8BJQ

Structure of a yeast 80S ribosome-bound N-Acetyltransferase B complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 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

The dynamic architecture of Map1- and NatB-ribosome complexes coordinates the sequential modifications of nascent polypeptide chains.

Knorr, A.G.Mackens-Kiani, T.Musial, J.Berninghausen, O.Becker, T.Beatrix, B.Beckmann, R.

(2023) PLoS Biol 21: e3001995-e3001995

  • DOI: https://doi.org/10.1371/journal.pbio.3001995
  • Primary Citation of Related Structures:  
    8BIP, 8BJQ, 8BQD, 8BQX

  • PubMed Abstract: 

    Cotranslational modification of the nascent polypeptide chain is one of the first events during the birth of a new protein. In eukaryotes, methionine aminopeptidases (MetAPs) cleave off the starter methionine, whereas N-acetyl-transferases (NATs) catalyze N-terminal acetylation. MetAPs and NATs compete with other cotranslationally acting chaperones, such as ribosome-associated complex (RAC), protein targeting and translocation factors (SRP and Sec61) for binding sites at the ribosomal tunnel exit. Yet, whereas well-resolved structures for ribosome-bound RAC, SRP and Sec61, are available, structural information on the mode of ribosome interaction of eukaryotic MetAPs or of the five cotranslationally active NATs is only available for NatA. Here, we present cryo-EM structures of yeast Map1 and NatB bound to ribosome-nascent chain complexes. Map1 is mainly associated with the dynamic rRNA expansion segment ES27a, thereby kept at an ideal position below the tunnel exit to act on the emerging substrate nascent chain. For NatB, we observe two copies of the NatB complex. NatB-1 binds directly below the tunnel exit, again involving ES27a, and NatB-2 is located below the second universal adapter site (eL31 and uL22). The binding mode of the two NatB complexes on the ribosome differs but overlaps with that of NatA and Map1, implying that NatB binds exclusively to the tunnel exit. We further observe that ES27a adopts distinct conformations when bound to NatA, NatB, or Map1, together suggesting a contribution to the coordination of a sequential activity of these factors on the emerging nascent chain at the ribosomal exit tunnel.


  • Organizational Affiliation

    Department of Biochemistry, Gene Center, Ludwig-Maximilians University Munich, University of Munich, Munich, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-terminal acetyltransferase B complex catalytic subunit NAT3A,
UA [auth C]
195Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.3.1.254
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
N-terminal acetyltransferase B complex subunit MDM20B,
VA [auth D]
796Saccharomyces cerevisiaeMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L2-AE [auth LA]251Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L3F [auth LB]386Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4-AG [auth LC]361Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L5H [auth LD]294Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6-BI [auth LE]175Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7-AJ [auth LF]222Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L8-AK [auth LG]233Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9-AL [auth LH]191Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L10M [auth LI]218Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11-BN [auth LJ]169Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13-AO [auth LL]193Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14-AP [auth LM]136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L15-AQ [auth LN]203Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L16-AR [auth LO]197Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17-AS [auth LP]183Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18-AT [auth LQ]185Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L19-AU [auth LR]188Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L20-AV [auth LS]171Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21-AW [auth LT]159Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22-AX [auth LU]100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23-AY [auth LV]136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L24-AZ [auth LW]126Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L25AA [auth LX]121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L26-ABA [auth LY]125Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27-ACA [auth LZ]135Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28DA [auth La]148Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29EA [auth Lb]58Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30FA [auth Lc]96Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31-AGA [auth Ld]109Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L32HA [auth Le]127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L33-AIA [auth Lf]106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34-AJA [auth Lg]112Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35-AKA [auth Lh]119Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36-ALA [auth Li]99Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37-AMA [auth Lj]85Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38NA [auth Lk]77Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39OA [auth Ll]50Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L40-APA [auth Lm]52Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41-AQA [auth Ln]25Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L42-ARA [auth Lo]103Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L43-ASA [auth Lp]91Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 3
MoleculeChains LengthOrganismImage
5S rRNAC [auth C4]121Saccharomyces cerevisiae
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Entity ID: 4
MoleculeChains LengthOrganismImage
5.8S rRNAD [auth C3]158Saccharomyces cerevisiae
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Entity ID: 46
MoleculeChains LengthOrganismImage
25S rRNATA [auth 1]3,395Saccharomyces cerevisiae
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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HB [auth Lg],
IB [auth Lj],
JB [auth Lm],
KB [auth Lo],
LB [auth Lp]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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AB [auth LB]
AC [auth 1]
AD [auth 1]
AE [auth 1]
AF [auth 1]
AB [auth LB],
AC [auth 1],
AD [auth 1],
AE [auth 1],
AF [auth 1],
AG [auth 1],
AH [auth 1],
AI [auth 1],
BB [auth LN],
BC [auth 1],
BD [auth 1],
BE [auth 1],
BF [auth 1],
BG [auth 1],
BH [auth 1],
BI [auth 1],
CB [auth LP],
CC [auth 1],
CD [auth 1],
CE [auth 1],
CF [auth 1],
CG [auth 1],
CH [auth 1],
CI [auth 1],
DB [auth LR],
DC [auth 1],
DD [auth 1],
DE [auth 1],
DF [auth 1],
DG [auth 1],
DH [auth 1],
DI [auth 1],
EB [auth LV],
EC [auth 1],
ED [auth 1],
EE [auth 1],
EF [auth 1],
EG [auth 1],
EH [auth 1],
EI [auth 1],
FB [auth La],
FC [auth 1],
FD [auth 1],
FE [auth 1],
FF [auth 1],
FG [auth 1],
FH [auth 1],
FI [auth 1],
GB [auth Le],
GC [auth 1],
GD [auth 1],
GE [auth 1],
GF [auth 1],
GG [auth 1],
GH [auth 1],
GI [auth 1],
HC [auth 1],
HD [auth 1],
HE [auth 1],
HF [auth 1],
HG [auth 1],
HH [auth 1],
HI [auth 1],
IC [auth 1],
ID [auth 1],
IE [auth 1],
IF [auth 1],
IG [auth 1],
IH [auth 1],
II [auth 1],
JC [auth 1],
JD [auth 1],
JE [auth 1],
JF [auth 1],
JG [auth 1],
JH [auth 1],
JI [auth 1],
KC [auth 1],
KD [auth 1],
KE [auth 1],
KF [auth 1],
KG [auth 1],
KH [auth 1],
KI [auth 1],
LC [auth 1],
LD [auth 1],
LE [auth 1],
LF [auth 1],
LG [auth 1],
LH [auth 1],
LI [auth 1],
MB [auth 1],
MC [auth 1],
MD [auth 1],
ME [auth 1],
MF [auth 1],
MG [auth 1],
MH [auth 1],
MI [auth 1],
NB [auth 1],
NC [auth 1],
ND [auth 1],
NE [auth 1],
NF [auth 1],
NG [auth 1],
NH [auth 1],
NI [auth 1],
OB [auth 1],
OC [auth 1],
OD [auth 1],
OE [auth 1],
OF [auth 1],
OG [auth 1],
OH [auth 1],
OI [auth 1],
PB [auth 1],
PC [auth 1],
PD [auth 1],
PE [auth 1],
PF [auth 1],
PG [auth 1],
PH [auth 1],
PI [auth 1],
QB [auth 1],
QC [auth 1],
QD [auth 1],
QE [auth 1],
QF [auth 1],
QG [auth 1],
QH [auth 1],
QI [auth 1],
RB [auth 1],
RC [auth 1],
RD [auth 1],
RE [auth 1],
RF [auth 1],
RG [auth 1],
RH [auth 1],
RI [auth 1],
SB [auth 1],
SC [auth 1],
SD [auth 1],
SE [auth 1],
SF [auth 1],
SG [auth 1],
SH [auth 1],
SI [auth 1],
TB [auth 1],
TC [auth 1],
TD [auth 1],
TE [auth 1],
TF [auth 1],
TG [auth 1],
TH [auth 1],
TI [auth 1],
UB [auth 1],
UC [auth 1],
UD [auth 1],
UE [auth 1],
UF [auth 1],
UG [auth 1],
UH [auth 1],
UI [auth 1],
VB [auth 1],
VC [auth 1],
VD [auth 1],
VE [auth 1],
VF [auth 1],
VG [auth 1],
VH [auth 1],
VI [auth 1],
WA [auth C4],
WB [auth 1],
WC [auth 1],
WD [auth 1],
WE [auth 1],
WF [auth 1],
WG [auth 1],
WH [auth 1],
WI [auth 1],
XA [auth C3],
XB [auth 1],
XC [auth 1],
XD [auth 1],
XE [auth 1],
XF [auth 1],
XG [auth 1],
XH [auth 1],
XI [auth 1],
YA [auth LA],
YB [auth 1],
YC [auth 1],
YD [auth 1],
YE [auth 1],
YF [auth 1],
YG [auth 1],
YH [auth 1],
YI [auth 1],
ZA [auth LA],
ZB [auth 1],
ZC [auth 1],
ZD [auth 1],
ZE [auth 1],
ZF [auth 1],
ZG [auth 1],
ZH [auth 1]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-08
    Type: Initial release
  • Version 1.1: 2023-05-03
    Changes: Database references
  • Version 1.2: 2024-07-24
    Changes: Data collection