8Z82 | pdb_00008z82

Photosynthetic LH1-RC-HiPIP complex from the purple bacterium Halorhodospira halophila


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 2.0 of the entry. See complete history

Literature

A Native LH1-RC-HiPIP Supercomplex from an Extremophilic Phototroph.

Tani, K.Kanno, R.Nagashima, K.V.P.Kawakami, M.Hiwatashi, N.Nakata, K.Nagashima, S.Inoue, K.Takaichi, S.Purba, E.R.Hall, M.Yu, L.J.Madigan, M.T.Mizoguchi, A.Humbel, B.M.Kimura, Y.Wang-Otomo, Z.Y.

(2025) Commun Biol 8: 42-42

  • DOI: https://doi.org/10.1038/s42003-024-07421-w
  • Primary Citation Related Structures: 
    8Z82, 8Z83

  • PubMed Abstract: 

    Halorhodospira (Hlr.) halophila strain BN9622 is an extremely halophilic and alkaliphilic purple phototrophic bacterium and has been widely used as a model for exploring the osmoadaptive and photosynthetic strategies employed by phototrophic extreme halophiles that enable them to thrive in hypersaline environments. Here we present the cryo-EM structures of (1) a unique native Hlr. halophila triple-complex formed from light-harvesting (LH1), the reaction center (RC), and high-potential iron-sulfur protein (HiPIP) at 2.44 Å resolution, and (2) a HiPIP-free LH1-RC complex at 2.64 Å resolution. Differing from the LH1 in the Hlr. halophila LH1-LH2 co-complex where LH1 encircles LH2, the RC-associated LH1 complex consists of 16 (rather than 18) αβ-subunits circularly surrounding the RC. These distinct forms of LH1 indicate that the number of subunits in a Hlr. halophila LH1 complex is flexible and its size is a function of the photocomplex it encircles. Like LH1 in the LH1-LH2 co-complex, the RC-associated LH1 complex also contained two forms of αβ-polypeptides and both dimeric and monomeric molecules of bacteriochlorophyll a. The majority of the isolated Hlr. halophila LH1-RC complexes contained the electron donor HiPIP bound to the surface of the RC cytochrome subunit near the heme-1 group. The bound HiPIP consisted of an N-terminal functional domain and a long C-terminal extension firmly attached to the cytochrome subunit. Despite overall highly negative surface-charge distributions for both the cytochrome subunit and HiPIP, the interface between the two proteins was relatively uncharged and neutral, forming a pathway for electron tunneling. The structure of the Hlr. halophila LH1-RC-HiPIP complex provides insights into the mechanism of light energy acquisition coupled with a long-distance electron donating process toward the charge separation site in a multi-extremophilic phototroph.


  • Organizational Affiliation
    • Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, Japan. ktani@ccs.tsukuba.ac.jp.

Macromolecule Content 

  • Total Structure Weight: 506.97 kDa 
  • Atom Count: 29,045 
  • Modeled Residue Count: 2,777 
  • Deposited Residue Count: 3,621 
  • Unique protein chains: 9

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosynthetic reaction center cytochrome c subunitA [auth C]362Halorhodospira halophilaMutation(s): 0 
UniProt
Find proteins for A1WXF5 (Halorhodospira halophila (strain DSM 244 / SL1))
Explore A1WXF5 
Go to UniProtKB:  A1WXF5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1WXF5
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Reaction center protein L chainB [auth L]276Halorhodospira halophilaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A1WXF7 (Halorhodospira halophila (strain DSM 244 / SL1))
Explore A1WXF7 
Go to UniProtKB:  A1WXF7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1WXF7
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Reaction center protein M chainC [auth M]323Halorhodospira halophilaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A1WXF6 (Halorhodospira halophila (strain DSM 244 / SL1))
Explore A1WXF6 
Go to UniProtKB:  A1WXF6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1WXF6
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosynthetic reaction centre, H-chainD [auth H]278Halorhodospira halophilaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A1WXI3 (Halorhodospira halophila (strain DSM 244 / SL1))
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Go to UniProtKB:  A1WXI3
Entity Groups
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UniProt GroupA1WXI3
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Antenna complex, alpha/beta subunit64Halorhodospira halophilaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A1WWW5 (Halorhodospira halophila (strain DSM 244 / SL1))
Explore A1WWW5 
Go to UniProtKB:  A1WWW5
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1WWW5
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Antenna complex, alpha/beta subunit75Halorhodospira halophilaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A1WWW6 (Halorhodospira halophila (strain DSM 244 / SL1))
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Go to UniProtKB:  A1WWW6
Entity Groups
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UniProt GroupA1WWW6
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Antenna complex, alpha/beta subunit67Halorhodospira halophilaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A1WXF8 (Halorhodospira halophila (strain DSM 244 / SL1))
Explore A1WXF8 
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Entity Groups
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UniProt GroupA1WXF8
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Antenna complex, alpha/beta subunit74Halorhodospira halophilaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A1WXF9 (Halorhodospira halophila (strain DSM 244 / SL1))
Explore A1WXF9 
Go to UniProtKB:  A1WXF9
Entity Groups
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UniProt GroupA1WXF9
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
High-potential iron-sulfur proteinKA [auth a]142Halorhodospira halophilaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A1WXH6 (Halorhodospira halophila (strain DSM 244 / SL1))
Explore A1WXH6 
Go to UniProtKB:  A1WXH6
Entity Groups
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UniProt GroupA1WXH6
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Reference Sequence

Small Molecules

Ligands 14 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL

Query on CDL



Download:Ideal Coordinates CCD File
GB [auth M]
LB [auth M]
MB [auth M]
NB [auth M]
QB [auth H]
GB [auth M],
LB [auth M],
MB [auth M],
NB [auth M],
QB [auth H],
RD [auth U],
SB [auth H],
SD [auth U],
ZC [auth O]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
BCL
(Subject of Investigation/LOI)

Query on BCL



Download:Ideal Coordinates CCD File
AE [auth X]
BD [auth O]
CC [auth D]
CD [auth O]
CE [auth Y]
AE [auth X],
BD [auth O],
CC [auth D],
CD [auth O],
CE [auth Y],
DB [auth L],
DC [auth D],
DD [auth P],
DE [auth Y],
DF [auth 7],
EB [auth L],
EC [auth E],
FF [auth 8],
GE [auth Z],
HB [auth M],
HD [auth Q],
HF [auth 9],
IC [auth F],
IF [auth 9],
JD [auth R],
KE [auth 1],
KF [auth 0],
LC [auth G],
LE [auth 1],
MD [auth S],
ME [auth 2],
ND [auth S],
OD [auth T],
PC [auth I],
QC [auth I],
QE [auth 3],
RC [auth J],
SE [auth 4],
TC [auth K],
TD [auth U],
UA [auth L],
VD [auth V],
WC [auth N],
WE [auth 5],
XB [auth A],
XD [auth W],
XE [auth 5],
YD [auth W],
ZB [auth B],
ZE [auth 6]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH

Query on BPH



Download:Ideal Coordinates CCD File
IB [auth M],
VA [auth L]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
PGV

Query on PGV



Download:Ideal Coordinates CCD File
AC [auth B]
AF [auth 6]
BB [auth L]
BC [auth B]
BE [auth X]
AC [auth B],
AF [auth 6],
BB [auth L],
BC [auth B],
BE [auth X],
BF [auth 6],
CB [auth L],
ED [auth P],
FC [auth E],
FD [auth P],
FE [auth Z],
GC [auth F],
GF [auth 8],
HE [auth Z],
IE [auth Z],
JC [auth G],
JE [auth 1],
JF [auth 0],
KD [auth R],
LD [auth R],
LF [auth 0],
MC [auth G],
MF [auth 0],
NC [auth G],
NE [auth 2],
OB [auth M],
OE [auth 2],
PD [auth T],
PE [auth 3],
QD [auth T],
RB [auth H],
SA [auth C],
SC [auth J],
TB [auth H],
TE [auth 4],
UC [auth N],
WD [auth V],
XA [auth L],
XC [auth N],
YC [auth N],
YE [auth 6],
ZD [auth X]
(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
UQ8

Query on UQ8



Download:Ideal Coordinates CCD File
WA [auth L],
YA [auth L],
ZA [auth L]
Ubiquinone-8
C49 H74 O4
ICFIZJQGJAJRSU-SGHXUWJISA-N
MQ8

Query on MQ8



Download:Ideal Coordinates CCD File
JB [auth M]MENAQUINONE 8
C51 H72 O2
LXKDFTDVRVLXFY-ACMRXAIVSA-N
HEC

Query on HEC



Download:Ideal Coordinates CCD File
LA [auth C],
MA [auth C],
NA [auth C],
OA [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
CRT

Query on CRT



Download:Ideal Coordinates CCD File
EE [auth Y]
EF [auth 8]
ID [auth R]
KB [auth M]
KC [auth G]
EE [auth Y],
EF [auth 8],
ID [auth R],
KB [auth M],
KC [auth G],
RE [auth 4],
UD [auth V],
VC [auth N],
YB [auth B]
SPIRILLOXANTHIN
C42 H60 O2
VAZQBTJCYODOSV-RISZBRKMSA-N
LMT

Query on LMT



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AB [auth L]
AD [auth O]
CF [auth 7]
GD [auth Q]
HC [auth F]
AB [auth L],
AD [auth O],
CF [auth 7],
GD [auth Q],
HC [auth F],
OC [auth I],
PB [auth M],
TA [auth L],
UB [auth H],
UE [auth 5],
VB [auth H],
VE [auth 5],
WB [auth H]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
LJQ

Query on LJQ



Download:Ideal Coordinates CCD File
QA [auth C][(2~{S})-1-dodecanoyloxy-3-oxidanyl-propan-2-yl] pentadecanoate
C30 H58 O5
IWQJHHBIHRVMSK-NDEPHWFRSA-N
SF4

Query on SF4



Download:Ideal Coordinates CCD File
NF [auth a]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
PLM

Query on PLM



Download:Ideal Coordinates CCD File
RA [auth C]PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
FE

Query on FE



Download:Ideal Coordinates CCD File
FB [auth M]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
PA [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



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: 2025-01-29
    Type: Initial release
  • Version 2.0: 2025-10-01
    Type: Coordinate replacement
    Reason: Polymer backbone linkage
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Refinement description, Structure summary