[English] 日本語
Yorodumi
- EMDB-9753: Cryo-EM density map of peptide deformylase and methionine aminope... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-9753
TitleCryo-EM density map of peptide deformylase and methionine aminopeptidase bound to the E. coli 70S ribosome
Map dataE.coli Peptide deformylsae and Methionine aminopeptidase bound to E.coli 70S ribosome at the polypeptide exit tunnel.
Sample
  • Complex: E. coli 70S ribosome in complex with peptide deformylase and methionine aminopeptidase
    • Protein or peptide: Peptide deformylase
    • Protein or peptide: Methionine aminopeptidaseMethionyl aminopeptidase
KeywordsE. coli 70S ribosome / Protein biogenesis / Peptide deformylase / Methionine aminopeptidase / Polypeptide exit tunnel / RIBOSOME
Function / homology
Function and homology information


co-translational protein modification / initiator methionyl aminopeptidase activity / peptide deformylase / peptide deformylase activity / methionyl aminopeptidase / metalloaminopeptidase activity / ferrous iron binding / ribosome binding / hydrolase activity / translation ...co-translational protein modification / initiator methionyl aminopeptidase activity / peptide deformylase / peptide deformylase activity / methionyl aminopeptidase / metalloaminopeptidase activity / ferrous iron binding / ribosome binding / hydrolase activity / translation / proteolysis / zinc ion binding / cytosol
Similarity search - Function
Methionine aminopeptidase subfamily 1 signature. / Peptidase M24A, methionine aminopeptidase, subfamily 1 / Peptide deformylase / Peptide deformylase superfamily / Polypeptide deformylase / Peptidase M24, methionine aminopeptidase / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like
Similarity search - Domain/homology
Peptide deformylase / Methionine aminopeptidase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 11.8 Å
AuthorsSengupta J / Bhakta S
Funding support India, 2 items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research India
Department of Science & Technology (India)SB/SO/BB-0025/2014 India
CitationJournal: J Mol Biol / Year: 2019
Title: Cryo-EM Structures Reveal Relocalization of MetAP in the Presence of Other Protein Biogenesis Factors at the Ribosomal Tunnel Exit.
Authors: Sayan Bhakta / Shirin Akbar / Jayati Sengupta /
Abstract: During protein biosynthesis in bacteria, one of the earliest events that a nascent polypeptide chain goes through is the co-translational enzymatic processing. The event includes two enzymatic ...During protein biosynthesis in bacteria, one of the earliest events that a nascent polypeptide chain goes through is the co-translational enzymatic processing. The event includes two enzymatic pathways: deformylation of the N-terminal methionine by the enzyme peptide deformylase (PDF), followed by methionine excision catalyzed by methionine aminopeptidase (MetAP). During the enzymatic processing, the emerging nascent protein likely remains shielded by the ribosome-associated chaperone trigger factor. The ribosome tunnel exit serves as a stage for recruiting proteins involved in maturation processes of the nascent chain. Co-translational processing of nascent chains is a critical step for subsequent folding and functioning of mature proteins. Here, we present cryo-electron microscopy structures of Escherichia coli (E. coli) ribosome in complex with the nascent chain processing proteins. The structures reveal overlapping binding sites for PDF and MetAP when they bind individually at the tunnel exit site, where L22-L32 protein region provides primary anchoring sites for both proteins. In the absence of PDF, trigger factor can access ribosomal tunnel exit when MetAP occupies its primary binding site. Interestingly, however, in the presence of PDF, when MetAP's primary binding site is already engaged, MetAP has a remarkable ability to occupy an alternative binding site adjacent to PDF. Our study, thus, discloses an unexpected mechanism that MetAP adopts for context-specific ribosome association.
History
DepositionDec 19, 2018-
Header (metadata) releaseApr 17, 2019-
Map releaseApr 17, 2019-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6izi
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6izi
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9753.png

Downloads & links

-
Map

FileDownload / File: emd_9753.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationE.coli Peptide deformylsae and Methionine aminopeptidase bound to E.coli 70S ribosome at the polypeptide exit tunnel.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.89 Å/pix.
x 220 pix.
= 415.8 Å		1.89 Å/pix.
x 220 pix.
= 415.8 Å		1.89 Å/pix.
x 220 pix.
= 415.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.89 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-16.639932999999999 - 25.309258
Average (Standard dev.)0.1254344 (±2.1281757)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 415.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.891.891.89
M x/y/z220220220
origin x/y/z0.0000.0000.000
length x/y/z415.800415.800415.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS220220220
D min/max/mean-16.64025.3090.125

-
Supplemental data

-
Sample components

-
Entire : E. coli 70S ribosome in complex with peptide deformylase and meth...

EntireName: E. coli 70S ribosome in complex with peptide deformylase and methionine aminopeptidase
Components
  • Complex: E. coli 70S ribosome in complex with peptide deformylase and methionine aminopeptidase
    • Protein or peptide: Peptide deformylase
    • Protein or peptide: Methionine aminopeptidaseMethionyl aminopeptidase

-
Supramolecule #1: E. coli 70S ribosome in complex with peptide deformylase and meth...

SupramoleculeName: E. coli 70S ribosome in complex with peptide deformylase and methionine aminopeptidase
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli K-12 (bacteria)

-
Macromolecule #1: Peptide deformylase

MacromoleculeName: Peptide deformylase / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: peptide deformylase
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K-12
Molecular weightTheoretical: 19.357447 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSVLQVLHIP DERLRKVAKP VEEVNAEIQR IVDDMFETMY AEEGIGLAAT QVDIHQRIIV IDVSENRDER LVLINPELLE KSGETGIEE GCLSIPEQRA LVPRAEKVKI RALDRDGKPF ELEADGLLAI CIQHEMDHLV GKLFMDYLSP LKQQRIRQKV E KLDRLKAR A

UniProtKB: Peptide deformylase

-
Macromolecule #2: Methionine aminopeptidase

MacromoleculeName: Methionine aminopeptidase / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: methionyl aminopeptidase
Source (natural)Organism: Escherichia coli K-12 (bacteria) / Strain: K-12
Molecular weightTheoretical: 29.341775 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAISIKTPED IEKMRVAGRL AAEVLEMIEP YVKPGVSTGE LDRICNDYIV NEQHAVSACL GYHGYPKSVC ISINEVVCHG IPDDAKLLK DGDIVNIDVT VIKDGFHGDT SKMFIVGKPT IMGERLCRIT QESLYLALRM VKPGINLREI GAAIQKFVEA E GFSVVREY ...String:
MAISIKTPED IEKMRVAGRL AAEVLEMIEP YVKPGVSTGE LDRICNDYIV NEQHAVSACL GYHGYPKSVC ISINEVVCHG IPDDAKLLK DGDIVNIDVT VIKDGFHGDT SKMFIVGKPT IMGERLCRIT QESLYLALRM VKPGINLREI GAAIQKFVEA E GFSVVREY CGHGIGQGFH EEPQVLHYDS RETNVVLKPG MTFTIEPMVN AGKKEIRTMK DGWTVKTKDR SLSAQYEHTI VV TDNGCEI LTLRKDDTIP AIISHDE

UniProtKB: Methionine aminopeptidase

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI EAGLE (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 10.0 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 11.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPIDER / Number images used: 35000
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

1bs7

chain_id: A, source_name: PDB, initial_model_type: experimental model

1c21

chain_id: A, source_name: PDB, initial_model_type: experimental model
Output model

PDB-6izi:
Crystal structure of E. coli peptide deformylase and methionine aminopeptidase fitted into the cryo-EM density map of the 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