7XXF

Structure of photosynthetic LH1-RC super-complex of Rhodopila globiformis


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.24 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

An LH1-RC photocomplex from an extremophilic phototroph provides insight into origins of two photosynthesis proteins.

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

(2022) Commun Biol 5: 1197-1197

  • DOI: https://doi.org/10.1038/s42003-022-04174-2
  • Primary Citation of Related Structures:  
    7XXF

  • PubMed Abstract: 

    Rhodopila globiformis is the most acidophilic of anaerobic purple phototrophs, growing optimally in culture at pH 5. Here we present a cryo-EM structure of the light-harvesting 1-reaction center (LH1-RC) complex from Rhodopila globiformis at 2.24 Å resolution. All purple bacterial cytochrome (Cyt, encoded by the gene pufC) subunit-associated RCs with known structures have their N-termini truncated. By contrast, the Rhodopila globiformis RC contains a full-length tetra-heme Cyt with its N-terminus embedded in the membrane forming an α-helix as the membrane anchor. Comparison of the N-terminal regions of the Cyt with PufX polypeptides widely distributed in Rhodobacter species reveals significant structural similarities, supporting a longstanding hypothesis that PufX is phylogenetically related to the N-terminus of the RC-bound Cyt subunit and that a common ancestor of phototrophic Proteobacteria contained a full-length tetra-heme Cyt subunit that evolved independently through partial deletions of its pufC gene. Eleven copies of a novel γ-like polypeptide were also identified in the bacteriochlorophyll a-containing Rhodopila globiformis LH1 complex; γ-polypeptides have previously been found only in the LH1 of bacteriochlorophyll b-containing species. These features are discussed in relation to their predicted functions of stabilizing the LH1 structure and regulating quinone transport under the warm acidic conditions.


  • Organizational Affiliation

    Graduate School of Medicine, Mie University, Tsu, 514-8507, Japan. ktani@doc.medic.mie-u.ac.jp.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic reaction center cytochrome c subunitA [auth C]344Rhodopila globiformisMutation(s): 0 
UniProt
Find proteins for A0A2S6NEK5 (Rhodopila globiformis)
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UniProt GroupA0A2S6NEK5
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein L chainB [auth L]275Rhodopila globiformisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2S6NEG7 (Rhodopila globiformis)
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UniProt GroupA0A2S6NEG7
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein M chainC [auth M]326Rhodopila globiformisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2S6NEP5 (Rhodopila globiformis)
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UniProt GroupA0A2S6NEP5
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic reaction center H subunitD [auth H]258Rhodopila globiformisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2S6MZS1 (Rhodopila globiformis)
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UniProt GroupA0A2S6MZS1
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting protein61Rhodopila globiformisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2S6NEK3 (Rhodopila globiformis)
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UniProt GroupA0A2S6NEK3
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting protein73Rhodopila globiformisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A2S6NEL9 (Rhodopila globiformis)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting protein LH1 Gamma-like22Rhodopila globiformisMutation(s): 0 
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Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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CC [auth H]
DC [auth A]
EE [auth 6]
HD [auth T]
HE [auth 6]
CC [auth H],
DC [auth A],
EE [auth 6],
HD [auth T],
HE [auth 6],
NE [auth 0],
TD [auth 2],
VB [auth M],
WB [auth M]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
BCL (Subject of Investigation/LOI)
Query on BCL

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BD [auth Q]
BE [auth 5]
CB [auth L]
DD [auth R]
EC [auth A]
BD [auth Q],
BE [auth 5],
CB [auth L],
DD [auth R],
EC [auth A],
ED [auth S],
GC [auth B],
GD [auth T],
GE [auth 6],
IC [auth D],
ID [auth U],
JE [auth 7],
KB [auth L],
KD [auth V],
LC [auth E],
LD [auth W],
LE [auth 8],
MC [auth F],
ME [auth 9],
ND [auth X],
OC [auth G],
OD [auth Y],
OE [auth 0],
PD [auth Z],
QB [auth M],
QC [auth I],
RB [auth M],
RD [auth 1],
SC [auth J],
UC [auth K],
UD [auth 2],
WD [auth 3],
XC [auth N],
YC [auth O],
ZC [auth P],
ZD [auth 4]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH
Query on BPH

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DB [auth L],
SB [auth M]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
U10
Query on U10

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EB [auth L],
HB [auth L],
IB [auth L],
IE [auth 7]
UBIQUINONE-10
C59 H90 O4
ACTIUHUUMQJHFO-UPTCCGCDSA-N
MQ9
Query on MQ9

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TB [auth M]MENAQUINONE-9
C56 H80 O2
WCRXHNIUHQUASO-ABFXHILCSA-N
PGV
Query on PGV

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AB [auth C]
AC [auth H]
AE [auth 5]
BB [auth C]
BC [auth H]
AB [auth C],
AC [auth H],
AE [auth 5],
BB [auth C],
BC [auth H],
CE [auth 5],
DE [auth 5],
FB [auth L],
GB [auth L],
JC [auth D],
LB [auth L],
MB [auth L],
NB [auth L],
NC [auth F],
VC [auth K],
YB [auth M],
ZA [auth C],
ZB [auth M]
(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
PEE
Query on PEE

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XB [auth M]1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
C41 H78 N O8 P
MWRBNPKJOOWZPW-NYVOMTAGSA-N
HEC
Query on HEC

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VA [auth C],
WA [auth C],
XA [auth C],
YA [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
I7D (Subject of Investigation/LOI)
Query on I7D

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AD [auth Q]
CD [auth R]
FC [auth A]
FD [auth T]
FE [auth 6]
AD [auth Q],
CD [auth R],
FC [auth A],
FD [auth T],
FE [auth 6],
HC [auth D],
JD [auth V],
KC [auth E],
KE [auth 8],
MD [auth X],
PC [auth I],
QD [auth 1],
TC [auth K],
UB [auth M],
VD [auth 3],
WC [auth N],
YD [auth 4]
(6~{E},8~{E},10~{E},12~{E},14~{E},16~{E},18~{E},20~{E},22~{E},24~{E},26~{E},28~{E})-2,31-dimethoxy-2,6,10,14,19,23,27,31-octamethyl-dotriaconta-6,8,10,12,14,16,18,20,22,24,26,28-dodecaen-5-one
C42 H60 O3
KSAQIRSWZGLSET-BOIKDPEESA-N
LMT
Query on LMT

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JB [auth L],
OB [auth L],
RC [auth I],
SD [auth 1],
XD [auth 3]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
FE
Query on FE

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PB [auth M]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
FME
Query on FME
AA [auth 1]
CA [auth 3]
E [auth A]
EA [auth 5]
G [auth D]
AA [auth 1],
CA [auth 3],
E [auth A],
EA [auth 5],
G [auth D],
GA [auth 7],
I [auth F],
IA [auth 9],
K [auth I],
M [auth K],
O,
Q,
S,
U,
W,
Y
L-PEPTIDE LINKINGC6 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.24 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION3.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)JapanJP21am0101118
Japan Agency for Medical Research and Development (AMED)JapanJP21am0101116
Japan Society for the Promotion of Science (JSPS)JapanJP16H04174
Japan Society for the Promotion of Science (JSPS)JapanJP18H05153
Japan Society for the Promotion of Science (JSPS)Japan20H05086
Japan Society for the Promotion of Science (JSPS)Japan20H02856

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-16
    Type: Initial release
  • Version 1.1: 2022-11-23
    Changes: Database references