Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 40-mer - ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmn Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 40-mer -A3B2C2DEFGHIJKLMNOPQRSTUVWXYZabcdefghij 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: authors reported there is no experimental evidence

Macromolecule Content

• Total Structure Weight: 2443793.75 
• Atom Count: 91742 
• Residue Count: 14615 
• Unique protein chains: 40
• Unique nucleic acid chains: 3

6C0F

Yeast nucleolar pre-60S ribosomal subunit (state 2)

• DOI: 10.2210/pdb6C0F/pdb
• EMDataResource: EMD-7324

• Classification: RIBOSOME
• Organism(s): Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Saccharomyces cerevisiae BY4741


• Deposited: 2017-12-29 Released: 2018-03-14 
• Deposition Author(s): Sanghai, Z.A., Miller, L., Barandun, J., Hunziker, M., Chaker-Margot, M., Klinge, S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences; Swiss National Science Foundation 

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.7 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Modular assembly of the nucleolar pre-60S ribosomal subunit.

Sanghai, Z.A., Miller, L., Molloy, K.R., Barandun, J., Hunziker, M., Chaker-Margot, M., Wang, J., Chait, B.T., Klinge, S.

(2018) Nature 556: 126-129

• PubMed: 29512650 
• DOI: 10.1038/nature26156
• Primary Citation of Related Structures:  
  6CB1


• PubMed Abstract: 
  

Early co-transcriptional events during eukaryotic ribosome assembly result in the formation of precursors of the small (40S) and large (60S) ribosomal subunits. A multitude of transient assembly factors regulate and chaperone the systematic folding of pre-ribosomal RNA subdomains. However, owing to a lack of structural information, the role of these factors during early nucleolar 60S assembly is not fully understood. Here we report cryo-electron microscopy (cryo-EM) reconstructions of the nucleolar pre-60S ribosomal subunit in different conformational states at resolutions of up to 3.4 Å. These reconstructions reveal how steric hindrance and molecular mimicry are used to prevent both premature folding states and binding of later factors. This is accomplished by the concerted activity of 21 ribosome assembly factors that stabilize and remodel pre-ribosomal RNA and ribosomal proteins. Among these factors, three Brix-domain proteins and their binding partners form a ring-like structure at ribosomal RNA (rRNA) domain boundaries to support the architecture of the maturing particle. The existence of mutually exclusive conformations of these pre-60S particles suggests that the formation of the polypeptide exit tunnel is achieved through different folding pathways during subsequent stages of ribosome assembly. These structures rationalize previous genetic and biochemical data and highlight the mechanisms that drive eukaryotic ribosome assembly in a unidirectional manner.

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Organizational Affiliation: 

Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, New York 10065, USA.,Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065, USA.,Tri-Institutional Training Program in Chemical Biology, The Rockefeller University, New York, New York 10065, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
Ribosome biogenesis protein NSA1	A	463	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: NSA1
Find proteins for P53136 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P53136

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L3	B	387	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL3 (MAK8, TCM1)
Find proteins for P14126 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: RPL3 Go to UniProtKB:  P14126

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L4-A	C	362	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL4A (RPL2, RPL2A)
Find proteins for P10664 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P10664

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details
Protein MAK16	D	306	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: MAK16
Find proteins for P10962 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: MAK16 Go to UniProtKB:  P10962

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L6-A	E	176	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL6A (RPL17A, YL16A)
Find proteins for Q02326 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  Q02326

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L7-A	F	244	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL7A (RPL6A, RPL8A, YL8A)
Find proteins for P05737 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: RPL7A Go to UniProtKB:  P05737

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L8-A	G	256	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL8A (MAK7, RPL4A)
Find proteins for P17076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P17076

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details
Ribosome production factor 1	I	295	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPF1
Find proteins for P38805 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: RPF1 Go to UniProtKB:  P38805

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details
Proteasome-interacting protein CIC1	K	376	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: CIC1 (NSA3)
Find proteins for P38779 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P38779

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L13-A	L	199	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL13A
Find proteins for Q12690 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: RPL13A Go to UniProtKB:  Q12690

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L14-A	M	138	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL14A
Find proteins for P36105 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P36105

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L15-A	N	204	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL15A (RPL10A, RPL13A, YL10A)
Find proteins for P05748 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P05748

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L16-A	O	199	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL16A (RPL13, RPL21A)
Find proteins for P26784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P26784

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L17-A	P	184	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL17A (RPL17, RPL20A)
Find proteins for P05740 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P05740

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L18-A	Q	186	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL18A (RP28A)
Find proteins for P0CX49 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: RPL18A Go to UniProtKB:  P0CX49

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L20-A	S	172	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL20A (RPL18A, RPL18A2)
Find proteins for P0CX23 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P0CX23

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L23-A	V	137	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL23A (RPL17A, RPL17AA)
Find proteins for P0CX41 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: RPL23A Go to UniProtKB:  P0CX41

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details
Nucleolar GTP-binding protein 1	W	647	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: NOG1
Find proteins for Q02892 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  Q02892

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L26-A	Y	127	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL26A (RPL26, RPL33A)
Find proteins for P05743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P05743

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details
Nucleolar protein 16	7	231	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: NOP16
Find proteins for P40007 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: NOP16 Go to UniProtKB:  P40007

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details
Ribosomal RNA-processing protein 14	8	434	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RRP14
Find proteins for P36080 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P36080

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details
Ribosome biogenesis protein BRX1	b	291	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: BRX1
Find proteins for Q08235 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  Q08235

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L32	e	130	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL32
Find proteins for P38061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: RPL32 Go to UniProtKB:  P38061

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L33-A	f	107	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL33A (RPL37A)
Find proteins for P05744 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P05744

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L35-A	h	120	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL35A (SOS1)
Find proteins for P0CX84 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: RPL35A Go to UniProtKB:  P0CX84

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L36-A	i	100	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL36A (RPL39A)
Find proteins for P05745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: RPL36A Go to UniProtKB:  P05745

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L37-A	j	88	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RPL37A (RPL35A)
Find proteins for P49166 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: RPL37A Go to UniProtKB:  P49166

Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details
Brx1-associated peptide	x	28	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details
rRNA-processing protein EBP2	m	74	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details
Pescadillo homolog	n	605	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: NOP7 (RRP13, YPH1)
Find proteins for P53261 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P53261

Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details
Ribosome biogenesis protein 15	o	220	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: NOP15
Find proteins for P53927 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P53927

Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details
ATP-dependent RNA helicase HAS1	p	505	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: HAS1 EC: 3.6.4.13
Find proteins for Q03532 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: HAS1 Go to UniProtKB:  Q03532

Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details
Protein MAK11	q	285	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details
Ribosome biogenesis protein ERB1	s	807	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: ERB1
Find proteins for Q04660 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  Q04660

Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details
Ribosome biogenesis protein RLP7	t	322	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RLP7 (RPL7)
Find proteins for P40693 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P40693

Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details
Ribosome biogenesis protein RLP24	u	199	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RLP24
Find proteins for Q07915 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  Q07915

Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details
Ribosome biogenesis protein SSF1	v	453	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: SSF1
Find proteins for P38789 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  P38789

Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details
Ribosomal RNA-processing protein 15	w	250	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RRP15
Find proteins for Q06511 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: RRP15 Go to UniProtKB:  Q06511

Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details
Eukaryotic translation initiation factor 6	y	245	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: TIF6 (CDC95)
Find proteins for Q12522 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to UniProtKB:  Q12522

Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details
Ribosomal RNA-processing protein 1	z	278	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: RRP1
Find proteins for P35178 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: RRP1 Go to UniProtKB:  P35178

Entity ID: 1
Molecule	Chains	Length	Organism
Saccharomyces cerevisiae S288c 35S pre-ribosomal RNA miscRNA	1	3395	Saccharomyces cerevisiae BY4741

Entity ID: 2
Molecule	Chains	Length	Organism
5.8S rRNA	2	158	Saccharomyces cerevisiae BY4741

Entity ID: 3
Molecule	Chains	Length	Organism
ITS2	6	232	Saccharomyces cerevisiae BY4741

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	D, j, u	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
UNK	b, m, q, s, x	L-PEPTIDE LINKING	C4 H9 N O2		--

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.7 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-12-29 
• Released Date: 2018-03-14 
• Deposition Author(s): Sanghai, Z.A., Miller, L., Barandun, J., Hunziker, M., Chaker-Margot, M., Klinge, S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences	United States	1DP2GM123459
Swiss National Science Foundation	Switzerland	155515
National Institutes of Health/National Institute of General Medical Sciences	United States	GM115327-Tan
National Institutes of Health/National Institute of General Medical Sciences	United States	P41GM103314
National Institutes of Health/National Institute of General Medical Sciences	United States	P41GM109824

Revision History 

• Version 1.0: 2018-03-14
  Type: Initial release
• Version 1.1: 2018-04-18
  Type: Data collection, Database references
• Version 1.2: 2019-02-20
  Type: Author supporting evidence, Data collection