Go to UniProtKB: P38861
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P38861
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L2-A	H [auth D]	254	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0CX45 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX45 Go to UniProtKB: P0CX45
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0CX45
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L3	I [auth E]	387	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P14126 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P14126 Go to UniProtKB: P14126
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UniProt Group	P14126
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L4-A	J [auth F]	362	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P10664 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P10664 Go to UniProtKB: P10664
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UniProt Group	P10664
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L5	K [auth G]	297	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P26321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P26321 Go to UniProtKB: P26321
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UniProt Group	P26321
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L6-A	L [auth H]	176	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q02326 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02326 Go to UniProtKB: Q02326
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UniProt Group	Q02326
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L7-A	M [auth I]	244	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P05737 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05737 Go to UniProtKB: P05737
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UniProt Group	P05737
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L8-A	N [auth J]	256	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P17076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P17076 Go to UniProtKB: P17076
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P17076
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L9-A	O [auth K]	191	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P05738 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05738 Go to UniProtKB: P05738
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P05738
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L11-A	P [auth M]	174	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0C0W9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0C0W9 Go to UniProtKB: P0C0W9
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UniProt Group	P0C0W9
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L13-A	Q [auth N]	199	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q12690 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12690 Go to UniProtKB: Q12690
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UniProt Group	Q12690
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L14-A	R [auth O]	138	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P36105 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36105 Go to UniProtKB: P36105
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UniProt Group	P36105
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L42-A	S [auth Q]	106	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0CX27 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX27 Go to UniProtKB: P0CX27
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UniProt Group	P0CX27
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L43-A	T [auth R]	92	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0CX25 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX25 Go to UniProtKB: P0CX25
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UniProt Group	P0CX25
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal Protein uL1	U [auth S]	217	Saccharomyces cerevisiae S288C	Mutation(s): 0

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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L15-A	V [auth a]	204	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P05748 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05748 Go to UniProtKB: P05748
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UniProt Group	P05748
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L16-A	W [auth b]	199	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P26784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P26784 Go to UniProtKB: P26784
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UniProt Group	P26784
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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L17-A	X [auth c]	184	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P05740 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05740 Go to UniProtKB: P05740
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UniProt Group	P05740
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L18-A	Y [auth d]	186	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0CX49 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX49 Go to UniProtKB: P0CX49
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UniProt Group	P0CX49
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L19-A	Z [auth e]	189	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0CX82 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX82 Go to UniProtKB: P0CX82
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UniProt Group	P0CX82
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L20-A	AA [auth f]	172	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0CX23 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX23 Go to UniProtKB: P0CX23
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UniProt Group	P0CX23
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L21-A	BA [auth g]	160	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for Q02753 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02753 Go to UniProtKB: Q02753
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UniProt Group	Q02753
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L22-A	CA [auth h]	121	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P05749 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05749 Go to UniProtKB: P05749
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UniProt Group	P05749
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L23-A	DA [auth i]	137	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0CX41 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX41 Go to UniProtKB: P0CX41
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UniProt Group	P0CX41
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L24-A	EA [auth j]	155	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P04449 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P04449 Go to UniProtKB: P04449
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UniProt Group	P04449
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L25	FA [auth k]	142	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P04456 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P04456 Go to UniProtKB: P04456
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UniProt Group	P04456
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L26-A	GA [auth l]	127	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P05743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05743 Go to UniProtKB: P05743
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UniProt Group	P05743
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L27-A	HA [auth m]	136	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0C2H6 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0C2H6 Go to UniProtKB: P0C2H6
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UniProt Group	P0C2H6
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Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L28	IA [auth n]	149	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P02406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P02406 Go to UniProtKB: P02406
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UniProt Group	P02406
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Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L29	JA [auth o]	59	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P05747 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05747 Go to UniProtKB: P05747
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UniProt Group	P05747
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Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L30	KA [auth p]	105	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P14120 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P14120 Go to UniProtKB: P14120
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UniProt Group	P14120
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Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L31-A	LA [auth q]	113	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0C2H8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0C2H8 Go to UniProtKB: P0C2H8
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UniProt Group	P0C2H8
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Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L32	MA [auth r]	130	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P38061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38061 Go to UniProtKB: P38061
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UniProt Group	P38061
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Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L33-A	NA [auth s]	107	Saccharomyces cerevisiae S288C	Mutation(s): 0
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Find proteins for P05744 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05744 Go to UniProtKB: P05744
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Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L34-A	OA [auth t]	121	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P87262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P87262 Go to UniProtKB: P87262
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UniProt Group	P87262
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Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L35-A	PA [auth u]	120	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0CX84 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX84 Go to UniProtKB: P0CX84
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UniProt Group	P0CX84
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Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L36-A	QA [auth v]	100	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P05745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05745 Go to UniProtKB: P05745
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UniProt Group	P05745
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Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L37-A	RA [auth w]	88	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P49166 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P49166 Go to UniProtKB: P49166
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UniProt Group	P49166
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Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L38	SA [auth x]	78	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P49167 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P49167 Go to UniProtKB: P49167
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UniProt Group	P49167
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Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L39	TA [auth y]	51	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P04650 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P04650 Go to UniProtKB: P04650
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UniProt Group	P04650
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Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-60S ribosomal protein L40	UA [auth z]	128	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0CH08 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CH08 Go to UniProtKB: P0CH08
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UniProt Group	P0CH08
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Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosomal protein L12	VA [auth L]	165	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P0CX53 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX53 Go to UniProtKB: P0CX53
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UniProt Group	P0CX53
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 1
Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), miscRNA	A	3,396	Saccharomyces cerevisiae S288C
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Molecule	Chains	Length	Organism
Entity ID: 2
5S rRNA	B	121	Saccharomyces cerevisiae S288C
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Molecule	Chains	Length	Organism
Entity ID: 3
5.8S rRNA	C	158	Saccharomyces cerevisiae S288C
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Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.80 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-03-13

Deposition Author(s):

Funding Organization	Location	Grant Number
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	RR160088
Robert A. Welch Foundation	United States	F-1938
Army Research Office	United States	W911NF-15-0120
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM53655
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM127127

Revision History (Full details and data files)

Version 1.0: 2019-03-13
Type: Initial release
Version 1.1: 2020-01-08
Changes: Author supporting evidence
Version 1.2: 2024-10-30
Changes: Data collection, Database references, Refinement description, Source and taxonomy, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

6N8N | pdb_00006n8n

Cryo-EM structure of Lsg1-engaged (LE) pre-60S ribosomal subunit

Literature

Tightly-orchestrated rearrangements govern catalytic center assembly of the ribosome.

Biological Assembly 1

Macromolecules

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