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


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