Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 46-mer - A1BCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrst Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 46-mer - A2B1CDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrs 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 2146.18 kDa 
• Atom Count: 141153 
• Residue Count: 11514 
• Unique protein chains: 46
• Unique nucleic acid chains: 5

6HD7

Cryo-EM structure of the ribosome-NatA complex

• DOI: 10.2210/pdb6HD7/pdb
• EMDataResource: EMD-0202

• Classification: TRANSLATION
• Organism(s): Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2018-08-17 Released: 2018-12-19 
• Deposition Author(s): Knorr, A.G., Becker, T., Beckmann, R.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Ribosome-NatA architecture reveals that rRNA expansion segments coordinate N-terminal acetylation.

Knorr, A.G., Schmidt, C., Tesina, P., Berninghausen, O., Becker, T., Beatrix, B., Beckmann, R.

(2019) Nat Struct Mol Biol 26: 35-39

• PubMed: 30559462 
• DOI: 10.1038/s41594-018-0165-y
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The majority of eukaryotic proteins are N-terminally α-acetylated by N-terminal acetyltransferases (NATs). Acetylation usually occurs co-translationally and defects have severe consequences. Nevertheless, it is unclear how these enzymes act in concert with the translating ribosome. Here, we report the structure of a native ribosome-NatA complex from Saccharomyces cerevisiae. NatA (comprising Naa10, Naa15 and Naa50) displays a unique mode of ribosome interaction by contacting eukaryotic-specific ribosomal RNA expansion segments in three out of four binding patches. Thereby, NatA is dynamically positioned directly underneath the ribosomal exit tunnel to facilitate modification of the emerging nascent peptide chain. Methionine amino peptidases, but not chaperones or signal recognition particle, would be able to bind concomitantly. This work assigns a function to the hitherto enigmatic ribosomal RNA expansion segments and provides mechanistic insights into co-translational protein maturation by N-terminal acetylation.

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Organizational Affiliation: 

Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany. [e-mail].

Macromolecules

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L43-A	D	92	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P0CX25 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX25  Go to UniProtKB:  P0CX25

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L2-A	E	254	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P0CX45 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX45  Go to UniProtKB:  P0CX45

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L4-A	G	362	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P10664 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P10664  Go to UniProtKB:  P10664

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L6-A	I	176	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for Q02326 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02326  Go to UniProtKB:  Q02326

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L7-A	J	244	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P05737 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05737  Go to UniProtKB:  P05737

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L8-A	K	256	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P17076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P17076  Go to UniProtKB:  P17076

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L11-A	M	174	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P0C0W9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0C0W9  Go to UniProtKB:  P0C0W9

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L13-A	N	199	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for Q12690 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12690  Go to UniProtKB:  Q12690

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L14-A	O	138	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P36105 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36105  Go to UniProtKB:  P36105

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L15-A	P	204	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P05748 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05748  Go to UniProtKB:  P05748

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L17-A	R	184	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P05740 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05740  Go to UniProtKB:  P05740

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L18-A	S	186	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P0CX49 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX49  Go to UniProtKB:  P0CX49

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L20-A	U	172	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P0CX23 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX23  Go to UniProtKB:  P0CX23

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L21-A	V	160	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for Q02753 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02753  Go to UniProtKB:  Q02753

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L23-A	X	137	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P0CX41 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX41  Go to UniProtKB:  P0CX41

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L24-A	Y	155	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P04449 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P04449  Go to UniProtKB:  P04449

Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L28	c	149	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P02406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P02406  Go to UniProtKB:  P02406

Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L31-A	f	109	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P0C2H8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0C2H8  Go to UniProtKB:  P0C2H8

Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L32	g	130	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P38061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38061  Go to UniProtKB:  P38061

Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L34-A	i	121	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P87262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P87262  Go to UniProtKB:  P87262

Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L36-A	k	100	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P05745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05745  Go to UniProtKB:  P05745

Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L38	m	78	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P49167 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P49167  Go to UniProtKB:  P49167

Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L39	n	51	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P04650 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P04650  Go to UniProtKB:  P04650

Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L41-A	p	25	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details
ribosomal protein RPL1	r	210	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L10	s	221	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P41805 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P41805  Go to UniProtKB:  P41805

Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details
N-terminal acetyltransferase A complex subunit NAT1	t	854	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P12945 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P12945  Go to UniProtKB:  P12945

Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details
N-alpha-acetyltransferase NAT5	v	176	Saccharomyces cerevisiae	Mutation(s): 0  EC: 2.3.1.258
Find proteins for Q08689 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08689  Go to UniProtKB:  Q08689

Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details
nascent polypeptide chain	z	23	Saccharomyces cerevisiae	Mutation(s): 0

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L5	H	297	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P26321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P26321  Go to UniProtKB:  P26321

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L9-A	L	191	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P05738 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05738  Go to UniProtKB:  P05738

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L16-A	Q	199	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P26784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P26784  Go to UniProtKB:  P26784

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L19-A	T	189	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P0CX82 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX82  Go to UniProtKB:  P0CX82

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L22-A	W	121	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P05749 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05749  Go to UniProtKB:  P05749

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L25	Z	142	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P04456 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P04456  Go to UniProtKB:  P04456

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L26-A	a	127	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P05743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05743  Go to UniProtKB:  P05743

Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L27-A	b	136	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P0C2H6 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0C2H6  Go to UniProtKB:  P0C2H6

Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L29	d	59	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P05747 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05747  Go to UniProtKB:  P05747

Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L30	e	105	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P14120 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P14120  Go to UniProtKB:  P14120

Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L33-A	h	107	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P05744 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05744  Go to UniProtKB:  P05744

Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L35-A	j	120	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P0CX84 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX84  Go to UniProtKB:  P0CX84

Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L37-A	l	88	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P49166 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P49166  Go to UniProtKB:  P49166

Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details
Ubiquitin-60S ribosomal protein L40	o	128	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P0CH08 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CH08  Go to UniProtKB:  P0CH08

Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details
N-terminal acetyltransferase A complex catalytic subunit ARD1	u	238	Saccharomyces cerevisiae	Mutation(s): 0  EC: 2.3.1.255
Find proteins for P07347 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P07347  Go to UniProtKB:  P07347

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L42-A	C	106	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P0CX27 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX27  Go to UniProtKB:  P0CX27

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details
60S ribosomal protein L3	F	387	Saccharomyces cerevisiae	Mutation(s): 0
Find proteins for P14126 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P14126  Go to UniProtKB:  P14126

Entity ID: 1
Molecule	Chains	Length	Organism
Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), miscRNA	1	3396	Saccharomyces cerevisiae

Entity ID: 2
Molecule	Chains	Length	Organism
5S rRNA	3	121	Saccharomyces cerevisiae

Entity ID: 3
Molecule	Chains	Length	Organism
5.8S rRNA	4	158	Saccharomyces cerevisiae

Entity ID: 5
Molecule	Chains	Length	Organism
P-site tRNA	B	77	Saccharomyces cerevisiae

Entity ID: 4
Molecule	Chains	Length	Organism
tRNA	A	76	Saccharomyces cerevisiae

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3HE	1	4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione C15 H23 N O4 YPHMISFOHDHNIV-FSZOTQKASA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-08-17 
• Released Date: 2018-12-19 
Deposition Author(s): Knorr, A.G., Becker, T., Beckmann, R.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	GRK1721
German Research Foundation	Germany	FOR1805

Revision History 

• Version 1.0: 2018-12-19
  Type: Initial release
  
• Version 1.1: 2018-12-26
  Changes: Advisory, Data collection, Database references, Derived calculations
• Version 1.2: 2019-01-16
  Changes: Data collection, Database references