7VY3 | pdb_00007vy3

STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF RHODOBACTER SPHAEROIDES LACKING PROTEIN-U

• PDB DOI: https://doi.org/10.2210/pdb7VY3/pdb
• EM Map EMD-32193: EMDB EMDataResource

• Classification: PHOTOSYNTHESIS
• Organism(s): Cereibacter sphaeroides f. sp. denitrificans
• Mutation(s): No 


• Deposited: 2021-11-13 Released: 2022-04-27 
• Deposition Author(s): Tani, K., Kanno, R., Kawamura, S., Kikuchi, R., Nagashima, K.V.P., Hall, M., Takahashi, A., Yu, L.-J., Kimura, Y., Madigan, M.T., Mizoguchi, A., Humbel, B.M., Wang-Otomo, Z.-Y.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.63 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Asymmetric structure of the native Rhodobacter sphaeroides dimeric LH1-RC complex.

Tani, K., Kanno, R., Kikuchi, R., Kawamura, S., Nagashima, K.V.P., Hall, M., Takahashi, A., Yu, L.J., Kimura, Y., Madigan, M.T., Mizoguchi, A., Humbel, B.M., Wang-Otomo, Z.Y.

(2022) Nat Commun 13: 1904-1904

• PubMed: 35393413 
• DOI: https://doi.org/10.1038/s41467-022-29453-8
• Primary Citation Related Structures: 
  7VY2, 7VY3


• PubMed Abstract: 
  

  Rhodobacter sphaeroides is a model organism in bacterial photosynthesis, and its light-harvesting-reaction center (LH1-RC) complex contains both dimeric and monomeric forms. Here we present cryo-EM structures of the native LH1-RC dimer and an LH1-RC monomer lacking protein-U (ΔU). The native dimer reveals several asymmetric features including the arrangement of its two monomeric components, the structural integrity of protein-U, the overall organization of LH1, and rigidities of the proteins and pigments. PufX plays a critical role in connecting the two monomers in a dimer, with one PufX interacting at its N-terminus with another PufX and an LH1 β-polypeptide in the other monomer. One protein-U was only partially resolved in the dimeric structure, signaling different degrees of disorder in the two monomers. The ΔU LH1-RC monomer was half-moon-shaped and contained 11 α- and 10 β-polypeptides, indicating a critical role for protein-U in controlling the number of αβ-subunits required for dimer assembly and stabilization. These features are discussed in relation to membrane topology and an assembly model proposed for the native dimeric complex.

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Organizational Affiliation: 
• Graduate School of Medicine, Mie University, Tsu, 514-8507, Japan. [e-mail].
Imaging Section, Research Support Division, Okinawa Institute of Science and Technology Graduate University (OIST), 1919-1, Tancha, Onna-son, Kunigami-gun, Okinawa, 904-0495, Japan.
Faculty of Science, Ibaraki University, Mito, 310-8512, Japan.
Research Institute for Integrated Science, Kanagawa University, 2946 Tsuchiya, Hiratsuka, Kanagawa, 259-1293, Japan.
Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe, 657-8501, Japan.
School of Biological Sciences, Department of Microbiology, Southern Illinois University, Carbondale, IL, 62901, USA.
Graduate School of Medicine, Mie University, Tsu, 514-8507, Japan.
Faculty of Science, Ibaraki University, Mito, 310-8512, Japan. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 25-mer - A10B9C1D1E1F1G1H1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 25-mer - A11B9C2D1E1F1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 288.91 kDa 
• Atom Count: 18,831 
• Modeled Residue Count: 1,846 
• Deposited Residue Count: 2,003 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic reaction center L subunit	A [auth L]	281	Cereibacter sphaeroides f. sp. denitrificans	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Reaction center protein M chain	B [auth M]	307	Cereibacter sphaeroides f. sp. denitrificans	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosynthetic reaction center subunit H	C [auth H]	260	Cereibacter sphaeroides f. sp. denitrificans	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Antenna pigment protein alpha chain	D [auth A], F [auth D], H [auth F], J [auth I], L [auth K], N [auth O], P [auth Q], R [auth S], T [auth V], V [auth Y], X [auth 1]	54	Cereibacter sphaeroides f. sp. denitrificans	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Antenna pigment protein beta chain	E [auth B], G [auth E], I [auth G], K [auth J], M [auth N], O [auth P], Q [auth R], S [auth T], U [auth W], W [auth Z]	48	Cereibacter sphaeroides f. sp. denitrificans	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
PufX	Y [auth X]	81	Cereibacter sphaeroides f. sp. denitrificans	Mutation(s): 0

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CDL	PA [auth M], YA [auth H], ZC [auth Y]	CARDIOLIPIN C81 H156 O17 P2 XVTUQDWPJJBEHJ-KZCWQMDCSA-L
BCL (Subject of Investigation/LOI)	AD [auth Y], BB [auth A], BC [auth K], DD [auth Z], EB [auth B], ED [auth 1], FC [auth N], GB [auth D], GC [auth O], HA [auth L], IA [auth M], IC [auth P], JA [auth M], LB [auth E], MB [auth F], NC [auth Q], PC [auth Q], QC [auth S], SB [auth G], TC [auth T], UC [auth V], WB [auth I], XC [auth W], YB [auth J], Z [auth L]	BACTERIOCHLOROPHYLL A C55 H74 Mg N4 O6 DSJXIQQMORJERS-AGGZHOMASA-M
BPH	AA [auth L], KA [auth M]	BACTERIOPHEOPHYTIN A C55 H76 N4 O6 KWOZSBGNAHVCKG-SZQBJALDSA-N
U10	BA [auth L], CA [auth L], KB [auth D], RA [auth M]	UBIQUINONE-10 C59 H90 O4 ACTIUHUUMQJHFO-UPTCCGCDSA-N
PGV	BD [auth Y], DA [auth L], DC [auth K], MC [auth Q], NB [auth F], OB [auth F], QA [auth M], SA [auth H]	(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE C40 H77 O10 P ADYWCMPUNIVOEA-GPJPVTGXSA-N
PTY	PB [auth F], XA [auth H]	PHOSPHATIDYLETHANOLAMINE C40 H80 N O8 P NJGIRBISCGPRPF-KXQOOQHDSA-N
SPO	CB [auth B], CC [auth K], CD [auth Z], EC [auth K], FB [auth B], HB [auth D], HC [auth O], JB [auth D], JC [auth P], MA [auth M], OC [auth Q], QB [auth F], RC [auth S], SC [auth S], TB [auth G], UB [auth G], VC [auth V], WC [auth V], ZB [auth J]	SPHEROIDENE C41 H60 O FJOCMTHZSURUFA-KXCOHNEYSA-N
LMT	AB [auth A], AC [auth K], DB [auth B], FA [auth L], GA [auth L], IB [auth D], KC [auth Q], LC [auth Q], NA [auth M], OA [auth M], RB [auth F], UA [auth H], VA [auth H], VB [auth I], WA [auth H], XB [auth I], ZA [auth A]	DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N
LDA	EA [auth L], FD [auth X], TA [auth H], YC [auth Y]	LAURYL DIMETHYLAMINE-N-OXIDE C14 H31 N O SYELZBGXAIXKHU-UHFFFAOYSA-N
FE	LA [auth M]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FME	D [auth A], F [auth D], H [auth F], J [auth I], L [auth K], N [auth O], P [auth Q], R [auth S], T [auth V], V [auth Y], X [auth 1]	L-PEPTIDE LINKING	C6 H11 N O3 S		MET

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.63 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	3.1

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-04-27 
Deposition Author(s): Tani, K., Kanno, R., Kawamura, S., Kikuchi, R., Nagashima, K.V.P., Hall, M., Takahashi, A., Yu, L.-J., Kimura, Y., Madigan, M.T., Mizoguchi, A., Humbel, B.M., Wang-Otomo, Z.-Y.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP21am0101118
Japan Agency for Medical Research and Development (AMED)	Japan	JP21am0101116
Japan Society for the Promotion of Science (JSPS)	Japan	JP16H04174
Japan Society for the Promotion of Science (JSPS)	Japan	JP18H05153
Japan Society for the Promotion of Science (JSPS)	Japan	20H05086
Japan Society for the Promotion of Science (JSPS)	Japan	20H02856

Revision History  

• Version 1.0: 2022-04-27
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Data collection, Refinement description, Structure summary