[English] 日本語
Yorodumi
- EMDB-14650: PucB-LH2 complex from Rps. palustris -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-14650
TitlePucB-LH2 complex from Rps. palustris
Map dataPucB-LH2
Sample
  • Complex: PucB-LH2 from Rps. palustris
    • Protein or peptide: Light-harvesting protein
    • Protein or peptide: Light-harvesting protein
    • Protein or peptide: PucA-LH2-gamma
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: 1,2-Dihydro-psi,psi-caroten-1-ol
Function / homology
Function and homology information


organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / 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
Uncharacterized protein / Light-harvesting protein / Light-harvesting protein
Similarity search - Component
Biological speciesRhodopseudomonas palustris ATCC 17001 (phototrophic) / Rhodopseudomonas palustris (phototrophic)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsQian P / Cogdell RJ / Nguyen-Phan TC
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/N016734/1 United Kingdom
Citation
Journal: Proc Natl Acad Sci U S A / Year: 2022
Title: Cryo-EM structures of light-harvesting 2 complexes from reveal the molecular origin of absorption tuning.
Authors: Pu Qian / Cam T Nguyen-Phan / Alastair T Gardiner / Tristan I Croll / Aleksander W Roszak / June Southall / Philip J Jackson / Cvetelin Vasilev / Pablo Castro-Hartmann / Kasim Sader / C Neil ...Authors: Pu Qian / Cam T Nguyen-Phan / Alastair T Gardiner / Tristan I Croll / Aleksander W Roszak / June Southall / Philip J Jackson / Cvetelin Vasilev / Pablo Castro-Hartmann / Kasim Sader / C Neil Hunter / Richard J Cogdell /
Abstract: The genomes of some purple photosynthetic bacteria contain a multigene family encoding a series of α- and β-polypeptides that together form a heterogeneous antenna of light-harvesting 2 (LH2) ...The genomes of some purple photosynthetic bacteria contain a multigene family encoding a series of α- and β-polypeptides that together form a heterogeneous antenna of light-harvesting 2 (LH2) complexes. To unravel this complexity, we generated four sets of deletion mutants in , each encoding a single type of gene pair and enabling the purification of complexes designated as PucA-LH2, PucB-LH2, PucD-LH2, and PucE-LH2. The structures of all four purified LH2 complexes were determined by cryogenic electron microscopy (cryo-EM) at resolutions ranging from 2.7 to 3.6 Å. Uniquely, each of these complexes contains a hitherto unknown polypeptide, γ, that forms an extended undulating ribbon that lies in the plane of the membrane and that encloses six of the nine LH2 αβ-subunits. The γ-subunit, which is located near to the cytoplasmic side of the complex, breaks the C9 symmetry of the LH2 complex and binds six extra bacteriochlorophylls (BChls) that enhance the 800-nm absorption of each complex. The structures show that all four complexes have two complete rings of BChls, conferring absorption bands centered at 800 and 850 nm on the PucA-LH2, PucB-LH2, and PucE-LH2 complexes, but, unusually, the PucD-LH2 antenna has only a single strong near-infared (NIR) absorption peak at 803 nm. Comparison of the cryo-EM structures of these LH2 complexes reveals altered patterns of hydrogen bonds between LH2 αβ-side chains and the bacteriochlorin rings, further emphasizing the major role that H bonds play in spectral tuning of bacterial antenna complexes.
#1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2018
Title: Real-space refinement in PHENIX for cryo-EM and crystallography
Authors: Qian P / Cogdell RJ
#2: Journal: To Be Published
Title: Cryo-EM structures of light harvesting complex 2 from Rhodopseudomonas palustris: a molecular origin of spectroscopic variation
Authors: Qian P / Cogdell RJ
History
DepositionMar 29, 2022-
Header (metadata) releaseOct 5, 2022-
Map releaseOct 5, 2022-
UpdateNov 23, 2022-
Current statusNov 23, 2022Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_14650.png

Downloads & links

-
Map

FileDownload / File: emd_14650.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPucB-LH2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 300 pix.
= 195. Å		0.65 Å/pix.
x 300 pix.
= 195. Å		0.65 Å/pix.
x 300 pix.
= 195. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0353
Minimum - Maximum-0.29295868 - 0.49085766
Average (Standard dev.)0.00046231394 (±0.01334908)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 195.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: PucB-LH2

Fileemd_14650_half_map_1.map
AnnotationPucB-LH2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: PucB-LH2

Fileemd_14650_half_map_2.map
AnnotationPucB-LH2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : PucB-LH2 from Rps. palustris

EntireName: PucB-LH2 from Rps. palustris
Components
  • Complex: PucB-LH2 from Rps. palustris
    • Protein or peptide: Light-harvesting protein
    • Protein or peptide: Light-harvesting protein
    • Protein or peptide: PucA-LH2-gamma
  • Ligand: BACTERIOCHLOROPHYLL A
  • Ligand: 1,2-Dihydro-psi,psi-caroten-1-ol

-
Supramolecule #1: PucB-LH2 from Rps. palustris

SupramoleculeName: PucB-LH2 from Rps. palustris / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / Details: Delt-pucBA(aced)
Source (natural)Organism: Rhodopseudomonas palustris ATCC 17001 (phototrophic)

-
Macromolecule #1: Light-harvesting protein

MacromoleculeName: Light-harvesting protein / type: protein_or_peptide / ID: 1 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Rhodopseudomonas palustris (phototrophic)
Molecular weightTheoretical: 6.873004 KDa
SequenceString:
(CXM)NQGRIWTVV NPGVGLPLLL GSVTVIAILV HYAVLSNTTW FPKYWNGATV AAPAAAPAPA APAAKK

-
Macromolecule #2: Light-harvesting protein

MacromoleculeName: Light-harvesting protein / type: protein_or_peptide / ID: 2 / Number of copies: 9 / Enantiomer: LEVO
Source (natural)Organism: Rhodopseudomonas palustris (phototrophic)
Molecular weightTheoretical: 5.73855 KDa
SequenceString:
MADDPNKVWP TGLTIAESEE LHKHVIDGTR IFGAIAIVAH FLAYVYSPWL H

-
Macromolecule #3: PucA-LH2-gamma

MacromoleculeName: PucA-LH2-gamma / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rhodopseudomonas palustris (phototrophic)
Molecular weightTheoretical: 10.848179 KDa
SequenceString:
MSEEYKGHSG HPLILKQEGE YKGYSGEPLI LKQEGEYKGY SGTPLILEQK GEYQSFSGTP LILKQEGEYR GFSGAPLILK QDGEYKSFS GYPLLLNI

-
Macromolecule #4: BACTERIOCHLOROPHYLL A

MacromoleculeName: BACTERIOCHLOROPHYLL A / type: ligand / ID: 4 / Number of copies: 33 / Formula: BCL
Molecular weightTheoretical: 911.504 Da
Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration7.0 mg/mL
BufferpH: 8 / Component - Concentration: 20.0 mM / Component - Formula: C4H11NO3 / Component - Name: Tris.HCl / Details: 0.1% LDAO in 20 mM Tris.Cl pH 8.0
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: Chamber humidity: 100%; Chamber temperature: 4 oC; Blotting time: 2.5; Blotting force: 3; Wait time: 30 sec.
Detailsprotein was purified using LDAO detergent.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 80.0 K
Specialist opticsDetails: No energy filter was applied.
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 5593 / Average exposure time: 12.21 sec. / Average electron dose: 44.1 e/Å2 / Details: Images were collected in AFIS mode.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 120000
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: 1946434
CTF correctionSoftware - Name: CTFFIND (ver. 4.0)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1lgh

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 402668
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7zdi:
PucB-LH2 complex from Rps. palustris

+
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