[English] 日本語
Yorodumi
- PDB-6zxa: LH2 complex from Marichromatium purpuratum -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zxa
TitleLH2 complex from Marichromatium purpuratum
Components
  • LHC domain-containing protein
  • Light-harvesting protein B:800-850 subunit beta
KeywordsPHOTOSYNTHESIS / purple bacteria / light harvesting complex / Marichromatium purpuratum / okenone.
Function / homology
Function and homology information


light-harvesting complex / 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, alpha subunit / Light-harvesting protein B beta chain / Antenna complex, beta domain superfamily / Antenna complex alpha/beta subunit / Light-harvesting complex
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL A / 9-cis-okenone / all-trans okenone / Light-harvesting protein B:800-850 subunit beta / Uncharacterized protein
Similarity search - Component
Biological speciesMarichromatium purpuratum 984 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.38 Å
AuthorsGardiner, A.T. / Naydenova, K. / Castro-Hartmann, P. / Nguyen-Phan, T.C. / Russo, C.J. / Sader, K. / Hunter, C.N. / Cogdell, R.J. / Qian, P.
Funding support United States, United Kingdom, 3items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0001035 United States
Medical Research Council (MRC, United Kingdom)MC_UP_120117 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Sci Adv / Year: 2021
Title: The 2.4 Å cryo-EM structure of a heptameric light-harvesting 2 complex reveals two carotenoid energy transfer pathways.
Authors: Alastair T Gardiner / Katerina Naydenova / Pablo Castro-Hartmann / Tu C Nguyen-Phan / Christopher J Russo / Kasim Sader / C Neil Hunter / Richard J Cogdell / Pu Qian /
Abstract: We report the 2.4 Ångström resolution structure of the light-harvesting 2 (LH2) complex from () determined by cryogenic electron microscopy. The structure contains a heptameric ring that is ...We report the 2.4 Ångström resolution structure of the light-harvesting 2 (LH2) complex from () determined by cryogenic electron microscopy. The structure contains a heptameric ring that is unique among all known LH2 structures, explaining the unusual spectroscopic properties of this bacterial antenna complex. We identify two sets of distinct carotenoids in the structure and describe a network of energy transfer pathways from the carotenoids to bacteriochlorophyll molecules. The geometry imposed by the heptameric ring controls the resonant coupling of the long-wavelength energy absorption band. Together, these details reveal key aspects of the assembly and oligomeric form of purple bacterial LH2 complexes that were previously inaccessible by any technique.
History
DepositionJul 29, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-11516
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LHC domain-containing protein
B: Light-harvesting protein B:800-850 subunit beta
C: LHC domain-containing protein
D: Light-harvesting protein B:800-850 subunit beta
E: LHC domain-containing protein
F: Light-harvesting protein B:800-850 subunit beta
G: LHC domain-containing protein
H: Light-harvesting protein B:800-850 subunit beta
I: LHC domain-containing protein
J: Light-harvesting protein B:800-850 subunit beta
K: LHC domain-containing protein
L: Light-harvesting protein B:800-850 subunit beta
M: LHC domain-containing protein
N: Light-harvesting protein B:800-850 subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,23349
Polymers94,98814
Non-polymers27,24635
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area79730 Å2
ΔGint-582 kcal/mol
Surface area31600 Å2
MethodPISA

-
Components

#1: Protein
LHC domain-containing protein


Mass: 8015.369 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Marichromatium purpuratum 984 (bacteria) / References: UniProt: W0E6A1
#2: Protein/peptide
Light-harvesting protein B:800-850 subunit beta


Mass: 5554.275 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Marichromatium purpuratum 984 (bacteria) / References: UniProt: W0E5B0
#3: Chemical...
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-QS2 / 9-cis-okenone


Mass: 578.866 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C41H54O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-QSE / all-trans okenone


Mass: 578.866 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C41H54O2 / Feature type: SUBJECT OF INVESTIGATION
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 2 (LH2) / Type: COMPLEX
Details: The LH2 complex from Mar. purpuratum forms a circular heptameter. Each subunit consists of an alpha/beta pair, in which all pigment molecules, three Bchl a and two carotenoids are bound non-covalently.
Entity ID: #1-#2 / Source: NATURAL
Molecular weightValue: 0.11 MDa / Experimental value: NO
Source (natural)Organism: Marichromatium purpuratum (bacteria) / Strain: BN5500
Buffer solutionpH: 8
Details: The final buffer contains 0.02 % n-dodecyl-beta-D-maltopyranoside (DDM)
Buffer componentConc.: 20 mM/L / Name: Tris.HCl
SpecimenConc.: 5.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The sample was mono disperse with detergent beta-DDM.
Specimen supportDetails: Fischione 1070 / Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Homemade
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: Blowing time, 10.0 sec.

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 120000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm / Calibrated defocus min: 400 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (min): 80 K
Image recordingAverage exposure time: 0.29 sec. / Electron dose: 43.7 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9543

-
Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.17.1_3660refinement
PHENIX1.17.1_3660refinement
EM software
IDNameVersionCategoryDetails
1cisTEM1particle selection
2EPU2.5image acquisition
4CTFFIND4.1CTF correction
7Coot0.9model fittingIn CCPEM 1.3.0
8UCSF Chimera1.13.1model fitting
10PHENIX1.17.1model refinement
11REFMACmodel refinementIn CCPEM 1.3.0
12RELION3.1initial Euler assignment
13RELION3.1final Euler assignment
14RELION3.1classification
15RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1330154
SymmetryPoint symmetry: C7 (7 fold cyclic)
3D reconstructionResolution: 2.38 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 414511 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 22.55 / Protocol: FLEXIBLE FIT / Space: REAL
Atomic model building

3D fitting-ID: 1 / Accession code: 1LGH / Initial refinement model-ID: 1 / PDB-ID: 1LGH

1lgh

/ Source name: PDB / Type: experimental model

IDPdb chain-IDPdb chain residue range
1A1-56
2B1-45
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 50.29 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00818876
ELECTRON MICROSCOPYf_angle_d1.29312418
ELECTRON MICROSCOPYf_chiral_restr0.06661141
ELECTRON MICROSCOPYf_plane_restr0.00751799
ELECTRON MICROSCOPYf_dihedral_angle_d12.05851736

+
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