[English] 日本語
Yorodumi
- EMDB-41307: KS-AT core of 6-deoxyerythronolide B synthase (DEBS) Module 3 cro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-41307
TitleKS-AT core of 6-deoxyerythronolide B synthase (DEBS) Module 3 crosslinked with its elongation ACP partner
Map data
Sample
  • Complex: KS-AT core of DEBS Module 3 crosslinked with its elongation ACP partner
    • Protein or peptide: EryAII
Keywordspolyketide synthase / antibody / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


macrolide biosynthetic process / DIM/DIP cell wall layer assembly / fatty acid synthase activity / phosphopantetheine binding / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / oxidoreductase activity / plasma membrane / cytoplasm
Similarity search - Function
Erythronolide synthase, docking / Erythronolide synthase, docking domain superfamily / Erythronolide synthase, docking / Zinc-binding dehydrogenase / Polyketide synthase, docking domain / Erythronolide synthase docking domain / : / : / Polyketide synthase dehydratase domain / : ...Erythronolide synthase, docking / Erythronolide synthase, docking domain superfamily / Erythronolide synthase, docking / Zinc-binding dehydrogenase / Polyketide synthase, docking domain / Erythronolide synthase docking domain / : / : / Polyketide synthase dehydratase domain / : / Polyketide and metazoan fatty acid synthase dehydratase (PKS/mFAS DH) domain profile. / 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 / Malonyl-CoA ACP transacylase, ACP-binding / Polyketide synthase, C-terminal extension / Ketoacyl-synthetase C-terminal extension / PKS_KR / Acyl transferase domain superfamily / Acyl transferase / Acyl transferase domain / Acyl transferase domain in polyketide synthase (PKS) enzymes. / Acyl transferase/acyl hydrolase/lysophospholipase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / 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 / GroES-like superfamily / 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
Biological speciesSaccharopolyspora erythraea (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.71 Å
AuthorsCogan DP / Soohoo AM / Chen M / Brodsky KL / Liu Y / Khosla C
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM141799 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM136039 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM129541 United States
National Science Foundation (NSF, United States)DGE-1656518 United States
CitationJournal: To Be Published
Title: Structural Basis for Intermodular Communication in Assembly-Line Polyketide Biosynthesis
Authors: Cogan DP / Soohoo AM / Chen M / Liu Y / Brodsky KL / Khosla C
History
DepositionJul 23, 2023-
Header (metadata) releaseJul 24, 2024-
Map releaseJul 24, 2024-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_41307.png

Downloads & links

-
Map

FileDownload / File: emd_41307.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 448 pix.
= 423.808 Å		0.95 Å/pix.
x 448 pix.
= 423.808 Å		0.95 Å/pix.
x 448 pix.
= 423.808 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.946 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.339
Minimum - Maximum-0.46599337 - 0.9122427
Average (Standard dev.)0.0002786378 (±0.02250235)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 423.80798 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_41307_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_41307_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : KS-AT core of DEBS Module 3 crosslinked with its elongation ACP p...

EntireName: KS-AT core of DEBS Module 3 crosslinked with its elongation ACP partner
Components
  • Complex: KS-AT core of DEBS Module 3 crosslinked with its elongation ACP partner
    • Protein or peptide: EryAII

-
Supramolecule #1: KS-AT core of DEBS Module 3 crosslinked with its elongation ACP p...

SupramoleculeName: KS-AT core of DEBS Module 3 crosslinked with its elongation ACP partner
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharopolyspora erythraea (bacteria)
Molecular weightTheoretical: 210 KDa

-
Macromolecule #1: EryAII

MacromoleculeName: EryAII / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharopolyspora erythraea (bacteria)
Molecular weightTheoretical: 99.76575 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MVTDSEKVAE YLRRATLDLR AARQRIRELE SDPIAIVSMA CRLPGGVNTP QRLWELLREG GETLSGFPTD RGWDLARLHH PDPDNPGTS YVDKGGFLDD AAGFDAEFFG VSPREAAAMD PQQRLLLETS WELVENAGID PHSLRGTATG VFLGVAKFGY G EDTAAAED ...String:
MVTDSEKVAE YLRRATLDLR AARQRIRELE SDPIAIVSMA CRLPGGVNTP QRLWELLREG GETLSGFPTD RGWDLARLHH PDPDNPGTS YVDKGGFLDD AAGFDAEFFG VSPREAAAMD PQQRLLLETS WELVENAGID PHSLRGTATG VFLGVAKFGY G EDTAAAED VEGYSVTGVA PAVASGRISY TMGLEGPSIS VDTACSSSLV ALHLAVESLR KGESSMAVVG GAAVMATPGV FV DFSRQRA LAADGRSKAF GAGADGFGFS EGVTLVLLER LSEARRNGHE VLAVVRGSAL NQDGASNGLS APSGPAQRRV IRQ ALESCG LEPGDVDAVE AHGTGTALGD PIEANALLDT YGRDRDADRP LWLGSVKSNI GHTQAAAGVT GLLKVVLALR NGEL PATLH VEEPTPHVDW SSGGVALLAG NQPWRRGERT RRAAVSAFGI SGTNAHVIVE EAPEREHRET TAHDGRPVPL VVSAR STAA LRAQAAQIAE LLERPDADLA GVGLGLATTR ARHEHRAAVV ASTREEAVRG LREIAAGAAT ADAVVEGVTE VDGRNV VFL FPGQGSQWAG MGAELLSSSP VFAGKIRACD ESMAPMQDWK VSDVLRQAPG APGLDRVDVV QPVLFAVMVS LAELWRS YG VEPAAVVGHS QGEIAAAHVA GALTLEDAAK LVVGRSRLMR SLSGEGGMAA VALGEAAVRE RLRPWQDRLS VAAVNGPR S VVVSGEPGAL RAFSEDCAAE GIRVRDIDVD YASHSPQIER VREELLETTG DIAPRPARVT FHSTVESRSM DGTELDARY WYRNLRETVR FADAVTRLAE SGYDAFIEVS PHPVVVQAVE EAVEEADGAE DAVVVGSLHR DGGDLSAFLR SMATAHVSGV DIRWDVALP GAAPFALPTY PFQRKRYWLQ PAAPAAASDE LAYRSSSVDK LAAALEHHHH HH

UniProtKB: EryAII

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration8 mg/mL
BufferpH: 7.2
Component:
ConcentrationFormulaName
100.0 mMC6H8O7citric acid
100.0 mMNaClsodium chloride
10.0 mMC8H18N2O4SHEPES
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 11 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: 30 s glow, 10 s hold, 15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 4601 / Average exposure time: 6.45 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 150.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 199350
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.71 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 199350
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: OTHER
Final 3D classificationNumber classes: 8 / Avg.num./class: 40000

-
Atomic model buiding 1

Initial modelPDB ID:

6c9u


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8tjp:
KS-AT core of 6-deoxyerythronolide B synthase (DEBS) Module 3 crosslinked with its elongation ACP partner

+
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://pdbjlvh1.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