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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: To Be Published
Title: Cryo EM structure of RC-dLH complex model II from Gemmatimonas groenlandica
Authors: Gardiner, A.T. / Jing, Y. / Bina, D. / Mujakic, I. / Gardian, Z. / Kaftan, D. / Joosten, M. / Jakobi, A. / Castro-Hartmann, P. / Qian, P. / Koblizek, M.
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
Revision 1.0Dec 3, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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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