[English] 日本語
Yorodumi
- EMDB-14793: Ketosynthase domain of module 4 from Brevibacillus Brevis orphan BGC11 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-14793
TitleKetosynthase domain of module 4 from Brevibacillus Brevis orphan BGC11
Map data
Sample
  • Complex: Ketosynthase domain 4 of Brevibacillus Brevis BGC 11
    • Protein or peptide: Putative polyketide synthase
Function / homology
Function and homology information


phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function
: / Methyltransferase type 12 / Methyltransferase domain / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily ...: / Methyltransferase type 12 / Methyltransferase domain / : / Polyketide synthase dehydratase domain / PKS_PP_betabranch / Polyketide synthase dehydratase N-terminal domain / PKS_DH / Polyketide synthase, dehydratase domain / Polyketide synthase, dehydratase domain superfamily / Polyketide synthase, ketoreductase domain / KR domain / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / PKS_KR / Ketosynthase family 3 (KS3) domain profile. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Thiolase-like / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / NAD(P)-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Putative polyketide synthase
Similarity search - Component
Biological speciesBrevibacillus brevis NBRC 100599 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsTittes YU / Herbst DA / Jakob RP / Maier T
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation179323, 159696, 177084 Switzerland
CitationJournal: Sci Adv / Year: 2022
Title: The structure of a polyketide synthase bimodule core.
Authors: Yves U Tittes / Dominik A Herbst / Solène F X Martin / Hugo Munoz-Hernandez / Roman P Jakob / Timm Maier /
Abstract: Polyketide synthases (PKSs) are predominantly microbial biosynthetic enzymes. They assemble highly potent bioactive natural products from simple carboxylic acid precursors. The most versatile ...Polyketide synthases (PKSs) are predominantly microbial biosynthetic enzymes. They assemble highly potent bioactive natural products from simple carboxylic acid precursors. The most versatile families of PKSs are organized as assembly lines of functional modules. Each module performs one round of precursor extension and optional modification, followed by directed transfer of the intermediate to the next module. While enzymatic domains and even modules of PKSs are well understood, the higher-order modular architecture of PKS assembly lines remains elusive. Here, we visualize a PKS bimodule core using cryo-electron microscopy and resolve a two-dimensional meshwork of the bimodule core formed by homotypic interactions between modules. The sheet-like organization provides the framework for efficient substrate transfer and for sequestration of trans-acting enzymes required for polyketide production.
History
DepositionApr 19, 2022-
Header (metadata) releaseSep 21, 2022-
Map releaseSep 21, 2022-
UpdateApr 5, 2023-
Current statusApr 5, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_14793.png

Downloads & links

-
Map

FileDownload / File: emd_14793.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 320 pix.
= 338.56 Å		1.06 Å/pix.
x 320 pix.
= 338.56 Å		1.06 Å/pix.
x 320 pix.
= 338.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.058 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-1.8913459 - 2.839848
Average (Standard dev.)-1.7320512e-05 (±0.04658154)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 338.56 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_14793_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_14793_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_14793_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Ketosynthase domain 4 of Brevibacillus Brevis BGC 11

EntireName: Ketosynthase domain 4 of Brevibacillus Brevis BGC 11
Components
  • Complex: Ketosynthase domain 4 of Brevibacillus Brevis BGC 11
    • Protein or peptide: Putative polyketide synthase

-
Supramolecule #1: Ketosynthase domain 4 of Brevibacillus Brevis BGC 11

SupramoleculeName: Ketosynthase domain 4 of Brevibacillus Brevis BGC 11 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Brevibacillus brevis NBRC 100599 (bacteria)
Molecular weightTheoretical: 160 KDa

-
Macromolecule #1: Putative polyketide synthase

MacromoleculeName: Putative polyketide synthase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Brevibacillus brevis NBRC 100599 (bacteria) / Strain: 47 / JCM 6285 / NBRC 100599
Molecular weightTheoretical: 187.424781 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GSPSSVVRDV AIIGLSGRYP QAKNVDEFWN RLKEGKNCIS EIPKDRWDWQ SFFDEEKGKK ESMYTKWGGF IDDMDKFDPL FFQISPKEA EEMDPQERLF LQEAYASIED AGYTPTTLCE SRKVGVFVGV MNGNYPTGAT YWSIANRLSY LLNFQGPSVA V DTACSASL ...String:
GSPSSVVRDV AIIGLSGRYP QAKNVDEFWN RLKEGKNCIS EIPKDRWDWQ SFFDEEKGKK ESMYTKWGGF IDDMDKFDPL FFQISPKEA EEMDPQERLF LQEAYASIED AGYTPTTLCE SRKVGVFVGV MNGNYPTGAT YWSIANRLSY LLNFQGPSVA V DTACSASL TAIHFALESL YSGTSECAIA GGVNLIVDPV HYMKLSALTM LSPSNQCKSF GDQADGFVDG EGVGAIVLKP LD KAIADGD HIYGVIKGSM MNAGGKTNGY TVPNPQAQAQ LVADALQRAN VHARTVSYLE AHGTGTELGD PIEVAGLTRA FEK DTQDKQ FCALGSAKSN IGHCESAAGI AGVTKILLQL KHAQLVPSLH SRTLNPNIDF TKTPFVVQQE LAEWRRPIVE INGT TNEYP RIAGISSFGA GGSNAHVIIE EYIPEEQKQS SLKITPQNPA IFVLSAKNAE RLYEIVQQLL AFIQEHSLSD EHLAD MAYT LQVGRVAMEE RIAVIAGTMK ELQQKLTAYV KGQEHIADLY RGQVNRNQEM LDILTSDDEL EETIARWMER GKYSKL LDL WVKGLSIDWN KLYQEEQPGR ISLPTYPFAK ESYWTHARSV SSSTGVGVIH PFLHQNTSDF MEQRFSSMFT GQEFFLS DH VIKGQRVLPS AAYLEMARAA IQQATGGLDS ERELEGLRFK NVVWTQPLAV GPEPVQAHIE LYPEANGEIV FEIYSDSK Q DRDQTTEIVH SQGSAVLCSI PDIPSFDLSV LQEQCSLRTL SAEQCYDAFK KMGVDYGPAH RGIEQILIGQ EQVLAKLSL PSSVVKTQGQ FGLHPSLLDA ALQSSLGLMM ATSDFSLILP FALEEMVIVG DCSSSMWALI RYREGSKAGD RVEKFDIDLC DENGNVQVR MKGFSTRKIA NVSVRSEVEV PKASVPLEEE KAIDSSSLME QATPYFKKLL SSVIKLPANK MEADASLEKY G VDSIVAMQ MTKELEKQFG SLPKTLFFEY QTIKELTGYF LENYRENLMH ILGMRENAEA SLTQESEATM VDEVKAQTER RS KKRKSQR FASLRMETQP PKGALDIAII GISGRYPQAR NIHDFWKNLR DGKDCITEIP KDRWDHSLYF DEAKDKLGKS YSK WGGFID GVDQFDPLFF HISPREAELM DPQERLFLQC VYETIEDAGY TRETLGKHEG LGGNVGVYVG VMYEEYQLYA SAEQ ALGRA LAIAGSPASI ANRVSYFCNF HGPSMAVDTM CSSSLTGIHL ACHSLQRGEC EVAIAGGVNV SIHPNKYLYL SQGKF ASSK GRCESFGEGG DGYVPGEGVG AVLLKPLARA IADGDHIYGV IKGSAINHGG KTNGYTVPNP HSQSRVIRRA FEEAGI HPR TVSYIEAHGT GTSLGDPIEI AGLTKTFQEY TKENQFCAIG SAKSNIGHGE SAAGIAGLTK ILLQMKYKRL VPSLHSR TL NPNIDFSKTP FVVQQELAEW KRPVIEIDGV TREYARIAGI SSFGAGGANA HLVIEEYIEA EHRPPSSISS KNPAVIVL S AKNKDRLREQ VQRLLSAIRE QVLTDNDLAE IAYTLQVGRE AMEERFAVIV KSISELEAKL TYYLKDEADS PDLFTGQVK RNKETMDVFA ADEDLQQAID TWITKGKYAK ILQMWVQGLI FDWNKLYGDT KPRRISLPAY PFARERYWLP KVESQAIGLT AGEPAYLHP L

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.18 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293 K / Instrument: LEICA PLUNGER

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 67.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE / Details: Ab initio calculated in cryosparc
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 171149

+
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