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- PDB-7vrj: STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF Allochromatiu... -

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Basic information

Entry
Database: PDB / ID: 7vrj
TitleSTRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF Allochromatium tepidum
Components
  • (Light-harvesting protein LH1 ...) x 5
  • (Photosynthetic reaction center ...Photosynthetic reaction centre) x 4
KeywordsPHOTOSYNTHESIS / LH1-RC COMPLEX / PURPLE BACTERIA
Function / homology
Function and homology information


BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / CARDIOLIPIN / SPIRILLOXANTHIN / DIACYL GLYCEROL / : / HEME C / MENAQUINONE 8 / Chem-PGV / PALMITIC ACID / Ubiquinone-8
Similarity search - Component
Biological speciesAllochromatium tepidum (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.81 Å
AuthorsTani, K. / Kobayashi, K. / Hosogi, N. / Ji, X.-C. / Nagashima, S. / Nagashima, K.V.P. / Tsukatani, Y. / Kanno, R. / Hall, M. / Yu, L.-J. ...Tani, K. / Kobayashi, K. / Hosogi, N. / Ji, X.-C. / Nagashima, S. / Nagashima, K.V.P. / Tsukatani, Y. / Kanno, R. / Hall, M. / Yu, L.-J. / Ishikawa, I. / Okura, Y. / Madigan, M.T. / Mizoguchi, A. / Humbel, B.M. / Kimura, Y. / Wang-Otomo, Z.-Y.
Funding support Japan, 6items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21am0101118 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101116 Japan
Japan Society for the Promotion of Science (JSPS)JP16H04174 Japan
Japan Society for the Promotion of Science (JSPS)JP18H05153 Japan
Japan Society for the Promotion of Science (JSPS)20H05086 Japan
Japan Society for the Promotion of Science (JSPS)20H02856 Japan
CitationJournal: J Biol Chem / Year: 2022
Title: A Ca-binding motif underlies the unusual properties of certain photosynthetic bacterial core light-harvesting complexes.
Authors: Kazutoshi Tani / Kazumi Kobayashi / Naoki Hosogi / Xuan-Cheng Ji / Sakiko Nagashima / Kenji V P Nagashima / Airi Izumida / Kazuhito Inoue / Yusuke Tsukatani / Ryo Kanno / Malgorzata Hall / ...Authors: Kazutoshi Tani / Kazumi Kobayashi / Naoki Hosogi / Xuan-Cheng Ji / Sakiko Nagashima / Kenji V P Nagashima / Airi Izumida / Kazuhito Inoue / Yusuke Tsukatani / Ryo Kanno / Malgorzata Hall / Long-Jiang Yu / Isamu Ishikawa / Yoshihiro Okura / Michael T Madigan / Akira Mizoguchi / Bruno M Humbel / Yukihiro Kimura / Zheng-Yu Wang-Otomo /
Abstract: The mildly thermophilic purple phototrophic bacterium Allochromatium tepidum provides a unique model for investigating various intermediate phenotypes observed between those of thermophilic and ...The mildly thermophilic purple phototrophic bacterium Allochromatium tepidum provides a unique model for investigating various intermediate phenotypes observed between those of thermophilic and mesophilic counterparts. The core light-harvesting (LH1) complex from A. tepidum exhibits an absorption maximum at 890 nm and mildly enhanced thermostability, both of which are Ca-dependent. However, it is unknown what structural determinants might contribute to these properties. Here, we present a cryo-EM structure of the reaction center-associated LH1 complex at 2.81 Å resolution, in which we identify multiple pigment-binding α- and β-polypeptides within an LH1 ring. Of the 16 α-polypeptides, we show that six (α1) bind Ca along with β1- or β3-polypeptides to form the Ca-binding sites. This structure differs from that of fully Ca-bound LH1 from Thermochromatium tepidum, enabling determination of the minimum structural requirements for Ca-binding. We also identified three amino acids (Trp44, Asp47, and Ile49) in the C-terminal region of the A. tepidum α1-polypeptide that ligate each Ca ion, forming a Ca-binding WxxDxI motif that is conserved in all Ca-bound LH1 α-polypeptides from other species with reported structures. The partial Ca-bound structure further explains the unusual phenotypic properties observed for this bacterium in terms of its Ca-requirements for thermostability, spectroscopy, and phototrophic growth, and supports the hypothesis that A. tepidum may represent a "transitional" species between mesophilic and thermophilic purple sulfur bacteria. The characteristic arrangement of multiple αβ-polypeptides also suggests a mechanism of molecular recognition in the expression and/or assembly of the LH1 complex that could be regulated through interactions with reaction center subunits.
History
DepositionOct 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2022Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Photosynthetic reaction center cytochrome c subunit
L: Photosynthetic reaction center L subunit
M: Photosynthetic reaction center M subunit
H: Photosynthetic reaction center H subunit
A: Light-harvesting protein LH1 alpha2
B: Light-harvesting protein LH1 beta1
D: Light-harvesting protein LH1 alpha1
E: Light-harvesting protein LH1 beta3
F: Light-harvesting protein LH1 alpha1
G: Light-harvesting protein LH1 beta3
I: Light-harvesting protein LH1 alpha2
J: Light-harvesting protein LH1 beta1
K: Light-harvesting protein LH1 alpha2
N: Light-harvesting protein LH1 beta1
O: Light-harvesting protein LH1 alpha2
P: Light-harvesting protein LH1 beta1
Q: Light-harvesting protein LH1 alpha2
R: Light-harvesting protein LH1 beta1
S: Light-harvesting protein LH1 alpha1
T: Light-harvesting protein LH1 beta3
U: Light-harvesting protein LH1 alpha1
V: Light-harvesting protein LH1 beta3
W: Light-harvesting protein LH1 alpha1
X: Light-harvesting protein LH1 beta3
Y: Light-harvesting protein LH1 alpha1
Z: Light-harvesting protein LH1 beta3
1: Light-harvesting protein LH1 alpha2
2: Light-harvesting protein LH1 beta1
3: Light-harvesting protein LH1 alpha3
4: Light-harvesting protein LH1 beta1
5: Light-harvesting protein LH1 alpha2
6: Light-harvesting protein LH1 beta1
7: Light-harvesting protein LH1 alpha2
8: Light-harvesting protein LH1 beta1
9: Light-harvesting protein LH1 alpha2
0: Light-harvesting protein LH1 beta1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)404,879150
Polymers322,49736
Non-polymers82,382114
Water86548
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Photosynthetic reaction center ... , 4 types, 4 molecules CLMH

#1: Protein Photosynthetic reaction center cytochrome c subunit


Mass: 43659.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Allochromatium tepidum (bacteria)
#2: Protein Photosynthetic reaction center L subunit


Mass: 31098.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Allochromatium tepidum (bacteria)
#3: Protein Photosynthetic reaction center M subunit


Mass: 36292.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Allochromatium tepidum (bacteria)
#4: Protein Photosynthetic reaction center H subunit


Mass: 28196.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Allochromatium tepidum (bacteria)

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Light-harvesting protein LH1 ... , 5 types, 32 molecules AIKOQ1579BJNPR24680DFSUWYEGTVXZ3

#5: Protein/peptide
Light-harvesting protein LH1 alpha2


Mass: 5136.131 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Allochromatium tepidum (bacteria)
#6: Protein/peptide
Light-harvesting protein LH1 beta1


Mass: 5269.103 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Allochromatium tepidum (bacteria)
#7: Protein
Light-harvesting protein LH1 alpha1


Mass: 7330.739 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Allochromatium tepidum (bacteria)
#8: Protein/peptide
Light-harvesting protein LH1 beta3


Mass: 5504.446 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Allochromatium tepidum (bacteria)
#9: Protein Light-harvesting protein LH1 alpha3


Mass: 7323.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Allochromatium tepidum (bacteria)

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Sugars , 1 types, 18 molecules

#22: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 15 types, 144 molecules

#10: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#11: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#12: Chemical ChemComp-DGA / DIACYL GLYCEROL / Diglyceride


Mass: 625.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H76O5
#13: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#14: Chemical
ChemComp-PGV / (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / PHOSPHATIDYLGLYCEROL / 2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL / Phosphatidylglycerol


Mass: 749.007 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#15: Chemical...
ChemComp-BCL / BACTERIOCHLOROPHYLL A / Bacteriochlorophyll


Mass: 911.504 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#16: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A / Pheophytin


Mass: 889.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H76N4O6
#17: Chemical ChemComp-UQ8 / Ubiquinone-8 / 2,3-dimethoxy-5-methyl-6-[(6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-oc taen-1-yl]cyclohexa-2,5-diene-1,4-dione


Mass: 727.109 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C49H74O4
#18: Chemical
ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL / Cardiolipin


Mass: 1464.043 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#19: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#20: 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 / Vitamin K2


Mass: 717.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C51H72O2
#21: Chemical
ChemComp-CRT / SPIRILLOXANTHIN / RHODOVIOLASCIN


Mass: 596.925 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C42H60O2
#23: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#24: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide


Mass: 229.402 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#25: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: Photosynthetic LH1-RC complex from the purple phototrophic bacterium Allochromatium tepidum
Type: COMPLEX / Entity ID: #1-#9 / Source: NATURAL
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Allochromatium tepidum (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse.
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Alignment procedure: BASIC
Specimen holderCryogen: NITROGEN / Specimen holder model: JEOL
Image recordingAverage exposure time: 1.5 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategory
2JADAS4.2.0image acquisition
4CTFFINDCTF correction
7UCSF Chimeramodel fitting
9RELION3.1initial Euler assignment
10RELION3.1final Euler assignment
11RELION3.1classification
12RELION3.13D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 309706
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 156992 / Symmetry type: POINT
Atomic model buildingB value: 62 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient
Atomic model buildingPDB-ID: 5Y5S

5y5s

Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00627271
ELECTRON MICROSCOPYf_angle_d2.76337460
ELECTRON MICROSCOPYf_dihedral_angle_d16.88110705
ELECTRON MICROSCOPYf_chiral_restr0.0853821
ELECTRON MICROSCOPYf_plane_restr0.0054429

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