7Y7B | pdb_00007y7b

Cryo-EM structure of cryptophyte photosystem I


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.66 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural basis and evolution of the photosystem I-light-harvesting supercomplex of cryptophyte algae.

Zhao, L.S.Wang, P.Li, K.Zhang, Q.B.He, F.Y.Li, C.Y.Su, H.N.Chen, X.L.Liu, L.N.Zhang, Y.Z.

(2023) Plant Cell 35: 2449-2463

  • DOI: https://doi.org/10.1093/plcell/koad087
  • Primary Citation of Related Structures:  
    7Y7B, 7Y8A

  • PubMed Abstract: 

    Cryptophyte plastids originated from a red algal ancestor through secondary endosymbiosis. Cryptophyte photosystem I (PSI) associates with transmembrane alloxanthin-chlorophyll a/c proteins (ACPIs) as light-harvesting complexes (LHCs). Here, we report the structure of the photosynthetic PSI-ACPI supercomplex from the cryptophyte Chroomonas placoidea at 2.7-Å resolution obtained by crygenic electron microscopy. Cryptophyte PSI-ACPI represents a unique PSI-LHCI intermediate in the evolution from red algal to diatom PSI-LHCI. The PSI-ACPI supercomplex is composed of a monomeric PSI core containing 14 subunits, 12 of which originated in red algae, 1 diatom PsaR homolog, and an additional peptide. The PSI core is surrounded by 14 ACPI subunits that form 2 antenna layers: an inner layer with 11 ACPIs surrounding the PSI core and an outer layer containing 3 ACPIs. A pigment-binding subunit that is not present in any other previously characterized PSI-LHCI complexes, ACPI-S, mediates the association and energy transfer between the outer and inner ACPIs. The extensive pigment network of PSI-ACPI ensures efficient light harvesting, energy transfer, and dissipation. Overall, the PSI-LHCI structure identified in this study provides a framework for delineating the mechanisms of energy transfer in cryptophyte PSI-LHCI and for understanding the evolution of photosynthesis in the red lineage, which occurred via secondary endosymbiosis.


  • Organizational Affiliation

    State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ACPI-1A [auth 1]222Chroomonas placoideaMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ACPI-2B [auth 2]216Chroomonas placoideaMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
ACPI-3C [auth 3]236Chroomonas placoideaMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
ACPI-4D [auth 4]217Chroomonas placoideaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
ACPI-5E [auth 5]229Chroomonas placoideaMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
ACPI-6F [auth 6]215Chroomonas placoideaMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
ACPI-7G [auth 7]230Chroomonas placoideaMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
ACPI-8H [auth 8]227Chroomonas placoideaMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
ACPI-12I [auth 9]220Chroomonas placoideaMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1J [auth A]752Chroomonas placoideaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
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UniProt GroupA0A222AIB4
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2K [auth B]734Chroomonas placoideaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerL [auth C]81Chroomonas placoideaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIM [auth D]141Chroomonas placoideaMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVN [auth E]64Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIIO [auth F]183Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIP [auth I]36Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXQ [auth J]42Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaKR [auth K]87Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIS [auth L]153Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIT [auth M]30Chroomonas placoideaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A222AI28 (Chroomonas placoidea)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
PsaOU [auth O]99Chroomonas placoideaMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
PsaRV [auth R]133Chroomonas placoideaMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Unk1W [auth X]164Chroomonas placoideaMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
ACPI-SX [auth Z]242Chroomonas placoideaMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
ACPI-13/10BA [auth d],
Y [auth a]
215Chroomonas placoideaMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
ACPI-14Z [auth b]218Chroomonas placoideaMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
ACPI-9AA [auth c]257Chroomonas placoideaMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
ACPI-11CA [auth e]208Chroomonas placoideaMutation(s): 0 
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Small Molecules
Ligands 13 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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IM [auth Z],
RK [auth B]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA (Subject of Investigation/LOI)
Query on CLA

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AB [auth 2]
AC [auth 3]
AE [auth 6]
AF [auth 7]
AH [auth A]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
SQD
Query on SQD

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AM [auth O],
KC [auth 3]
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG
Query on LMG

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AG [auth 8]
BL [auth F]
DL [auth I]
HC [auth 3]
JC [auth 3]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

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DD [auth 4]
FD [auth 4]
HN [auth a]
IC [auth 3]
KF [auth 7]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
KC2 (Subject of Investigation/LOI)
Query on KC2

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CF [auth 7]
DP [auth d]
FB [auth 2]
IO [auth c]
JE [auth 6]
Chlorophyll c2
C35 H28 Mg N4 O5
QDRBYWCRXZZVLY-QIEHNWLWSA-L
II3 (Subject of Investigation/LOI)
Query on II3

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RA [auth 1],
VN [auth b],
ZP [auth e]
(1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol
C40 H54 O2
VAGYSFRRYPPSFX-RLVOMNFVSA-N
II0 (Subject of Investigation/LOI)
Query on II0

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AD [auth 4]
AQ [auth e]
BD [auth 4]
BQ [auth e]
CC [auth 3]
(1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-3,5,7,9,11,13,15-heptaen-1,17-diynyl]cyclohex-3-en-1-ol
C40 H52 O2
DVICWXUADSCSLL-DDEWRDOISA-N
IHT (Subject of Investigation/LOI)
Query on IHT

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GN [auth a]
HM [auth Z]
KP [auth d]
LB [auth 2]
LL [auth K]
(1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-(2,6,6-trimethylcyclohexen-1-yl)octadeca-3,5,7,9,11,13,15,17-octaen-1-ynyl]cyclohex-3-en-1-ol
C40 H54 O
UNJKJDIRJWIHLL-BQLQDKTLSA-N
8CT (Subject of Investigation/LOI)
Query on 8CT

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CD [auth 4]
CL [auth I]
CM [auth R]
CQ [auth e]
EM [auth R]
(6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene
C40 H56
ANVAOWXLWRTKGA-GZSHKXEASA-N
LMU
Query on LMU

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BM [auth O],
DQ [auth e],
ED [auth 4],
HL [auth J],
MF [auth 7]
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
PQN
Query on PQN

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LK [auth B],
SI [auth A]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4

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VK [auth C],
WI [auth B],
WK [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.66 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China--

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-12
    Type: Initial release
  • Version 1.1: 2023-04-19
    Changes: Database references
  • Version 1.2: 2023-04-26
    Changes: Structure summary
  • Version 1.3: 2023-07-12
    Changes: Database references
  • Version 1.4: 2024-10-16
    Changes: Data collection, Structure summary