[English] 日本語
Yorodumi
- EMDB-5651: Cryo-EM structure pentaketide-ACP4-PikAIII/C209A/delta ACP5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-5651
TitleCryo-EM structure pentaketide-ACP4-PikAIII/C209A/delta ACP5
Map dataReconstruction of the 5th module from the pikromycin biosynthetic pathway (PikAIII) lacking the ACP domain with an N-terminal fusion to the ACP domain from module 4 of the pikromycin pathway (ACP4). The ACP4 domain was loaded with the pentaketide intermediate.
Sample
  • Sample: pentaketide-ACP4-PikAIII/C209A/delta ACP5
  • Protein or peptide: PikAIII
  • Ligand: pentaketide
KeywordsType I polyketide synthase module
Function / homology
Function and homology information


10-deoxymethynolide synthase / narbonolide synthase / macrolide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / identical protein binding
Similarity search - Function
Polyketide synthase, docking domain superfmaily / Polyketide synthase, docking domain / Erythronolide synthase docking domain / PKS_PP_betabranch / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / : ...Polyketide synthase, docking domain superfmaily / Polyketide synthase, docking domain / Erythronolide synthase docking domain / PKS_PP_betabranch / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / Polyketide synthase, ketoreductase domain / KR domain / Malonyl-CoA ACP transacylase, ACP-binding / : / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase domain superfamily / Acyl transferase/acyl hydrolase/lysophospholipase / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / PKS_KR / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Pikromycin polyketide synthase component PikAIII
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria) / unidentified (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.6 Å
AuthorsDutta S / Whicher JR / Hansen DA / Hale WA / Chemler JA / Narayan AR / Hakansson K / Sherman DH / Smith JL / Skiniotis G
CitationJournal: Nature / Year: 2014
Title: Structure of a modular polyketide synthase.
Authors: Somnath Dutta / Jonathan R Whicher / Douglas A Hansen / Wendi A Hale / Joseph A Chemler / Grady R Congdon / Alison R H Narayan / Kristina Håkansson / David H Sherman / Janet L Smith / Georgios Skiniotis /
Abstract: Polyketide natural products constitute a broad class of compounds with diverse structural features and biological activities. Their biosynthetic machinery, represented by type I polyketide synthases ...Polyketide natural products constitute a broad class of compounds with diverse structural features and biological activities. Their biosynthetic machinery, represented by type I polyketide synthases (PKSs), has an architecture in which successive modules catalyse two-carbon linear extensions and keto-group processing reactions on intermediates covalently tethered to carrier domains. Here we used electron cryo-microscopy to determine sub-nanometre-resolution three-dimensional reconstructions of a full-length PKS module from the bacterium Streptomyces venezuelae that revealed an unexpectedly different architecture compared to the homologous dimeric mammalian fatty acid synthase. A single reaction chamber provides access to all catalytic sites for the intramodule carrier domain. In contrast, the carrier from the preceding module uses a separate entrance outside the reaction chamber to deliver the upstream polyketide intermediate for subsequent extension and modification. This study reveals for the first time, to our knowledge, the structural basis for both intramodule and intermodule substrate transfer in polyketide synthases, and establishes a new model for molecular dissection of these multifunctional enzyme systems.
History
DepositionMay 1, 2013-
Header (metadata) releaseJul 3, 2013-
Map releaseJun 25, 2014-
UpdateOct 22, 2014-
Current statusOct 22, 2014Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 7.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 7.4
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_5651.gif

Downloads & links

-
Map

FileDownload / File: emd_5651.map.gz / Format: CCP4 / Size: 26.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the 5th module from the pikromycin biosynthetic pathway (PikAIII) lacking the ACP domain with an N-terminal fusion to the ACP domain from module 4 of the pikromycin pathway (ACP4). The ACP4 domain was loaded with the pentaketide intermediate.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.24 Å/pix.
x 192 pix.
= 430.08 Å		2.24 Å/pix.
x 192 pix.
= 430.08 Å		2.24 Å/pix.
x 192 pix.
= 430.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.24 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.4 / Movie #1: 7.4
Minimum - Maximum-25.489131929999999 - 42.894367219999999
Average (Standard dev.)0.0 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-16-16-16
Dimensions192192192
Spacing192192192
CellA=B=C: 430.08002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.242.242.24
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z430.080430.080430.080
α/β/γ90.00090.00090.000
start NX/NY/NZ-132-122-147
NX/NY/NZ250274261
MAP C/R/S123
start NC/NR/NS-16-16-16
NC/NR/NS192192192
D min/max/mean-25.48942.894-0.000

-
Supplemental data

-
Sample components

-
Entire : pentaketide-ACP4-PikAIII/C209A/delta ACP5

EntireName: pentaketide-ACP4-PikAIII/C209A/delta ACP5
Components
  • Sample: pentaketide-ACP4-PikAIII/C209A/delta ACP5
  • Protein or peptide: PikAIII
  • Ligand: pentaketide

-
Supramolecule #1000: pentaketide-ACP4-PikAIII/C209A/delta ACP5

SupramoleculeName: pentaketide-ACP4-PikAIII/C209A/delta ACP5 / type: sample / ID: 1000
Details: Sample was not frozen prior to loading on the grid. The sample was monodisperse.
Oligomeric state: Dimer / Number unique components: 2
Molecular weightExperimental: 348 KDa / Theoretical: 348 KDa / Method: Gel filtration chromatography.

-
Macromolecule #1: PikAIII

MacromoleculeName: PikAIII / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: Yes
Source (natural)Organism: Streptomyces venezuelae (bacteria)
Molecular weightExperimental: 348 KDa / Theoretical: 348 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET28b
SequenceUniProtKB: Pikromycin polyketide synthase component PikAIII

-
Macromolecule #2: pentaketide

MacromoleculeName: pentaketide / type: ligand / ID: 2 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: unidentified (others)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.4 / Details: 50 mM HEPES, 100mM NaCl
GridDetails: Glow-discharged Quantifoil R2/200 mesh grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 89 K / Instrument: FEI VITROBOT MARK IV
Method: Blot for 1.5-2.0 seconds before plunging (3 microliter sample).

-
Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureMin: 89 K / Max: 89 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 135,000 times magnification
DateMar 3, 2012
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 365 / Average electron dose: 22 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 66964 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Oxford holder / Specimen holder model: OTHER
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

DetailsThe particles were selected manually.
CTF correctionDetails: Each micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.6 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN1, EMAN2 / Number images used: 43946

-
Atomic model buiding 1

Initial modelPDB ID:

2hg4


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B
SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT

-
Atomic model buiding 2

Initial modelPDB ID:

2ju1

SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT

-
Atomic model buiding 3

Initial modelPDB ID:

2fr0

SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT

+
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