6HD7

Cryo-EM structure of the ribosome-NatA complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1038/s41594-018-0165-y
  • Primary Citation of Related Structures:  

  • 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 concer ...

    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.


    Organizational Affiliation

    Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany. becker@genzentrum.lmu.de.,Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan.,Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany. beckmann@genzentrum.lmu.de.,Laboratory of Drug Design and Medicinal Chemistry, Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo 194-8543, Japan. Electronic address: titoh@ac.shoyaku.ac.jp.,Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany. beatrix@genzentrum.lmu.de.,Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L42-A
C
106Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL42A (RPL41A, SCL41A)
Find proteins for P0CX27 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX27
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L43-A
D
92Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL43A
Find proteins for P0CX25 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX25
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L2-A
E
254Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL2A (RPL5B)
Find proteins for P0CX45 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX45
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L3
F
387Saccharomyces 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: 10
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4-A
G
362Saccharomyces 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: 11
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5
H
297Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL5 (RPL1, RPL1A)
Find proteins for P26321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL5
Go to UniProtKB:  P26321
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6-A
I
176Saccharomyces 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: 13
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7-A
J
244Saccharomyces 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: 14
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L8-A
K
256Saccharomyces 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: 15
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L9-A
L
191Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL9A (RPL8A, RPL9)
Find proteins for P05738 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05738
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L11-A
M
174Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL11A (RP39A, RPL16A)
Find proteins for P0C0W9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0C0W9
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13-A
N
199Saccharomyces 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: 18
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L14-A
O
138Saccharomyces 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: 19
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L15-A
P
204Saccharomyces 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: 20
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L16-A
Q
199Saccharomyces 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: 21
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17-A
R
184Saccharomyces 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: 22
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18-A
S
186Saccharomyces 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: 23
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L19-A
T
189Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL19A (RPL23A, YL14A)
Find proteins for P0CX82 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX82
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L20-A
U
172Saccharomyces 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: 25
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L21-A
V
160Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL21A (URP1)
Find proteins for Q02753 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q02753
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L22-A
W
121Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL22A
Find proteins for P05749 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05749
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23-A
X
137Saccharomyces 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: 28
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L24-A
Y
155Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL24A (RP29, RPL30A)
Find proteins for P04449 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P04449
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L25
Z
142Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL25
Find proteins for P04456 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P04456
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26-A
a
127Saccharomyces 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: 31
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27-A
b
136Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL27A (RPL27)
Find proteins for P0C2H6 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL27A
Go to UniProtKB:  P0C2H6
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L28
c
149Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL28 (CYH2)
Find proteins for P02406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL28
Go to UniProtKB:  P02406
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L29
d
59Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL29 (YL43)
Find proteins for P05747 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL29
Go to UniProtKB:  P05747
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L30
e
105Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL30 (RPL32)
Find proteins for P14120 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL30
Go to UniProtKB:  P14120
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L31-A
f
109Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL31A (RPL34, RPL34A)
Find proteins for P0C2H8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0C2H8
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32
g
130Saccharomyces 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: 37
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L33-A
h
107Saccharomyces 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: 38
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L34-A
i
121Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL34A
Find proteins for P87262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P87262
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35-A
j
120Saccharomyces 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: 40
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36-A
k
100Saccharomyces 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: 41
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37-A
l
88Saccharomyces 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: 42
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L38
m
78Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL38
Find proteins for P49167 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL38
Go to UniProtKB:  P49167
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L39
n
51Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL39 (RPL46, SPB2)
Find proteins for P04650 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL39
Go to UniProtKB:  P04650
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-60S ribosomal protein L40
o
128Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL40A (UBI1)
Find proteins for P0CH08 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CH08
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L41-A
p
25N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
ribosomal protein RPL1
r
210N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L10
s
221Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL10 (GRC5, QSR1)
Find proteins for P41805 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL10
Go to UniProtKB:  P41805
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
N-terminal acetyltransferase A complex subunit NAT1
t
854Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: NAT1 (AAA1)
Find proteins for P12945 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: NAT1
Go to UniProtKB:  P12945
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
N-terminal acetyltransferase A complex catalytic subunit ARD1
u
238Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ARD1
EC: 2.3.1.255
Find proteins for P07347 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P07347
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
N-alpha-acetyltransferase NAT5
v
176Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: NAT5
EC: 2.3.1.258
Find proteins for Q08689 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q08689
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
nascent polypeptide chain
z
23N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 1
MoleculeChainsLengthOrganism
Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), miscRNA13396Saccharomyces cerevisiae
Entity ID: 2
MoleculeChainsLengthOrganism
5S rRNA3121Saccharomyces cerevisiae
Entity ID: 3
MoleculeChainsLengthOrganism
5.8S rRNA4158Saccharomyces cerevisiae
Entity ID: 4
MoleculeChainsLengthOrganism
tRNAA76Saccharomyces cerevisiae
Entity ID: 5
MoleculeChainsLengthOrganism
P-site tRNAB77Saccharomyces cerevisiae
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3HE
Query on 3HE

Download SDF File 
Download CCD File 
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
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
r, z
L-PEPTIDE LINKINGC4 H9 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyGRK1721
German Research FoundationGermanyFOR1805

Revision History 

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