[English] 日本語
Yorodumi
- PDB-7pbw: Cryo-EM structure of light harvesting complex 2 from Rba. sphaeroides. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7pbw
TitleCryo-EM structure of light harvesting complex 2 from Rba. sphaeroides.
Components(Light-harvesting protein B-800/850 ...) x 2
KeywordsPHOTOSYNTHESIS / Purple bacteria / Light harvesting complex 2 / LH2 / Membrane protein / Cryo-EM.
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 / membrane => GO:0016020 / 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, beta domain superfamily / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Light-harvesting protein B beta chain / Antenna complex, alpha/beta subunit / Light-harvesting complex / Antenna complex alpha/beta subunit
Similarity search - Domain/homology
SPHEROIDENE / BACTERIOCHLOROPHYLL A / Light-harvesting protein B-800/850 alpha chain / Light-harvesting protein B-800/850 beta chain
Similarity search - Component
Biological speciesCereibacter sphaeroides 2.4.1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsQian, P. / Swainsbury, D.J.K. / Croll, T.I. / Castro-Hartmann, P. / Sader, K. / Divitini, G. / Hunter, C.N.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M000265/1 United Kingdom
CitationJournal: Biochemistry / Year: 2021
Title: Cryo-EM Structure of the Light-Harvesting 2 Complex at 2.1 Å.
Authors: Pu Qian / David J K Swainsbury / Tristan I Croll / Pablo Castro-Hartmann / Giorgio Divitini / Kasim Sader / C Neil Hunter /
Abstract: Light-harvesting 2 (LH2) antenna complexes augment the collection of solar energy in many phototrophic bacteria. Despite its frequent role as a model for such complexes, there has been no three- ...Light-harvesting 2 (LH2) antenna complexes augment the collection of solar energy in many phototrophic bacteria. Despite its frequent role as a model for such complexes, there has been no three-dimensional (3D) structure available for the LH2 from the purple phototroph . We used cryo-electron microscopy (cryo-EM) to determine the 2.1 Å resolution structure of this LH2 antenna, which is a cylindrical assembly of nine αβ heterodimer subunits, each of which binds three bacteriochlorophyll (BChl) molecules and one carotenoid. The high resolution of this structure reveals all of the interpigment and pigment-protein interactions that promote the assembly and energy-transfer properties of this complex. Near the cytoplasmic face of the complex there is a ring of nine BChls, which absorb maximally at 800 nm and are designated as B800; each B800 is coordinated by the N-terminal carboxymethionine of LH2-α, part of a network of interactions with nearby residues on both LH2-α and LH2-β and with the carotenoid. Nine carotenoids, which are spheroidene in the strain we analyzed, snake through the complex, traversing the membrane and interacting with a ring of 18 BChls situated toward the periplasmic side of the complex. Hydrogen bonds with C-terminal aromatic residues modify the absorption of these pigments, which are red-shifted to 850 nm. Overlaps between the macrocycles of the B850 BChls ensure rapid transfer of excitation energy around this ring of pigments, which act as the donors of energy to neighboring LH2 and reaction center light-harvesting 1 (RC-LH1) complexes.
History
DepositionAug 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-13307
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-13307
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AA: Light-harvesting protein B-800/850 alpha chain
AB: Light-harvesting protein B-800/850 alpha chain
AC: Light-harvesting protein B-800/850 alpha chain
AD: Light-harvesting protein B-800/850 alpha chain
AE: Light-harvesting protein B-800/850 alpha chain
AF: Light-harvesting protein B-800/850 alpha chain
AG: Light-harvesting protein B-800/850 alpha chain
AH: Light-harvesting protein B-800/850 alpha chain
AI: Light-harvesting protein B-800/850 alpha chain
BA: Light-harvesting protein B-800/850 beta chain
BB: Light-harvesting protein B-800/850 beta chain
BC: Light-harvesting protein B-800/850 beta chain
BD: Light-harvesting protein B-800/850 beta chain
BE: Light-harvesting protein B-800/850 beta chain
BF: Light-harvesting protein B-800/850 beta chain
BG: Light-harvesting protein B-800/850 beta chain
BH: Light-harvesting protein B-800/850 beta chain
BI: Light-harvesting protein B-800/850 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,74499
Polymers92,39418
Non-polymers38,35081
Water4,143230
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, Reference-free 2D classification shows that a top view of the complex has C9 symmetry.
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area119200 Å2
ΔGint-699 kcal/mol
Surface area28350 Å2

-
Components

-
Light-harvesting protein B-800/850 ... , 2 types, 18 molecules AAABACADAEAFAGAHAIBABBBCBDBEBFBGBHBI

#1: Protein/peptide
Light-harvesting protein B-800/850 alpha chain / Antenna pigment protein alpha chain / LH-2


Mass: 5275.187 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides 2.4.1 (bacteria) / References: UniProt: Q3J144
#2: Protein/peptide
Light-harvesting protein B-800/850 beta chain / Antenna pigment protein beta chain / LH-3B


Mass: 4990.840 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Cereibacter sphaeroides 2.4.1 (bacteria) / References: UniProt: Q3J145

-
Non-polymers , 5 types, 311 molecules

#3: Chemical...
ChemComp-BCL / BACTERIOCHLOROPHYLL A / Bacteriochlorophyll


Mass: 911.504 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-7OT / SPHEROIDENE / (6E,10E,12E,14E,16E,18E,20E,22E,24E,26E,28E)-31-methoxy-2,6,10,14,19,23,27,31-octamethyl-dotriaconta-2,6,10,12,14,16,18,20,22,24,26,28-dodecaene


Mass: 568.914 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C41H60O
#5: Chemical...
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide


Mass: 229.402 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Light harvesting complex 2Light-harvesting complex / Type: COMPLEX / Entity ID: #1-#2 / Source: NATURAL
Molecular weightValue: 0.1237 MDa / Experimental value: YES
Source (natural)Organism: Cereibacter sphaeroides 2.4.1 (bacteria)
Buffer solutionpH: 7.8
Details: The final sample buffer: 20 mM Hepes, pH 7.8, 0.1%LDAO
Buffer componentConc.: 20 mmol / Name: Hepes / Formula: C8H18N2O4S
SpecimenConc.: 4.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Sample was solubilised and purified with detergent of LDAO
Specimen supportDetails: easiGlow was used for glow discharge. / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 130000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.37 sec. / Electron dose: 41.6 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3138
Details: A total doe 41.6 was fractioned into 40 frames, resulting in an electron fluency of 1.04 e/A2/frame.
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

-
Processing

Software
NameVersionClassificationNB
phenix.real_space_refinedev_4234refinement
PHENIXdev_4234refinement
EM software
IDNameVersionCategory
1cisTEM1particle selection
4CTFFIND4CTF correction
10RELION3.1initial Euler assignment
11RELION3.1final Euler assignment
12RELION3.1classification
13RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1717608
SymmetryPoint symmetry: C9 (9 fold cyclic)
3D reconstructionResolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 835641 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 12.34 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0049603
ELECTRON MICROSCOPYf_angle_d0.941413365
ELECTRON MICROSCOPYf_chiral_restr0.04661359
ELECTRON MICROSCOPYf_plane_restr0.00871530
ELECTRON MICROSCOPYf_dihedral_angle_d17.7873348

+
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