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- PDB-9h22: Cryo EM structure of RC-dLH complex model II from Gemmatimonas gr... -

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Basic information

Entry
Database: PDB / ID: 9h22
TitleCryo EM structure of RC-dLH complex model II from Gemmatimonas groenlandica
Components
  • (Light-harvesting ...) x 3
  • (Reaction center protein ...) x 2
  • (reaction centre ...) x 3
  • Photosynthetic reaction center cytochrome c subunit
KeywordsPHOTOSYNTHESIS / photosynthetic bacteria / reaction cennter light harvesting complex / RC-LH1 / RC-dLH / cryo-EM / Gemmatimonas groenlandica
Function / homology
Function and homology information


organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / endomembrane system / electron transfer activity / iron ion binding / heme binding / metal ion binding ...organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / endomembrane system / electron transfer activity / iron ion binding / heme binding / metal ion binding / membrane / plasma membrane
Similarity search - Function
Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / 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 ...Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / 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 / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, L subunit / Multiheme cytochrome superfamily / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / Chem-CD4 / SPIRILLOXANTHIN / : / HEME C / MENAQUINONE 8 / 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Chem-V7N / Reaction center protein M chain ...BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / Chem-CD4 / SPIRILLOXANTHIN / : / HEME C / MENAQUINONE 8 / 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Chem-V7N / Reaction center protein M chain / Light-harvesting protein / Reaction center protein L chain / Uncharacterized protein / Light-harvesting protein / Light-harvesting protein / Photosynthetic reaction center cytochrome c subunit
Similarity search - Component
Biological speciesGemmatimonas groenlandica (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsGardiner, A.T. / Jing, Y. / Bina, D. / Mujakic, I. / Gardian, Z. / Kaftan, D. / Joosten, M. / Jakobi, A. / Castro-Hartmann, P. / Qian, P. / Koblizek, M.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Czech Academy of Sciences19-28778X Czech Republic
CitationJournal: mSystems / Year: 2025
Title: Two solutions for efficient light-harvesting in phototrophic .
Authors: Alastair T Gardiner / Yibo Jin / David Bína / Maarten Joosten / David Kaftan / Izabela Mujakić / Zdenko Gardian / Pablo Castro-Hartmann / Pu Qian / Michal Koblížek /
Abstract: Phototrophic Gemmatimonadota represent a unique group of phototrophic bacteria that acquired a complete set of photosynthetic genes via horizontal gene transfer and later evolved independently. () ...Phototrophic Gemmatimonadota represent a unique group of phototrophic bacteria that acquired a complete set of photosynthetic genes via horizontal gene transfer and later evolved independently. () contains photosynthetic complexes with two concentric light-harvesting antenna rings that absorb at 816 and 868 nm, allowing it to better exploit the light conditions found deeper in the water column. The closely related species , with highly similar photosynthetic genes, harvests infrared light using a single 860 nm absorption band. The cryo-electron microscopy structure of the photosynthetic complex reveals that the outer antenna lacks monomeric bacteriochlorophylls, resulting in a smaller optical antenna cross-section. The spectrum is red-shifted relative to due to the formation of a H-bond enabled by a different rotamer conformation of αTrp in the outer ring. This H-bond forms with a neighboring bacteriochlorophyll and increases the intra-dimer exciton coupling, affecting the exciton localization probability within the rings and increasing exciton cooperativity between the complexes. The functional consequences of the spectral shift, caused solely by a subtle conformational change of a single residue, represent a novel mechanism in which phototrophic organisms adjust their antennae for particular light conditions and enable to grow higher in the water column where more photons are available.IMPORTANCEThe photoheterotrophic species of the phylum Gemmatimonadota employ unique photosynthetic complexes with two concentric antenna rings around a central reaction center. In contrast to other phototrophic species, these organisms have not evolved any regulatory systems to control the expression of their photosynthetic apparatus under different light conditions. Despite the overall similarity, the complexes present in and have different absorption properties in the near-infrared region of the spectrum that make them more suitable for low or medium light, respectively. The main difference in absorption depends on the conformation of a single tryptophan residue that can form an H-bond with a neighboring bacteriochlorophyll. The presence or absence of this H-bond affects how the protein scaffold interacts with the bacteriochlorophylls, which in turn determines how light energy is transferred within and between the photosynthetic complexes.
History
DepositionOct 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Dec 3, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 3, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 1.1Dec 17, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / EM metadata / Category: citation / citation_author / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata / EM metadata
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
S: reaction centre S sub unit
L: Reaction center protein L chain
M: Reaction center protein M chain
H: reaction centre Ht su unit
K: reaction centre Hc sub unit
C: Photosynthetic reaction center cytochrome c subunit
AA: Light-harvesting protein
BA: Light-harvesting protein
BB: Light-harvesting protein
AB: Light-harvesting protein
AC: Light-harvesting protein
BC: Light-harvesting protein
BD: Light-harvesting protein
AD: Light-harvesting protein
AE: Light-harvesting protein
BE: Light-harvesting protein
BF: Light-harvesting protein
AF: Light-harvesting protein
AG: Light-harvesting protein
BG: Light-harvesting protein
AH: Light-harvesting protein
BH: Light-harvesting protein
AI: Light-harvesting protein
BI: Light-harvesting protein
AJ: Light-harvesting protein
BJ: Light-harvesting protein
AK: Light-harvesting protein
BK: Light-harvesting protein
AL: Light-harvesting protein
BL: Light-harvesting protein
AM: Light-harvesting protein
BM: Light-harvesting protein
BN: Light-harvesting protein
AN: Light-harvesting protein
AO: Light-harvesting protein
BO: Light-harvesting protein
BP: Light-harvesting protein
AP: Light-harvesting protein
AQ: Light-harvesting protein
BQ: Light-harvesting protein
BR: Light-harvesting protein
AR: Light-harvesting protein
BS: Light-harvesting protein
AS: Light-harvesting protein
BT: Light-harvesting protein
AT: Light-harvesting protein
BU: Light-harvesting protein
AU: Light-harvesting protein
AV: Light-harvesting protein
BV: Light-harvesting protein
AW: Light-harvesting protein
BW: Light-harvesting protein
AX: Light-harvesting protein
BX: Light-harvesting protein
Aa: Light-harvesting protein
Ba: Light-harvesting protein
Ab: Light-harvesting protein
Bb: Light-harvesting protein
Ac: Light-harvesting protein
Bc: Light-harvesting protein
Ad: Light-harvesting protein
Bd: Light-harvesting protein
Ae: Light-harvesting protein
Be: Light-harvesting protein
Af: Light-harvesting protein
Bf: Light-harvesting protein
Ag: Light-harvesting protein
Bg: Light-harvesting protein
Ah: Light-harvesting protein
Bh: Light-harvesting protein
Ai: Light-harvesting protein
Bi: Light-harvesting protein
Aj: Light-harvesting protein
Bj: Light-harvesting protein
Ak: Light-harvesting protein
Bk: Light-harvesting protein
Al: Light-harvesting protein
Bl: Light-harvesting protein
Am: Light-harvesting protein
Bm: Light-harvesting protein
An: Light-harvesting protein
Bn: Light-harvesting protein
Ao: Light-harvesting protein
Bo: Light-harvesting protein
Ap: Light-harvesting protein
Bp: Light-harvesting protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)791,699288
Polymers647,76486
Non-polymers143,935202
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, gel filtration profile only shows a single peak
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Reaction centre ... , 3 types, 3 molecules SHK

#1: Protein reaction centre S sub unit


Mass: 21641.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: native protein / Source: (natural) Gemmatimonas groenlandica (bacteria) / References: UniProt: A0A6M4IPJ3
#4: Protein reaction centre Ht su unit


Mass: 7771.843 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: a single helix / Source: (natural) Gemmatimonas groenlandica (bacteria)
#5: Protein reaction centre Hc sub unit


Mass: 19669.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: native protein / Source: (natural) Gemmatimonas groenlandica (bacteria)

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Reaction center protein ... , 2 types, 2 molecules LM

#2: Protein Reaction center protein L chain / Photosynthetic reaction center L subunit


Mass: 30542.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: native protein / Source: (natural) Gemmatimonas groenlandica (bacteria) / References: UniProt: A0A6M4IPC7
#3: Protein Reaction center protein M chain / Photosynthetic reaction center M subunit


Mass: 43396.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: native protein / Source: (natural) Gemmatimonas groenlandica (bacteria) / References: UniProt: A0A6M4ILR2

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Light-harvesting ... , 3 types, 80 molecules AAABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAUAVAWAXBABBBCBDBEBF...

#7: Protein ...
Light-harvesting protein


Mass: 6413.583 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Details: helix / Source: (natural) Gemmatimonas groenlandica (bacteria) / References: UniProt: A0A6M4IQ17
#8: Protein/peptide ...
Light-harvesting protein


Mass: 5183.985 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Details: helix / Source: (natural) Gemmatimonas groenlandica (bacteria) / References: UniProt: A0A6M4IQ93
#9: Protein
Light-harvesting protein


Mass: 7697.123 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Details: helix / Source: (natural) Gemmatimonas groenlandica (bacteria) / References: UniProt: A0A6M4INU2

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Protein / Sugars , 2 types, 49 molecules C

#12: Sugar...
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#6: Protein Photosynthetic reaction center cytochrome c subunit


Mass: 40302.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: native protein / Source: (natural) Gemmatimonas groenlandica (bacteria) / References: UniProt: A0A6M4ITL7

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Non-polymers , 10 types, 192 molecules

#10: Chemical...
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 84 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A


Mass: 889.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H76N4O6
#13: Chemical ChemComp-MQ8 / MENAQUINONE 8 / 2-METHYL-3-(3,7,11,15,19,23,27,31-OCTAMETHYL-DOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL)-[1,4]NAPTHOQUINONE


Mass: 717.116 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C51H72O2
#14: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#15: Chemical ChemComp-CD4 / (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(tetradecanoyloxy)-4,6,10,12,16-pentaoxa-5,11-diphosphatriacont-1-yl tetradecanoate / tetramyristoyl-cardiolipin


Mass: 1241.633 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C65H126O17P2
#16: Chemical ChemComp-CRT / SPIRILLOXANTHIN / RHODOVIOLASCIN


Mass: 596.925 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H60O2
#17: Chemical
ChemComp-PEX / 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE


Mass: 522.632 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C25H49NO8P
#18: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#19: Chemical...
ChemComp-V7N / (2~{E},4~{E},6~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{Z},24~{E},26~{E},28~{E})-23-methanoyl-31-methoxy-2,6,10,14,19,27,31-heptamethyl-dotriaconta-2,4,6,10,12,14,16,18,20,22,24,26,28-tridecaenoic acid


Mass: 610.865 Da / Num. of mol.: 40 / Source method: obtained synthetically / Formula: C41H54O4
#20: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: RC-dLH complex model II from Gemmatimonas groenlandica
Type: COMPLEX / Details: a monomer complex / Entity ID: #7, #9, #8, #6, #4-#5, #2-#3, #1 / Source: NATURAL
Molecular weightValue: 0.65 MDa / Experimental value: NO
Source (natural)Organism: Gemmatimonas groenlandica (bacteria)
Buffer solutionpH: 8 / Details: 10mM Tris-HCl buffer, 20 mM NaCl, pH 8.0
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: in buffer solution with detergent beta-DDM. ~4 mg/ml
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: blot time, 3 sec blot force, 3

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 92 K / Temperature (min): 88 K
Image recordingAverage exposure time: 5.13 sec. / Electron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 23012 / Details: images were collected in AFIS model
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.2.1particle selection
2EPUimage acquisition
4CTFFIND4CTF correction
7Coot0.8.9.2model fitting
9cryoSPARC4.2.1initial Euler assignment
10cryoSPARC4.2.1final Euler assignment
11cryoSPARC4.2.1classification
12cryoSPARC4.2.13D reconstruction
13PHENIX1.20.1-4487model refinement
Image processingDetails: with energy filter slit of 10 eV
CTF correctionDetails: CTF collection was performed within cryosparc / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 935540
Details: cryosparc blob selection first, then model reference selection for final 3d reconstruction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 116858 / Algorithm: BACK PROJECTION / Details: performed in cryosparc / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingB value: 60 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: map to model
Details: Initial model was established with coot. The model was fitted into map using chimera. The refinement was performed y the use of Phenix.
Atomic model buildingSource name: AlphaFold / Type: in silico model

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