8J0D

FCP heterodimer, Lhca2, and Lhcf5 together as the M1 side binds to the PSII core in the diatom Thalassiosira pseudonana

PDB DOI: https://doi.org/10.2210/pdb8J0D/pdb
EM Map EMD-35899: EMDB EMDataResource

Classification: PHOTOSYNTHESIS
Organism(s): Thalassiosira pseudonana
Mutation(s): No
Membrane Protein: Yes PDBTM

Deposited: 2023-04-10 Released: 2023-10-25
Deposition Author(s): Li, Z., Feng, Y., Wang, W., Shen, J.R.
Funding Organization(s): Chinese Academy of Sciences

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.19 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

Structure of a diatom photosystem II supercomplex containing a member of Lhcx family and dimeric FCPII.

Feng, Y., Li, Z., Li, X., Shen, L., Liu, X., Zhou, C., Zhang, J., Sang, M., Han, G., Yang, W., Kuang, T., Wang, W., Shen, J.R.

(2023) Sci Adv 9: eadi8446-eadi8446

PubMed: 37878698 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1126/sciadv.adi8446
Primary Citation of Related Structures:
8IWH, 8J0D

PubMed Abstract:
Diatoms rely on fucoxanthin chlorophyll a/c -binding proteins (FCPs) for their great success in oceans, which have a great diversity in their pigment, protein compositions, and subunit organizations. We report a unique structure of photosystem II (PSII)-FCPII supercomplex from Thalassiosira pseudonana at 2.68-Å resolution by cryo-electron microscopy. FCPIIs within this PSII-FCPII supercomplex exist in dimers and monomers, and a homodimer and a heterodimer were found to bind to a PSII core. The FCPII homodimer is formed by Lhcf7 and associates with PSII through an Lhcx family antenna Lhcx6_1, whereas the heterodimer is formed by Lhcf6 and Lhcf11 and connects to the core together with an Lhcf5 monomer through Lhca2 monomer. An extended pigment network consisting of diatoxanthins, diadinoxanthins, fucoxanthins, and chlorophylls a/c is revealed, which functions in efficient light harvesting, energy transfer, and dissipation. These results provide a structural basis for revealing the energy transfer and dissipation mechanisms and also for the structural diversity of FCP antennas in diatoms.

Organizational Affiliation

Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.

Macromolecule Content

Total Structure Weight: 135.94 kDa
Atom Count: 9,105
Modelled Residue Count: 711
Deposited Residue Count: 711
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucoxanthin chl a/c protein, lhca clade	A [auth 3]	220	Thalassiosira pseudonana	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for B8BUU4 (Thalassiosira pseudonana) Explore B8BUU4 Go to UniProtKB: B8BUU4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B8BUU4
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucoxanthin-chlorophyll a-c binding protein, plastid	B [auth 4]	163	Thalassiosira pseudonana	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for B8BVI1 (Thalassiosira pseudonana) Explore B8BVI1 Go to UniProtKB: B8BVI1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B8BVI1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucoxanthin chlorophyll a/c protein 6	C [auth 5]	160	Thalassiosira pseudonana	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for B8BX92 (Thalassiosira pseudonana) Explore B8BX92 Go to UniProtKB: B8BX92
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B8BX92
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucoxanthin chlorophyll a/c protein 5	D [auth 6]	168	Thalassiosira pseudonana	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for B8CEV5 (Thalassiosira pseudonana) Explore B8CEV5 Go to UniProtKB: B8CEV5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B8CEV5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 9 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DGD (Subject of Investigation/LOI) Query on DGD Download Ideal Coordinates CCD File SDF format, chain X [auth 3] MOL2 format, chain X [auth 3]	X [auth 3]	DIGALACTOSYL DIACYL GLYCEROL (DGDG) C₅₁ H₉₆ O₁₅ LDQFLSUQYHBXSX-HXXRYREZSA-N		Interactions Focus chain X [auth 3] Interactions & Density Focus chain X [auth 3]
CLA (Subject of Investigation/LOI) Query on CLA Download Ideal Coordinates CCD File SDF format, chain AB [auth 5] SDF format, chain BB [auth 5] SDF format, chain CA [auth 4] SDF format, chain CB [auth 5] SDF format, chain DA [auth 4] SDF format, chain DB [auth 5] SDF format, chain E [auth 3] SDF format, chain F [auth 3] SDF format, chain FA [auth 4] SDF format, chain FB [auth 5] SDF format, chain G [auth 3] SDF format, chain GA [auth 4] SDF format, chain GB [auth 5] SDF format, chain H [auth 3] SDF format, chain HA [auth 4] SDF format, chain I [auth 3] SDF format, chain IA [auth 4] SDF format, chain J [auth 3] SDF format, chain JA [auth 4] SDF format, chain K [auth 3] SDF format, chain KA [auth 4] SDF format, chain L [auth 3] SDF format, chain LA [auth 4] SDF format, chain MA [auth 4] SDF format, chain N [auth 3] SDF format, chain NA [auth 4] SDF format, chain O [auth 3] SDF format, chain P [auth 3] SDF format, chain QB [auth 6] SDF format, chain RB [auth 6] SDF format, chain TB [auth 6] SDF format, chain UB [auth 6] SDF format, chain VB [auth 6] SDF format, chain W [auth 3] SDF format, chain WB [auth 6] SDF format, chain XA [auth 5] SDF format, chain YA [auth 5] SDF format, chain YB [auth 6] SDF format, chain ZB [auth 6] MOL2 format, chain AB [auth 5] MOL2 format, chain BB [auth 5] MOL2 format, chain CA [auth 4] MOL2 format, chain CB [auth 5] MOL2 format, chain DA [auth 4] MOL2 format, chain DB [auth 5] MOL2 format, chain E [auth 3] MOL2 format, chain F [auth 3] MOL2 format, chain FA [auth 4] MOL2 format, chain FB [auth 5] MOL2 format, chain G [auth 3] MOL2 format, chain GA [auth 4] MOL2 format, chain GB [auth 5] MOL2 format, chain H [auth 3] MOL2 format, chain HA [auth 4] MOL2 format, chain I [auth 3] MOL2 format, chain IA [auth 4] MOL2 format, chain J [auth 3] MOL2 format, chain JA [auth 4] MOL2 format, chain K [auth 3] MOL2 format, chain KA [auth 4] MOL2 format, chain L [auth 3] MOL2 format, chain LA [auth 4] MOL2 format, chain MA [auth 4] MOL2 format, chain N [auth 3] MOL2 format, chain NA [auth 4] MOL2 format, chain O [auth 3] MOL2 format, chain P [auth 3] MOL2 format, chain QB [auth 6] MOL2 format, chain RB [auth 6] MOL2 format, chain TB [auth 6] MOL2 format, chain UB [auth 6] MOL2 format, chain VB [auth 6] MOL2 format, chain W [auth 3] MOL2 format, chain WB [auth 6] MOL2 format, chain XA [auth 5] MOL2 format, chain YA [auth 5] MOL2 format, chain YB [auth 6] MOL2 format, chain ZB [auth 6]	AB [auth 5] BB [auth 5] CA [auth 4] CB [auth 5] DA [auth 4] AB [auth 5], BB [auth 5], CA [auth 4], CB [auth 5], DA [auth 4], DB [auth 5], E [auth 3], F [auth 3], FA [auth 4], FB [auth 5], G [auth 3], GA [auth 4], GB [auth 5], H [auth 3], HA [auth 4], I [auth 3], IA [auth 4], J [auth 3], JA [auth 4], K [auth 3], KA [auth 4], L [auth 3], LA [auth 4], MA [auth 4], N [auth 3], NA [auth 4], O [auth 3], P [auth 3], QB [auth 6], RB [auth 6], TB [auth 6], UB [auth 6], VB [auth 6], W [auth 3], WB [auth 6], XA [auth 5], YA [auth 5], YB [auth 6], ZB [auth 6]	CHLOROPHYLL A C₅₅ H₇₂ Mg N₄ O₅ ATNHDLDRLWWWCB-AENOIHSZSA-M		Interactions Focus chain AB [auth 5] Focus chain BB [auth 5] Focus chain CA [auth 4] Focus chain CB [auth 5] Focus chain DA [auth 4] Focus chain DB [auth 5] Focus chain E [auth 3] Focus chain F [auth 3] Focus chain FA [auth 4] Focus chain FB [auth 5] Focus chain G [auth 3] Focus chain GA [auth 4] Focus chain GB [auth 5] Focus chain H [auth 3] Focus chain HA [auth 4] Focus chain I [auth 3] Focus chain IA [auth 4] Focus chain J [auth 3] Focus chain JA [auth 4] Focus chain K [auth 3] Focus chain KA [auth 4] Focus chain L [auth 3] Focus chain LA [auth 4] Focus chain MA [auth 4] Focus chain N [auth 3] Focus chain NA [auth 4] Focus chain O [auth 3] Focus chain P [auth 3] Focus chain QB [auth 6] Focus chain RB [auth 6] Focus chain TB [auth 6] Focus chain UB [auth 6] Focus chain VB [auth 6] Focus chain W [auth 3] Focus chain WB [auth 6] Focus chain XA [auth 5] Focus chain YA [auth 5] Focus chain YB [auth 6] Focus chain ZB [auth 6] Interactions & Density Focus chain AB [auth 5] Focus chain BB [auth 5] Focus chain CA [auth 4] Focus chain CB [auth 5] Focus chain DA [auth 4] Focus chain DB [auth 5] Focus chain E [auth 3] Focus chain F [auth 3] Focus chain FA [auth 4] Focus chain FB [auth 5] Focus chain G [auth 3] Focus chain GA [auth 4] Focus chain GB [auth 5] Focus chain H [auth 3] Focus chain HA [auth 4] Focus chain I [auth 3] Focus chain IA [auth 4] Focus chain J [auth 3] Focus chain JA [auth 4] Focus chain K [auth 3] Focus chain KA [auth 4] Focus chain L [auth 3] Focus chain LA [auth 4] Focus chain MA [auth 4] Focus chain N [auth 3] Focus chain NA [auth 4] Focus chain O [auth 3] Focus chain P [auth 3] Focus chain QB [auth 6] Focus chain RB [auth 6] Focus chain TB [auth 6] Focus chain UB [auth 6] Focus chain VB [auth 6] Focus chain W [auth 3] Focus chain WB [auth 6] Focus chain XA [auth 5] Focus chain YA [auth 5] Focus chain YB [auth 6] Focus chain ZB [auth 6]
LMG (Subject of Investigation/LOI) Query on LMG Download Ideal Coordinates CCD File SDF format, chain IB [auth 5] SDF format, chain S [auth 3] SDF format, chain T [auth 3] MOL2 format, chain IB [auth 5] MOL2 format, chain S [auth 3] MOL2 format, chain T [auth 3]	IB [auth 5], S [auth 3], T [auth 3]	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C₄₅ H₈₆ O₁₀ DCLTVZLYPPIIID-CVELTQQQSA-N		Interactions Focus chain IB [auth 5] Focus chain S [auth 3] Focus chain T [auth 3] Interactions & Density Focus chain IB [auth 5] Focus chain S [auth 3] Focus chain T [auth 3]
LHG (Subject of Investigation/LOI) Query on LHG Download Ideal Coordinates CCD File SDF format, chain HB [auth 5] SDF format, chain PA [auth 4] SDF format, chain U [auth 3] SDF format, chain V [auth 3] MOL2 format, chain HB [auth 5] MOL2 format, chain PA [auth 4] MOL2 format, chain U [auth 3] MOL2 format, chain V [auth 3]	HB [auth 5], PA [auth 4], U [auth 3], V [auth 3]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C₃₈ H₇₅ O₁₀ P BIABMEZBCHDPBV-MPQUPPDSSA-N		Interactions Focus chain HB [auth 5] Focus chain PA [auth 4] Focus chain U [auth 3] Focus chain V [auth 3] Interactions & Density Focus chain HB [auth 5] Focus chain PA [auth 4] Focus chain U [auth 3] Focus chain V [auth 3]
A86 (Subject of Investigation/LOI) Query on A86 Download Ideal Coordinates CCD File SDF format, chain BA [auth 4] SDF format, chain KB [auth 5] SDF format, chain LB [auth 6] SDF format, chain MB [auth 6] SDF format, chain NB [auth 6] SDF format, chain OB [auth 6] SDF format, chain PB [auth 6] SDF format, chain Q [auth 3] SDF format, chain QA [auth 5] SDF format, chain RA [auth 5] SDF format, chain SA [auth 5] SDF format, chain TA [auth 5] SDF format, chain UA [auth 5] SDF format, chain VA [auth 5] SDF format, chain WA [auth 5] SDF format, chain Y [auth 4] SDF format, chain Z [auth 4] MOL2 format, chain BA [auth 4] MOL2 format, chain KB [auth 5] MOL2 format, chain LB [auth 6] MOL2 format, chain MB [auth 6] MOL2 format, chain NB [auth 6] MOL2 format, chain OB [auth 6] MOL2 format, chain PB [auth 6] MOL2 format, chain Q [auth 3] MOL2 format, chain QA [auth 5] MOL2 format, chain RA [auth 5] MOL2 format, chain SA [auth 5] MOL2 format, chain TA [auth 5] MOL2 format, chain UA [auth 5] MOL2 format, chain VA [auth 5] MOL2 format, chain WA [auth 5] MOL2 format, chain Y [auth 4] MOL2 format, chain Z [auth 4]	BA [auth 4] KB [auth 5] LB [auth 6] MB [auth 6] NB [auth 6] BA [auth 4], KB [auth 5], LB [auth 6], MB [auth 6], NB [auth 6], OB [auth 6], PB [auth 6], Q [auth 3], QA [auth 5], RA [auth 5], SA [auth 5], TA [auth 5], UA [auth 5], VA [auth 5], WA [auth 5], Y [auth 4], Z [auth 4]	(3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate C₄₂ H₅₈ O₆ SJWWTRQNNRNTPU-XJUZQKKNSA-N		Interactions Focus chain BA [auth 4] Focus chain KB [auth 5] Focus chain LB [auth 6] Focus chain MB [auth 6] Focus chain NB [auth 6] Focus chain OB [auth 6] Focus chain PB [auth 6] Focus chain Q [auth 3] Focus chain QA [auth 5] Focus chain RA [auth 5] Focus chain SA [auth 5] Focus chain TA [auth 5] Focus chain UA [auth 5] Focus chain VA [auth 5] Focus chain WA [auth 5] Focus chain Y [auth 4] Focus chain Z [auth 4] Interactions & Density Focus chain BA [auth 4] Focus chain KB [auth 5] Focus chain LB [auth 6] Focus chain MB [auth 6] Focus chain NB [auth 6] Focus chain OB [auth 6] Focus chain PB [auth 6] Focus chain Q [auth 3] Focus chain QA [auth 5] Focus chain RA [auth 5] Focus chain SA [auth 5] Focus chain TA [auth 5] Focus chain UA [auth 5] Focus chain VA [auth 5] Focus chain WA [auth 5] Focus chain Y [auth 4] Focus chain Z [auth 4]
KC1 (Subject of Investigation/LOI) Query on KC1 Download Ideal Coordinates CCD File SDF format, chain EB [auth 5] SDF format, chain M [auth 3] SDF format, chain XB [auth 6] MOL2 format, chain EB [auth 5] MOL2 format, chain M [auth 3] MOL2 format, chain XB [auth 6]	EB [auth 5], M [auth 3], XB [auth 6]	Chlorophyll c1 C₃₅ H₃₀ Mg N₄ O₅ DGNIJJSSARBJSH-QIEHNWLWSA-L		Interactions Focus chain EB [auth 5] Focus chain M [auth 3] Focus chain XB [auth 6] Interactions & Density Focus chain EB [auth 5] Focus chain M [auth 3] Focus chain XB [auth 6]
KC2 (Subject of Investigation/LOI) Query on KC2 Download Ideal Coordinates CCD File SDF format, chain EA [auth 4] SDF format, chain SB [auth 6] SDF format, chain ZA [auth 5] MOL2 format, chain EA [auth 4] MOL2 format, chain SB [auth 6] MOL2 format, chain ZA [auth 5]	EA [auth 4], SB [auth 6], ZA [auth 5]	Chlorophyll c2 C₃₅ H₂₈ Mg N₄ O₅ QDRBYWCRXZZVLY-QIEHNWLWSA-L		Interactions Focus chain EA [auth 4] Focus chain SB [auth 6] Focus chain ZA [auth 5] Interactions & Density Focus chain EA [auth 4] Focus chain SB [auth 6] Focus chain ZA [auth 5]
DD6 (Subject of Investigation/LOI) Query on DD6 Download Ideal Coordinates CCD File SDF format, chain AA [auth 4] SDF format, chain R [auth 3] MOL2 format, chain AA [auth 4] MOL2 format, chain R [auth 3]	AA [auth 4], R [auth 3]	(3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol C₄₀ H₅₄ O₃ OGHZCSINIMWCSB-WMTIXGNLSA-N		Interactions Focus chain AA [auth 4] Focus chain R [auth 3] Interactions & Density Focus chain AA [auth 4] Focus chain R [auth 3]
LMT (Subject of Investigation/LOI) Query on LMT Download Ideal Coordinates CCD File SDF format, chain JB [auth 5] SDF format, chain OA [auth 4] MOL2 format, chain JB [auth 5] MOL2 format, chain OA [auth 4]	JB [auth 5], OA [auth 4]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain JB [auth 5] Focus chain OA [auth 4] Interactions & Density Focus chain JB [auth 5] Focus chain OA [auth 4]