[English] 日本語
Yorodumi
- EMDB-65526: LH2 complex from Ectothiorhodospira haloalkaliphila with inhibite... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-65526
TitleLH2 complex from Ectothiorhodospira haloalkaliphila with inhibited carotenoid biosynthesis
Map data
Sample
  • Complex: LH2 complex from Ectothiorhodospira haloalkaliphila
    • Protein or peptide: Light-harvesting protein B:800-850 subunit beta
    • Protein or peptide: Light-harvesting protein B-800/850 alpha chain
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: Phytoene
  • Ligand: water
KeywordsPHOTOSYNTHESIS / Light-harvesing / purple sulfur bacteria / cryo-EM
Function / homology
Function and homology information


plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / metal ion binding / plasma membrane
Similarity search - Function
Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, alpha/beta subunit / Light-harvesting protein B beta chain / Antenna complex, beta domain superfamily / Antenna complex alpha/beta subunit / Light-harvesting complex
Similarity search - Domain/homology
Antenna complex alpha/beta subunit domain-containing protein / Light-harvesting protein B:800-850 subunit beta
Similarity search - Component
Biological speciesEctothiorhodospira haloalkaliphila ATCC 51935 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.92 Å
AuthorsBurtseva AD / Baymukhametov TN / Popov VO / Ashikhmin AA / Boyko KM
Funding support Russian Federation, 1 items
OrganizationGrant numberCountry
Russian Science Foundation23-74-00062 Russian Federation
CitationJournal: FEBS Lett / Year: 2025
Title: Structural insights into LH2 complexes formed by a purple sulfur bacterium with inhibited carotenoid biosynthesis.
Authors: Anna D Burtseva / Timur N Baymukhametov / Maxim A Bolshakov / Aleksandr S Starodubov / Huawei Zhang / Vladimir O Popov / Aleksandr A Ashikhmin / Konstantin M Boyko /
Abstract: The LH2 complex is essential for light harvesting in many photosynthetic bacteria. To elucidate the specific structural role of carotenoids, we analyzed LH2 complexes from Ectothiorhodospira ...The LH2 complex is essential for light harvesting in many photosynthetic bacteria. To elucidate the specific structural role of carotenoids, we analyzed LH2 complexes from Ectothiorhodospira haloalkaliphila with inhibited carotenoid biosynthesis. This approach allowed us to study complexes incorporating the colorless carotenoid phytoene instead of the native, colored pigments. A 1.92 Å cryo-EM reconstruction revealed that phytoene fully substitutes for the native carotenoids while maintaining the octameric symmetry of the complex and the precise arrangement of bacteriochlorophylls. These results demonstrate that the architectural function of carotenoids in LH2 complexes is maintained even when their light-absorption capability is altered, providing new mechanistic insight into the structural basis of pigment-protein interactions in photosynthetic antenna complexes.
History
DepositionJul 25, 2025-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_65526.png

Downloads & links

-
Map

FileDownload / File: emd_65526.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.67 Å/pix.
x 400 pix.
= 268. Å		0.67 Å/pix.
x 400 pix.
= 268. Å		0.67 Å/pix.
x 400 pix.
= 268. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.67 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.35
Minimum - Maximum-1.3050765 - 1.8637816
Average (Standard dev.)0.00031934277 (±0.038146213)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 268.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: #1

Fileemd_65526_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_65526_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_65526_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : LH2 complex from Ectothiorhodospira haloalkaliphila

EntireName: LH2 complex from Ectothiorhodospira haloalkaliphila
Components
  • Complex: LH2 complex from Ectothiorhodospira haloalkaliphila
    • Protein or peptide: Light-harvesting protein B:800-850 subunit beta
    • Protein or peptide: Light-harvesting protein B-800/850 alpha chain
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: Phytoene
  • Ligand: water

-
Supramolecule #1: LH2 complex from Ectothiorhodospira haloalkaliphila

SupramoleculeName: LH2 complex from Ectothiorhodospira haloalkaliphila / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Ectothiorhodospira haloalkaliphila ATCC 51935 (bacteria)

-
Macromolecule #1: Light-harvesting protein B:800-850 subunit beta

MacromoleculeName: Light-harvesting protein B:800-850 subunit beta / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Ectothiorhodospira haloalkaliphila ATCC 51935 (bacteria)
Molecular weightTheoretical: 5.468237 KDa
SequenceString:
MYDNSISGLT EEQAKEFHEQ FKTTFTVFMV LAAAAHFLVF LWRPFY

UniProtKB: Light-harvesting protein B:800-850 subunit beta

-
Macromolecule #2: Light-harvesting protein B-800/850 alpha chain

MacromoleculeName: Light-harvesting protein B-800/850 alpha chain / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Ectothiorhodospira haloalkaliphila ATCC 51935 (bacteria)
Molecular weightTheoretical: 7.855903 KDa
SequenceString:
MSEYRPSKPS NPRDDWKLWL VVNPGTWLMP ILMAVLVVAL VVHAFVYSND NYNPLTFDAS AEVAAEEAAE

UniProtKB: Antenna complex alpha/beta subunit domain-containing protein

-
Macromolecule #3: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 3 / Number of copies: 24 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A

-
Macromolecule #4: Phytoene

MacromoleculeName: Phytoene / type: ligand / ID: 4 / Number of copies: 8 / Formula: A1MBA
Molecular weightTheoretical: 544.936 Da

-
Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 88 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
GridModel: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsSpherical aberration corrector: Microscope was modified with a Cs corrector (CEOS GmbH, Germany).
Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 15 eV
DetailsPreliminary grid screening was performed manually.
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 12334 / Average exposure time: 2.5 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
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: 1589688
CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C8 (8 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 1.92 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 445556
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9w1c:
LH2 complex from Ectothiorhodospira haloalkaliphila with inhibited carotenoid biosynthesis

+
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