[English] 日本語
Yorodumi
- EMDB-0201: Cryo-EM structure of the ribosome-NatA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0201
TitleCryo-EM structure of the ribosome-NatA complex
Map dataRibosome-NatA complex refined on NatA. Postprocessed map was low pass filtered to 6 Angstrom.
Sample
  • Complex: Ribosome-NatA complex
    • Protein or peptide: N-terminal acetyltransferase A complex subunit NAT1
    • Protein or peptide: N-terminal acetyltransferase A complex catalytic subunit ARD1
    • Protein or peptide: N-alpha-acetyltransferase NAT5
KeywordsN-terminal acetylation / protein modification / ribosome / expansion segments / TRANSLATION
Function / homology
Function and homology information


peptide-glutamate-alpha-N-acetyltransferase activity / N-terminal methionine Nalpha-acetyltransferase NatE / N-terminal amino-acid Nalpha-acetyltransferase NatA / peptide-serine-alpha-N-acetyltransferase activity / NatA complex / peptide alpha-N-acetyltransferase activity / mitotic sister chromatid cohesion / ribosome binding / mitochondrion / identical protein binding / cytoplasm
Similarity search - Function
N-terminal acetyltransferase A, auxiliary subunit / N-terminal acetyltransferase A, auxiliary subunit / : / N-acetyltransferase Ard1-like / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
N-terminal acetyltransferase A complex catalytic subunit ARD1 / N-terminal acetyltransferase A complex subunit NAT1 / N-alpha-acetyltransferase NAT5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsKnorr AG / Becker T / Berninghausen O / Beckmann R
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research FoundationGRK1721 Germany
German Research FoundationFOR1805 Germany
CitationJournal: Nat Struct Mol Biol / Year: 2019
Title: Ribosome-NatA architecture reveals that rRNA expansion segments coordinate N-terminal acetylation.
Authors: Alexandra G Knorr / Christian Schmidt / Petr Tesina / Otto Berninghausen / Thomas Becker / Birgitta Beatrix / Roland Beckmann /
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. ...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.
History
DepositionAug 17, 2018-
Header (metadata) releaseOct 24, 2018-
Map releaseDec 19, 2018-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0331
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0331
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6hd5
  • Surface level: 0.0331
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6hd5
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0201.png

Downloads & links

-
Map

FileDownload / File: emd_0201.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRibosome-NatA complex refined on NatA. Postprocessed map was low pass filtered to 6 Angstrom.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 420 pix.
= 455.28 Å		1.08 Å/pix.
x 420 pix.
= 455.28 Å		1.08 Å/pix.
x 420 pix.
= 455.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.084 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0331 / Movie #1: 0.0331
Minimum - Maximum-0.14963268 - 0.27869624
Average (Standard dev.)0.00051754306 (±0.010154534)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 455.28 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0841.0841.084
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z455.280455.280455.280
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS420420420
D min/max/mean-0.1500.2790.001

-
Supplemental data

-
Sample components

-
Entire : Ribosome-NatA complex

EntireName: Ribosome-NatA complex
Components
  • Complex: Ribosome-NatA complex
    • Protein or peptide: N-terminal acetyltransferase A complex subunit NAT1
    • Protein or peptide: N-terminal acetyltransferase A complex catalytic subunit ARD1
    • Protein or peptide: N-alpha-acetyltransferase NAT5

-
Supramolecule #1: Ribosome-NatA complex

SupramoleculeName: Ribosome-NatA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Map was refined on NatA. Coordinates are deposited for NatA only.
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)

-
Macromolecule #1: N-terminal acetyltransferase A complex subunit NAT1

MacromoleculeName: N-terminal acetyltransferase A complex subunit NAT1 / type: protein_or_peptide / ID: 1 / Details: ribosome binding subunit / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 99.050133 KDa
SequenceString: MSRKRSTKPK PAAKIALKKE NDQFLEALKL YEGKQYKKSL KLLDAILKKD GSHVDSLALK GLDLYSVGEK DDAASYVANA IRKIEGASA SPICCHVLGI YMRNTKEYKE SIKWFTAALN NGSTNKQIYR DLATLQSQIG DFKNALVSRK KYWEAFLGYR A NWTSLAVA ...String:
MSRKRSTKPK PAAKIALKKE NDQFLEALKL YEGKQYKKSL KLLDAILKKD GSHVDSLALK GLDLYSVGEK DDAASYVANA IRKIEGASA SPICCHVLGI YMRNTKEYKE SIKWFTAALN NGSTNKQIYR DLATLQSQIG DFKNALVSRK KYWEAFLGYR A NWTSLAVA QDVNGERQQA INTLSQFEKL AEGKISDSEK YEHSECLMYK NDIMYKAASD NQDKLQNVLK HLNDIEPCVF DK FGLLERK ATIYMKLGQL KDASIVYRTL IKRNPDNFKY YKLLEVSLGI QGDNKLKKAL YGKLEQFYPR CEPPKFIPLT FLQ DKEELS KKLREYVLPQ LERGVPATFS NVKPLYQRRK SKVSPLLEKI VLDYLSGLDP TQDPIPFIWT NYYLSQHFLF LKDF PKAQE YIDAALDHTP TLVEFYILKA RILKHLGLMD TAAGILEEGR QLDLQDRFIN CKTVKYFLRA NNIDKAVEVA SLFTK NDDS VNGIKDLHLV EASWFIVEQA EAYYRLYLDR KKKLDDLASL KKEVESDKSE QIANDIKENQ WLVRKYKGLA LKRFNA IPK FYKQFEDDQL DFHSYCMRKG TPRAYLEMLE WGKALYTKPM YVRAMKEASK LYFQMHDDRL KRKSDSLDEN SDEIQNN GQ NSSSQKKKAK KEAAAMNKRK ETEAKSVAAY PSDQDNDVFG EKLIETSTPM EDFATEFYNN YSMQVREDER DYILDFEF N YRIGKLALCF ASLNKFAKRF GTTSGLFGSM AIVLLHATRN DTPFDPILKK VVTKSLEKEY SENFPLNEIS NNSFDWLNF YQEKFGKNDI NGLLFLYRYR DDVPIGSSNL KEMIISSLSP LEPHSQNEIL QYYL

UniProtKB: N-terminal acetyltransferase A complex subunit NAT1

-
Macromolecule #2: N-terminal acetyltransferase A complex catalytic subunit ARD1

MacromoleculeName: N-terminal acetyltransferase A complex catalytic subunit ARD1
type: protein_or_peptide / ID: 2 / Details: catalytic subunit / Number of copies: 1 / Enantiomer: LEVO
EC number: N-terminal amino-acid Nalpha-acetyltransferase NatA
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 27.635168 KDa
SequenceString: MPINIRRATI NDIICMQNAN LHNLPENYMM KYYMYHILSW PEASFVATTT TLDCEDSDEQ DENDKLELTL DGTNDGRTIK LDPTYLAPG EKLVGYVLVK MNDDPDQQNE PPNGHITSLS VMRTYRRMGI AENLMRQALF ALREVHQAEY VSLHVRQSNR A ALHLYRDT ...String:
MPINIRRATI NDIICMQNAN LHNLPENYMM KYYMYHILSW PEASFVATTT TLDCEDSDEQ DENDKLELTL DGTNDGRTIK LDPTYLAPG EKLVGYVLVK MNDDPDQQNE PPNGHITSLS VMRTYRRMGI AENLMRQALF ALREVHQAEY VSLHVRQSNR A ALHLYRDT LAFEVLSIEK SYYQDGEDAY AMKKVLKLEE LQISNFTHRR LKENEEKLED DLESDLLEDI IKQGVNDIIV

UniProtKB: N-terminal acetyltransferase A complex catalytic subunit ARD1

-
Macromolecule #3: N-alpha-acetyltransferase NAT5

MacromoleculeName: N-alpha-acetyltransferase NAT5 / type: protein_or_peptide / ID: 3 / Details: ribosome binding subunit / Number of copies: 1 / Enantiomer: LEVO
EC number: N-terminal methionine Nalpha-acetyltransferase NatE
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Molecular weightTheoretical: 19.753727 KDa
SequenceString:
MGRDICTLDN VYANNLGMLT KLAHVTVPNL YQDAFFSALF AEDSLVAKNK KPSSKKDVHF TQMAYYSEIP VGGLVAKLVP KKQNELSLK GIQIEFLGVL PNYRHKSIGS KLLKFAEDKC SECHQHNVFV YLPAVDDLTK QWFIAHGFEQ VGETVNNFIK G VNGDEQDA ILLKKHIS

UniProtKB: N-alpha-acetyltransferase NAT5

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 2.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 262507
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION

-
Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-6hd5:
Cryo-EM structure of the ribosome-NatA complex

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more