[English] 日本語
Yorodumi
- EMDB-47275: Light Harvesting complex 3 (LH3), B800-B820, of Rhodoblastus (Rbl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-47275
TitleLight Harvesting complex 3 (LH3), B800-B820, of Rhodoblastus (Rbl.) acidophilus strain 7750
Map dataLight Harvesting complex 3 (LH3), B800-B820, of Rhodoblastus (Rbl.) acidophilus strain 7750
Sample
  • Complex: Nonameric complex of the low-light induced Light Harvesting complex 3 (LH3)
    • Protein or peptide: Light-harvesting protein B-800/820 alpha chain
    • Protein or peptide: Light-harvesting protein B-800/820 beta-2 chain
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: LAURYL DIMETHYLAMINE-N-OXIDE
  • Ligand: 1,2-Dihydro-psi,psi-caroten-1-ol
  • Ligand: DODECYL-BETA-D-MALTOSIDE
KeywordsLight Harvesting / acclimation / stress / PHOTOSYNTHESIS
Function / homology
Function and homology information


organelle inner membrane / 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 subunit conserved site / Antenna complexes alpha subunits signature. / 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
Light-harvesting protein B-800/820 alpha chain / Light-harvesting protein B-800/820 beta-2 chain
Similarity search - Component
Biological speciesRhodoblastus acidophilus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.35 Å
AuthorsHarris D / Schlau-Cohen GS
Funding support United States, 2 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0018097 United States
National Science Foundation (NSF, United States)DMR-1419807 United States
CitationJournal: To Be Published
Title: Robust light-harvesting properties upon chromatic acclimation in purple bacteria
Authors: Wang D / Harris D / Chuang C / Schmidt GP / Feibig OC / Schlau-Cohen GS
History
DepositionOct 10, 2024-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_47275.png

Downloads & links

-
Map

FileDownload / File: emd_47275.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLight Harvesting complex 3 (LH3), B800-B820, of Rhodoblastus (Rbl.) acidophilus strain 7750
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 380 pix.
= 248.52 Å		0.65 Å/pix.
x 380 pix.
= 248.52 Å		0.65 Å/pix.
x 380 pix.
= 248.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.654 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.06
Minimum - Maximum-0.20645632 - 21.2941
Average (Standard dev.)-0.040562715 (±0.57616717)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 248.51999 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half Map A

Fileemd_47275_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half Map B

Fileemd_47275_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Nonameric complex of the low-light induced Light Harvesting compl...

EntireName: Nonameric complex of the low-light induced Light Harvesting complex 3 (LH3)
Components
  • Complex: Nonameric complex of the low-light induced Light Harvesting complex 3 (LH3)
    • Protein or peptide: Light-harvesting protein B-800/820 alpha chain
    • Protein or peptide: Light-harvesting protein B-800/820 beta-2 chain
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: LAURYL DIMETHYLAMINE-N-OXIDE
  • Ligand: 1,2-Dihydro-psi,psi-caroten-1-ol
  • Ligand: DODECYL-BETA-D-MALTOSIDE

-
Supramolecule #1: Nonameric complex of the low-light induced Light Harvesting compl...

SupramoleculeName: Nonameric complex of the low-light induced Light Harvesting complex 3 (LH3)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Rhodoblastus acidophilus (bacteria) / Strain: 7750
Molecular weightTheoretical: 130 KDa

-
Macromolecule #1: Light-harvesting protein B-800/820 alpha chain

MacromoleculeName: Light-harvesting protein B-800/820 alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Rhodoblastus acidophilus (bacteria) / Strain: 7750
Molecular weightTheoretical: 5.113006 KDa
SequenceString:
(FME)NQGKIWTVV NPAVGLPLLL GSVAITALLV HLAVLTHTTW FPAFQQGG

UniProtKB: Light-harvesting protein B-800/820 alpha chain

-
Macromolecule #2: Light-harvesting protein B-800/820 beta-2 chain

MacromoleculeName: Light-harvesting protein B-800/820 beta-2 chain / type: protein_or_peptide / ID: 2 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Rhodoblastus acidophilus (bacteria)
Molecular weightTheoretical: 4.553242 KDa
SequenceString:
AVLSPEQSEE LHKYVIDGAR AFLGIALVAH FLAFSLTPWL H

UniProtKB: Light-harvesting protein B-800/820 beta-2 chain

-
Macromolecule #3: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 3 / Number of copies: 27 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A

-
Macromolecule #4: LAURYL DIMETHYLAMINE-N-OXIDE

MacromoleculeName: LAURYL DIMETHYLAMINE-N-OXIDE / type: ligand / ID: 4 / Number of copies: 9 / Formula: LDA
Molecular weightTheoretical: 229.402 Da
Chemical component information

ChemComp-LDA:
LAURYL DIMETHYLAMINE-N-OXIDE / LDAO, detergent*YM

-
Macromolecule #5: 1,2-Dihydro-psi,psi-caroten-1-ol

MacromoleculeName: 1,2-Dihydro-psi,psi-caroten-1-ol / type: ligand / ID: 5 / Number of copies: 9 / Formula: IRM
Molecular weightTheoretical: 554.888 Da
Chemical component information

ChemComp-IRM:
1,2-Dihydro-psi,psi-caroten-1-ol

-
Macromolecule #6: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 6 / Number of copies: 9 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.75 mg/mL
BufferpH: 7.8
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 1.0 sec. / Average electron dose: 43.37 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.35 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 49453
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

+
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