[English] 日本語
Yorodumi
- PDB-7zdi: PucB-LH2 complex from Rps. palustris -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zdi
TitlePucB-LH2 complex from Rps. palustris
Components
  • (Light-harvesting protein) x 2
  • PucA-LH2-gamma
KeywordsPHOTOSYNTHESIS / light harvesting complex 2 / LH2 / Rps. palustris / purple bacteria / cryo-EM / single particle analysis
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
BACTERIOCHLOROPHYLL A / 1,2-Dihydro-psi,psi-caroten-1-ol / Uncharacterized protein / Light-harvesting protein / Light-harvesting protein
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsQian, P. / Cogdell, R.J. / Nguyen-Phan, T.C.
Funding support United Kingdom, 1items
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, R.J.
#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, R.J.
History
DepositionMar 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Derived calculations / Structure summary / Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2Nov 23, 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
Revision 1.3Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Light-harvesting protein
B: Light-harvesting protein
S: PucA-LH2-gamma
C: Light-harvesting protein
D: Light-harvesting protein
E: Light-harvesting protein
F: Light-harvesting protein
G: Light-harvesting protein
H: Light-harvesting protein
I: Light-harvesting protein
J: Light-harvesting protein
K: Light-harvesting protein
L: Light-harvesting protein
M: Light-harvesting protein
N: Light-harvesting protein
O: Light-harvesting protein
P: Light-harvesting protein
Q: Light-harvesting protein
R: Light-harvesting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,42661
Polymers124,35219
Non-polymers35,07442
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area101820 Å2
ΔGint-727 kcal/mol
Surface area40170 Å2

-
Components

#1: Protein
Light-harvesting protein


Mass: 6873.004 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Rhodopseudomonas palustris (phototrophic) / References: UniProt: A0A323UGK7
#2: Protein
Light-harvesting protein / Light-harvesting protein B-800-850 beta chain / Light-harvesting protein B-800-850 subunit beta B


Mass: 5738.550 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Rhodopseudomonas palustris (phototrophic) / References: UniProt: A0A2R4GZC1
#3: Protein PucA-LH2-gamma


Mass: 10848.179 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhodopseudomonas palustris (phototrophic) / References: UniProt: A0A2R4GRK2
#4: Chemical...
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-IRM / 1,2-Dihydro-psi,psi-caroten-1-ol / Rhodopin / (6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},24~{E},26~{E})-2,6,10,14,19,23,27,31-octamethyldotriaconta-6,8,10,12,14,16,18,20,22,24,26,30-dodecaen-2-ol


Mass: 554.888 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C40H58O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: PucB-LH2 from Rps. palustris / Type: COMPLEX / Details: Delt-pucBA(aced) / Entity ID: #1-#3 / Source: NATURAL
Source (natural)Organism: Rhodopseudomonas palustris ATCC 17001 (phototrophic)
Buffer solutionpH: 8 / Details: 0.1% LDAO in 20 mM Tris.Cl pH 8.0
Buffer componentConc.: 20 mM / Name: Tris.HCl / Formula: C4H11NO3
SpecimenConc.: 7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: protein was purified using LDAO detergent.
Specimen supportGrid 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
Details: Chamber humidity: 100%; Chamber temperature: 4 oC; Blotting time: 2.5; Blotting force: 3; Wait time: 30 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 / 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: 12.21 sec. / Electron dose: 44.1 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5593 / Details: Images were collected in AFIS mode.
EM imaging opticsDetails: No energy filter was applied.

-
Processing

Software
NameVersionClassificationNB
phenix.real_space_refinedev_4386refinement
PHENIXdev_4386refinement
EM software
IDNameVersionCategory
1cisTEM1particle selection
2EPUimage acquisition
4CTFFIND4CTF correction
7ISOLDEmodel fitting
10RELION3.1final Euler assignment
11RELION3.1classification
12RELION3.13D reconstruction
13PHENIXmodel refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 1946434
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 402668 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 39.44 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.003610792
ELECTRON MICROSCOPYf_angle_d0.894815206
ELECTRON MICROSCOPYf_chiral_restr0.04251507
ELECTRON MICROSCOPYf_plane_restr0.00881997
ELECTRON MICROSCOPYf_dihedral_angle_d13.1033689

+
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