EMDB-51788: Cryo EM structure of RC-dLH complex model II from Gemmatimonas gr...

Basic information

Entry

Database: EMDB / ID: EMD-51788

• Title: Cryo EM structure of RC-dLH complex model II from Gemmatimonas groenlandica

Sample

• Complex: RC-dLH complex model II from Gemmatimonas groenlandica
  • Protein or peptide: x 9 types
• Ligand: x 11 types

• Keywords: photosynthetic bacteria / photosynthesis / reaction cennter light harvesting complex / RC-LH1 / RC-dLH / cryo-EM / Gemmatimonas groenlandica

Function / homology

Function:

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

Domain/homology:

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.

Component:

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

• Biological species: Gemmatimonas groenlandica (bacteria)
• Method: single particle reconstruction / cryo EM / Resolution: 2.3 Å
• Authors: Gardiner AT / 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, 1 items

Organization	Grant number	Country
Czech Academy of Sciences	19-28778X	Czech Republic

• Citation: Journal: 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. () 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

Deposition	Oct 10, 2024	-
Header (metadata) release	Dec 3, 2025	-
Map release	Dec 3, 2025	-
Update	Dec 17, 2025	-
Current status	Dec 17, 2025	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_51788.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 0.732 Å

Density

Contour Level	By AUTHOR: 0.0687
Minimum - Maximum	-0.22641595 - 0.54656935
Average (Standard dev.)	0.0005516693 (±0.012068127)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 600 600 600 Spacing 600 600 600
Cell	A=B=C: 439.19998 Å α=β=γ: 90.0 °

Supplemental data

Half map: #1

• File: emd_51788_half_map_1.map

Half map: #2

• File: emd_51788_half_map_2.map

Sample components

Entire : RC-dLH complex model II from Gemmatimonas groenlandica

• Entire: Name: RC-dLH complex model II from Gemmatimonas groenlandica

Components

• Complex: RC-dLH complex model II from Gemmatimonas groenlandica
  • Protein or peptide: Light-harvesting protein
  • Protein or peptide: Light-harvesting protein
  • Protein or peptide: Light-harvesting protein
  • Protein or peptide: Photosynthetic reaction center cytochrome c subunit
  • Protein or peptide: reaction centre Ht su unit
  • Protein or peptide: reaction centre Hc sub unit
  • Protein or peptide: Reaction center protein L chain
  • Protein or peptide: Reaction center protein M chain
  • Protein or peptide: reaction centre S sub unit
• Ligand: BACTERIOCHLOROPHYLL A
• Ligand: BACTERIOPHEOPHYTIN A
• Ligand: DODECYL-BETA-D-MALTOSIDE
• Ligand: MENAQUINONE 8
• Ligand: FE (III) ION
• Ligand: (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
• Ligand: SPIRILLOXANTHIN
• Ligand: 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE
• Ligand: HEME C
• Ligand: (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
• Ligand: water

Supramolecule #1: RC-dLH complex model II from Gemmatimonas groenlandica

• Supramolecule: Name: RC-dLH complex model II from Gemmatimonas groenlandica; type: complex / ID: 1 / Parent: 0 / Macromolecule list: #7, #9, #8, #6, #4-#5, #2-#3, #1 / Details: a monomer complex
• Source (natural): Organism: Gemmatimonas groenlandica (bacteria)
• Molecular weight: Theoretical: 650 KDa

Macromolecule #1: reaction centre S sub unit

• Macromolecule: Name: reaction centre S sub unit / type: protein_or_peptide / ID: 1 / Details: native protein / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Gemmatimonas groenlandica (bacteria)
• Molecular weight: Theoretical: 21.641564 KDa

Sequence

String:

MMLRQDRPRV LSRVSTVVGI GALVAVAMAA RSQGGQQATP PSAPQPPVAA PSAAPAATDS TMQDSTQRAD TTAKADSMLA MPDSMMMQH TAAAPAPQAS AMWPVDPVTG QTIINGEPVV GRVFIMQKTD GTVKLGKWQA QYDGEPTAPE AANVGSSYTV P APEHTRRM RGIMIQSTLW SIDGKRSARE RRHYRPQTTG AALGQQ

UniProtKB: Uncharacterized protein

Macromolecule #2: Reaction center protein L chain

• Macromolecule: Name: Reaction center protein L chain / type: protein_or_peptide / ID: 2 / Details: native protein / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Gemmatimonas groenlandica (bacteria)
• Molecular weight: Theoretical: 30.54274 KDa

Sequence

String:

MAMLSFEKKY RVRGGTLIGG DLFDFWFGPF YVGFFGVTTI FFVTLGTLLC VWGAAMGPTW NLWQISIAPP DLKYGLGLAP LREGGLWQI ITLCALGAFG SWALRQAEIS RKLGMGMHIP WAYGGAVLAY ATLVVIRPML LGAWGHGFPY GIFSHLDWVS N VGYQYLHF HYNPAHMIAV TFFFTNCLAL AMHGSLILSV TNPKKGTPVG TSETENVFFR DLLGYSIGAI GIHRLGLFLA VG AAVWSAI CIVISGPFWT KGWPEWWNWW LNLPIWR

UniProtKB: Reaction center protein L chain

Macromolecule #3: Reaction center protein M chain

• Macromolecule: Name: Reaction center protein M chain / type: protein_or_peptide / ID: 3 / Details: native protein / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Gemmatimonas groenlandica (bacteria)
• Molecular weight: Theoretical: 43.396742 KDa

Sequence

String:

MLEYQNLFTR VQVRTVPEAG IEIDESTGTR YGTGTFSYLA GKFGDAQIGP IYLGWAGVLS LIFGFMAFEI IGLNMWASVG WDPVEFIRQ LPWLALEPPP PQYGLRVPPL AQGGWYLMAG FFLTISILLW WVRVYRRARA LNMGTHLPWA FASAIFLYST F FFQPLLVG SWSEMVPFGI FPHLDWTSAF SIRYGNLYYN PFHALSIAFL YGSAVLFAMH GATILAVARL GGEREIEQIT DR GTAAERS MLFWRWTMGF NATMESIHRW SWWFAVLTTF SGGIGILLTG TVVDNWYLWG VKHGLVAPYP AQNTLTEEQQ QLL RGRYQG TAPDSFPSYV APQPAMMLDS TAMMAPADSM KADSTKVDSA AAPSAPAAAA PPPAKPPAPS VGGKTP

UniProtKB: Reaction center protein M chain

Macromolecule #4: reaction centre Ht su unit

• Macromolecule: Name: reaction centre Ht su unit / type: protein_or_peptide / ID: 4 / Details: a single helix / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Gemmatimonas groenlandica (bacteria)
• Molecular weight: Theoretical: 7.771843 KDa

Sequence

String:

MQYIDGAQIA LYAFWLFFFG LIIYIRREDK REGYPLESPQ GPREGWPAMP EKKTYIHRPT SGEGTH

Macromolecule #5: reaction centre Hc sub unit

• Macromolecule: Name: reaction centre Hc sub unit / type: protein_or_peptide / ID: 5 / Details: native protein / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Gemmatimonas groenlandica (bacteria)
• Molecular weight: Theoretical: 19.669318 KDa

Sequence

String:

MSDIKAVPAD SYNGSALIPT GDPMIDGVGP SSWANRSDTP DMTFHNTAKI VPMRLDPTYS IAKGDPDPRG LPVVAADKQV AGTVIELWV NRAEPQVTYY EVQLTGSERR VMLPAGFVQW PNFGLWGNDK LLVKAITAAQ FANVPALKRD DQITLLEEDM V CAYYAGGH LYAMAERSEP II

Macromolecule #6: Photosynthetic reaction center cytochrome c subunit

• Macromolecule: Name: Photosynthetic reaction center cytochrome c subunit / type: protein_or_peptide / ID: 6 / Details: native protein / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Gemmatimonas groenlandica (bacteria)
• Molecular weight: Theoretical: 40.302758 KDa

Sequence

String:

MSILRRSIGL VAPLALLSLG ACGDTATDSV QVGYRGTGME QNYDHGDLKK QFAQVKIPTP LPPAGESPPG PLPWQNVQVL NDISVGEFN RTMVAMSTWV AGTGNCAYCH NIANLAADTL PNGKPLYTKL VARRMLQMTR QINGQYSQHV KNTGVTCYTC H MGKPLPNG LWFYSSQTDY LRHYLDRDGA RVVTRDVAPS NANRSSVKQT EWTYALMISQ SRSLGVNCTY CHNTRQFASW KE APPARVT AYHGILMLRD VNQNYLSPLQ PVYPSVRLGT QGDAPKAQCV TCHNGNYKPL YGAQMVKDYP ALWGRADWNG VPF QGLSPK ADTTSAGAAP AAPAAAAPVP AVKRSSARTV PAPTVIGGAV GSPNTPK

UniProtKB: Photosynthetic reaction center cytochrome c subunit

Macromolecule #7: Light-harvesting protein

• Macromolecule: Name: Light-harvesting protein / type: protein_or_peptide / ID: 7 / Details: helix / Number of copies: 24 / Enantiomer: LEVO
• Source (natural): Organism: Gemmatimonas groenlandica (bacteria)
• Molecular weight: Theoretical: 6.413583 KDa

Sequence

String:

MHRIWQGMDP QIIMSGLGFF LAGLALIIHM WAYSITGWPK YKKAQYNAQT PPTAVR

UniProtKB: Light-harvesting protein

Macromolecule #8: Light-harvesting protein

• Macromolecule: Name: Light-harvesting protein / type: protein_or_peptide / ID: 8 / Details: helix / Number of copies: 40 / Enantiomer: LEVO
• Source (natural): Organism: Gemmatimonas groenlandica (bacteria)
• Molecular weight: Theoretical: 5.183985 KDa

Sequence

String:

MMEKGGMTED EARRFHGYFV TGTLGYIIVA AVAHFLAWQW RPWF

UniProtKB: Light-harvesting protein

Macromolecule #9: Light-harvesting protein

• Macromolecule: Name: Light-harvesting protein / type: protein_or_peptide / ID: 9 / Details: helix / Number of copies: 16 / Enantiomer: LEVO
• Source (natural): Organism: Gemmatimonas groenlandica (bacteria)
• Molecular weight: Theoretical: 7.697123 KDa

Sequence

String:

MHRIWLMFDP RRVMVAMVGF LAVLALVIHF ILLSSQRYSW IENGTLSAAQ APVGASAPAA AAEMSPLPPG R

UniProtKB: Light-harvesting protein

Macromolecule #10: BACTERIOCHLOROPHYLL A

• Macromolecule: Name: BACTERIOCHLOROPHYLL A / type: ligand / ID: 10 / Number of copies: 84 / Formula: BCL
• Molecular weight: Theoretical: 911.504 Da

Chemical component information

ChemComp-BCL:
BACTERIOCHLOROPHYLL A

Macromolecule #11: BACTERIOPHEOPHYTIN A

• Macromolecule: Name: BACTERIOPHEOPHYTIN A / type: ligand / ID: 11 / Number of copies: 2 / Formula: BPH
• Molecular weight: Theoretical: 889.215 Da

Chemical component information

ChemComp-BPH:
BACTERIOPHEOPHYTIN A

Macromolecule #12: DODECYL-BETA-D-MALTOSIDE

• Macromolecule: Name: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 12 / Number of copies: 48 / Formula: LMT
• Molecular weight: Theoretical: 510.615 Da

Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

Macromolecule #13: MENAQUINONE 8

• Macromolecule: Name: MENAQUINONE 8 / type: ligand / ID: 13 / Number of copies: 3 / Formula: MQ8
• Molecular weight: Theoretical: 717.116 Da

Chemical component information

ChemComp-MQ8:
MENAQUINONE 8

Macromolecule #14: FE (III) ION

• Macromolecule: Name: FE (III) ION / type: ligand / ID: 14 / Number of copies: 1 / Formula: FE
• Molecular weight: Theoretical: 55.845 Da

Macromolecule #15: (2R,5R,11R,14R)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-2,14-bis(te...

• Macromolecule: Name: (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; type: ligand / ID: 15 / Number of copies: 2 / Formula: CD4
• Molecular weight: Theoretical: 1.241633 KDa

Chemical component information

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

Macromolecule #16: SPIRILLOXANTHIN

• Macromolecule: Name: SPIRILLOXANTHIN / type: ligand / ID: 16 / Number of copies: 1 / Formula: CRT
• Molecular weight: Theoretical: 596.925 Da

Chemical component information

ChemComp-CRT:
SPIRILLOXANTHIN

Macromolecule #17: 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE

• Macromolecule: Name: 1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / type: ligand / ID: 17 / Number of copies: 17 / Formula: PEX
• Molecular weight: Theoretical: 522.632 Da

Chemical component information

ChemComp-PEX:
1,2-DIDECANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE

Macromolecule #18: HEME C

• Macromolecule: Name: HEME C / type: ligand / ID: 18 / Number of copies: 4 / Formula: HEC
• Molecular weight: Theoretical: 618.503 Da

Chemical component information

ChemComp-HEC:
HEME C

Macromolecule #19: (2~{E},4~{E},6~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{...

• Macromolecule: Name: (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; type: ligand / ID: 19 / Number of copies: 40 / Formula: V7N
• Molecular weight: Theoretical: 610.865 Da

Chemical component information

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

Macromolecule #20: water

• Macromolecule: Name: water / type: ligand / ID: 20 / Number of copies: 38 / Formula: HOH
• Molecular weight: Theoretical: 18.015 Da

Chemical component information

ChemComp-HOH:
WATER

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Buffer: pH: 8 / Details: 10mM Tris-HCl buffer, 20 mM NaCl, pH 8.0
• Grid: Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
• Vitrification: Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK III / Details: blot time, 3 sec blot force, 3.
• Details: in buffer solution with detergent beta-DDM. ~4 mg/ml

Electron microscopy

• Microscope: TFS KRIOS
• Temperature: Min: 88.0 K / Max: 92.0 K
• Specialist optics: Energy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV
• Image recording: Film or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 23012 / Average exposure time: 5.13 sec. / Average electron dose: 60.0 e/Ų / Details: images were collected in AFIS model
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000
• Sample stage: Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Details: with energy filter slit of 10 eV
• Particle selection: Number selected: 935540 ; Details: cryosparc blob selection first, then model reference selection for final 3d reconstruction
• CTF correction: Software - Name: CTFFIND (ver. 4.0) / Details: CTF collection was performed within cryosparc / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
• Startup model: Type of model: INSILICO MODEL / In silico model: cryosparc ab-init; Details: a subset of randomly picked-up particles were used for initial model generation.
• Final reconstruction: Number classes used: 1 / Applied symmetry - Point group: C₁ (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Details: performed in cryosparc / Number images used: 116858
• Initial angle assignment: Type: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.2.1) / Details: cryosparc Ab-init
• Final angle assignment: Type: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 4.2.1)
• Final 3D classification: Number classes: 2 / Avg.num./class: 120000 / Software - Name: cryoSPARC (ver. 4.2.1); Details: This complex has two confirmations. 2 classs 3D classification was used for the final separation of the two confirmation.

Atomic model buiding 1

• Initial model: Chain - Source name: AlphaFold / Chain - Initial model type: in silico 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.
• Refinement: Space: REAL / Protocol: RIGID BODY FIT / Overall B value: 60 / Target criteria: map to model

Output model

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