8WCL | pdb_00008wcl

FCP pentamer in Chaetoceros gracilis

PDB DOI: https://doi.org/10.2210/pdb8WCL/pdb
EM Map EMD-37442: EMDB EMDataResource

Classification: PHOTOSYNTHESIS
Organism(s): Chaetoceros neogracilis
Mutation(s): No
Membrane Protein: Yes PDBTM

Deposited: 2023-09-12 Released: 2024-07-31
Deposition Author(s): Feng, Y., Li, Z., Zhou, C., Liu, C., Shen, J.-R., Wang, W.
Funding Organization(s): Chinese Academy of Sciences

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.65 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

Structural and spectroscopic insights into fucoxanthin chlorophyll a/c-binding proteins of diatoms in diverse oligomeric states.

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

(2024) Plant Commun 5: 101041-101041

PubMed: 39030906 Search on PubMed
DOI: https://doi.org/10.1016/j.xplc.2024.101041
Primary Citation Related Structures:
8JP3, 8WCK, 8WCL

PubMed Abstract:
Diatoms, a group of prevalent marine algae, significantly contribute to global primary productivity. Their substantial biomass is linked to enhanced absorption of blue-green light underwater, facilitated by fucoxanthin chlorophyll a/c-binding proteins (FCPs), exhibiting oligomeric diversity across diatom species. Utilizing mild CN-PAGE analysis on solubilized thylakoid membranes, we displayed monomeric, dimeric, trimeric, tetrameric and pentameric FCPs in diatoms. Mass spectrometry analysis revealed each oligomeric FCP has specific protein compositions, constituting a large Lhcf family of FCP antennas. In addition, we resolved the structures of Thalassiosira pseudonana FCP (Tp-FCP) homotrimer and Chaetoceros gracilis FCP (Cg-FCP) pentamer by cryo-electron microscopy at 2.73 Å and 2.65 Å resolutions, respectively. The distinct pigment composition and organization in various oligomeric FCPs change their blue-green light-harvesting, excitation energy transfer pathways. In comparison to dimeric and trimeric FCPs, Cg-FCP tetramer and Cg-FCP pentamer exhibit stronger absorption by Chls c, red-shifted and broader Chl a fluorescence emission, as well as more robust circular dichroism signals originating from Chl a-carotenoid dimers. These spectroscopic characteristics indicate that Chl a molecules in Cg-FCP tetramer and Cg-FCP pentamer are more heterogeneous than in both dimers and Tp-FCP trimer. The structural and spectroscopic insights provided by this study contribute to a better understanding of the mechanisms that empower diatoms to adapt to fluctuating light environments.

Organizational Affiliation

Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, P. R. China; University of Chinese Academy of Sciences, Beijing 100049, P. R. China.

Macromolecule Content

Total Structure Weight: 171.18 kDa
Atom Count: 10,662
Modeled Residue Count: 847
Deposited Residue Count: 1,027
Unique protein chains: 4

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorophyll a/c-binding protein Lhcf6	A [auth 6]	211	Chaetoceros neogracilis	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorophyll a/b-binding protein	B [auth 8], D [auth 5]	207	Chaetoceros neogracilis	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A679BXP6 (Chaetoceros neogracilis) Explore A0A679BXP6 Go to UniProtKB: A0A679BXP6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A679BXP6
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fucoxanthin-chlorophyll a/c protein	C [auth 9]	195	Chaetoceros neogracilis	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A8S0JDZ7 (Chaetoceros neogracilis) Explore A0A8S0JDZ7 Go to UniProtKB: A0A8S0JDZ7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8S0JDZ7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Chlorophyll a/c-binding protein Lhcf7	E [auth 7]	207	Chaetoceros neogracilis	Mutation(s): 0

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLA (Subject of Investigation/LOI) Query on CLA Download:Ideal Coordinates CCD File SDF format, chain CC [auth 7] SDF format, chain FC [auth 7] SDF format, chain J [auth 6] SDF format, chain NB [auth 5] SDF format, chain YA [auth 9] SDF format, chain ZB [auth 7] SDF format, chain Z [auth 8] SDF format, chain WA [auth 9] SDF format, chain VA [auth 9] SDF format, chain UA [auth 9] SDF format, chain TA [auth 9] SDF format, chain S [auth 6] SDF format, chain RA [auth 9] SDF format, chain R [auth 6] SDF format, chain QA [auth 9] SDF format, chain P [auth 6] SDF format, chain OB [auth 5] SDF format, chain M [auth 6] SDF format, chain LB [auth 5] SDF format, chain K [auth 6] SDF format, chain IB [auth 5] SDF format, chain HC [auth 7] SDF format, chain HA [auth 8] SDF format, chain GB [auth 5] SDF format, chain GA [auth 8] SDF format, chain FB [auth 5] SDF format, chain EA [auth 8] SDF format, chain BA [auth 8] SDF format, chain AC [auth 7] MOL2 format, chain CC [auth 7] MOL2 format, chain FC [auth 7] MOL2 format, chain J [auth 6] MOL2 format, chain NB [auth 5] MOL2 format, chain YA [auth 9] MOL2 format, chain ZB [auth 7] MOL2 format, chain Z [auth 8] MOL2 format, chain WA [auth 9] MOL2 format, chain VA [auth 9] MOL2 format, chain UA [auth 9] MOL2 format, chain TA [auth 9] MOL2 format, chain S [auth 6] MOL2 format, chain RA [auth 9] MOL2 format, chain R [auth 6] MOL2 format, chain QA [auth 9] MOL2 format, chain P [auth 6] MOL2 format, chain OB [auth 5] MOL2 format, chain M [auth 6] MOL2 format, chain LB [auth 5] MOL2 format, chain K [auth 6] MOL2 format, chain IB [auth 5] MOL2 format, chain HC [auth 7] MOL2 format, chain HA [auth 8] MOL2 format, chain GB [auth 5] MOL2 format, chain GA [auth 8] MOL2 format, chain FB [auth 5] MOL2 format, chain EA [auth 8] MOL2 format, chain BA [auth 8] MOL2 format, chain AC [auth 7] mmCIF format, chain CC [auth 7] mmCIF format, chain FC [auth 7] mmCIF format, chain J [auth 6] mmCIF format, chain NB [auth 5] mmCIF format, chain YA [auth 9] mmCIF format, chain ZB [auth 7] mmCIF format, chain Z [auth 8] mmCIF format, chain WA [auth 9] mmCIF format, chain VA [auth 9] mmCIF format, chain UA [auth 9] mmCIF format, chain TA [auth 9] mmCIF format, chain S [auth 6] mmCIF format, chain RA [auth 9] mmCIF format, chain R [auth 6] mmCIF format, chain QA [auth 9] mmCIF format, chain P [auth 6] mmCIF format, chain OB [auth 5] mmCIF format, chain M [auth 6] mmCIF format, chain LB [auth 5] mmCIF format, chain K [auth 6] mmCIF format, chain IB [auth 5] mmCIF format, chain HC [auth 7] mmCIF format, chain HA [auth 8] mmCIF format, chain GB [auth 5] mmCIF format, chain GA [auth 8] mmCIF format, chain FB [auth 5] mmCIF format, chain EA [auth 8] mmCIF format, chain BA [auth 8] mmCIF format, chain AC [auth 7]	AC [auth 7] BA [auth 8] CC [auth 7] EA [auth 8] FB [auth 5] AC [auth 7], BA [auth 8], CC [auth 7], EA [auth 8], FB [auth 5], FC [auth 7], GA [auth 8], GB [auth 5], HA [auth 8], HC [auth 7], IB [auth 5], J [auth 6], K [auth 6], LB [auth 5], M [auth 6], NB [auth 5], OB [auth 5], P [auth 6], QA [auth 9], R [auth 6], RA [auth 9], S [auth 6], TA [auth 9], UA [auth 9], VA [auth 9], WA [auth 9], YA [auth 9], Z [auth 8], ZB [auth 7]	CHLOROPHYLL A C₅₅ H₇₂ Mg N₄ O₅ ATNHDLDRLWWWCB-AENOIHSZSA-M		Interactions Focus chain AC [auth 7] Focus chain BA [auth 8] Focus chain CC [auth 7] Focus chain EA [auth 8] Focus chain FB [auth 5] Focus chain FC [auth 7] Focus chain GA [auth 8] Focus chain GB [auth 5] Focus chain HA [auth 8] Focus chain HC [auth 7] Focus chain IB [auth 5] Focus chain J [auth 6] Focus chain K [auth 6] Focus chain LB [auth 5] Focus chain M [auth 6] Focus chain NB [auth 5] Focus chain OB [auth 5] Focus chain P [auth 6] Focus chain QA [auth 9] Focus chain R [auth 6] Focus chain RA [auth 9] Focus chain S [auth 6] Focus chain TA [auth 9] Focus chain UA [auth 9] Focus chain VA [auth 9] Focus chain WA [auth 9] Focus chain YA [auth 9] Focus chain Z [auth 8] Focus chain ZB [auth 7] Interactions & Density Focus chain AC [auth 7] Focus chain BA [auth 8] Focus chain CC [auth 7] Focus chain EA [auth 8] Focus chain FB [auth 5] Focus chain FC [auth 7] Focus chain GA [auth 8] Focus chain GB [auth 5] Focus chain HA [auth 8] Focus chain HC [auth 7] Focus chain IB [auth 5] Focus chain J [auth 6] Focus chain K [auth 6] Focus chain LB [auth 5] Focus chain M [auth 6] Focus chain NB [auth 5] Focus chain OB [auth 5] Focus chain P [auth 6] Focus chain QA [auth 9] Focus chain R [auth 6] Focus chain RA [auth 9] Focus chain S [auth 6] Focus chain TA [auth 9] Focus chain UA [auth 9] Focus chain VA [auth 9] Focus chain WA [auth 9] Focus chain YA [auth 9] Focus chain Z [auth 8] Focus chain ZB [auth 7]
LMG (Subject of Investigation/LOI) Query on LMG Download:Ideal Coordinates CCD File SDF format, chain ZA [auth 9] SDF format, chain IC [auth 7] MOL2 format, chain ZA [auth 9] MOL2 format, chain IC [auth 7] mmCIF format, chain ZA [auth 9] mmCIF format, chain IC [auth 7]	IC [auth 7], ZA [auth 9]	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C₄₅ H₈₆ O₁₀ DCLTVZLYPPIIID-CVELTQQQSA-N		Interactions Focus chain IC [auth 7] Focus chain ZA [auth 9] Interactions & Density Focus chain IC [auth 7] Focus chain ZA [auth 9]
A86 (Subject of Investigation/LOI) Query on A86 Download:Ideal Coordinates CCD File SDF format, chain AB [auth 5] SDF format, chain EB [auth 5] SDF format, chain G [auth 6] SDF format, chain JA [auth 9] SDF format, chain RB [auth 5] SDF format, chain U [auth 8] SDF format, chain V [auth 8] SDF format, chain Y [auth 8] SDF format, chain YB [auth 7] SDF format, chain XB [auth 7] SDF format, chain X [auth 8] SDF format, chain WB [auth 7] SDF format, chain W [auth 8] SDF format, chain VB [auth 7] SDF format, chain UB [auth 7] SDF format, chain TB [auth 7] SDF format, chain T [auth 8] SDF format, chain SB [auth 7] SDF format, chain PA [auth 9] SDF format, chain OA [auth 9] SDF format, chain NA [auth 9] SDF format, chain MA [auth 9] SDF format, chain LA [auth 9] SDF format, chain KA [auth 9] SDF format, chain I [auth 6] SDF format, chain H [auth 6] SDF format, chain F [auth 6] SDF format, chain DB [auth 5] SDF format, chain CB [auth 5] SDF format, chain BB [auth 5] MOL2 format, chain AB [auth 5] MOL2 format, chain EB [auth 5] MOL2 format, chain G [auth 6] MOL2 format, chain JA [auth 9] MOL2 format, chain RB [auth 5] MOL2 format, chain U [auth 8] MOL2 format, chain V [auth 8] MOL2 format, chain Y [auth 8] MOL2 format, chain YB [auth 7] MOL2 format, chain XB [auth 7] MOL2 format, chain X [auth 8] MOL2 format, chain WB [auth 7] MOL2 format, chain W [auth 8] MOL2 format, chain VB [auth 7] MOL2 format, chain UB [auth 7] MOL2 format, chain TB [auth 7] MOL2 format, chain T [auth 8] MOL2 format, chain SB [auth 7] MOL2 format, chain PA [auth 9] MOL2 format, chain OA [auth 9] MOL2 format, chain NA [auth 9] MOL2 format, chain MA [auth 9] MOL2 format, chain LA [auth 9] MOL2 format, chain KA [auth 9] MOL2 format, chain I [auth 6] MOL2 format, chain H [auth 6] MOL2 format, chain F [auth 6] MOL2 format, chain DB [auth 5] MOL2 format, chain CB [auth 5] MOL2 format, chain BB [auth 5] mmCIF format, chain AB [auth 5] mmCIF format, chain EB [auth 5] mmCIF format, chain G [auth 6] mmCIF format, chain JA [auth 9] mmCIF format, chain RB [auth 5] mmCIF format, chain U [auth 8] mmCIF format, chain V [auth 8] mmCIF format, chain Y [auth 8] mmCIF format, chain YB [auth 7] mmCIF format, chain XB [auth 7] mmCIF format, chain X [auth 8] mmCIF format, chain WB [auth 7] mmCIF format, chain W [auth 8] mmCIF format, chain VB [auth 7] mmCIF format, chain UB [auth 7] mmCIF format, chain TB [auth 7] mmCIF format, chain T [auth 8] mmCIF format, chain SB [auth 7] mmCIF format, chain PA [auth 9] mmCIF format, chain OA [auth 9] mmCIF format, chain NA [auth 9] mmCIF format, chain MA [auth 9] mmCIF format, chain LA [auth 9] mmCIF format, chain KA [auth 9] mmCIF format, chain I [auth 6] mmCIF format, chain H [auth 6] mmCIF format, chain F [auth 6] mmCIF format, chain DB [auth 5] mmCIF format, chain CB [auth 5] mmCIF format, chain BB [auth 5]	AB [auth 5] BB [auth 5] CB [auth 5] DB [auth 5] EB [auth 5] AB [auth 5], BB [auth 5], CB [auth 5], DB [auth 5], EB [auth 5], F [auth 6], G [auth 6], H [auth 6], I [auth 6], JA [auth 9], KA [auth 9], LA [auth 9], MA [auth 9], NA [auth 9], OA [auth 9], PA [auth 9], RB [auth 5], SB [auth 7], T [auth 8], TB [auth 7], U [auth 8], UB [auth 7], V [auth 8], VB [auth 7], W [auth 8], WB [auth 7], X [auth 8], XB [auth 7], Y [auth 8], YB [auth 7]	(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 AB [auth 5] Focus chain BB [auth 5] Focus chain CB [auth 5] Focus chain DB [auth 5] Focus chain EB [auth 5] Focus chain F [auth 6] Focus chain G [auth 6] Focus chain H [auth 6] Focus chain I [auth 6] Focus chain JA [auth 9] Focus chain KA [auth 9] Focus chain LA [auth 9] Focus chain MA [auth 9] Focus chain NA [auth 9] Focus chain OA [auth 9] Focus chain PA [auth 9] Focus chain RB [auth 5] Focus chain SB [auth 7] Focus chain T [auth 8] Focus chain TB [auth 7] Focus chain U [auth 8] Focus chain UB [auth 7] Focus chain V [auth 8] Focus chain VB [auth 7] Focus chain W [auth 8] Focus chain WB [auth 7] Focus chain X [auth 8] Focus chain XB [auth 7] Focus chain Y [auth 8] Focus chain YB [auth 7] Interactions & Density Focus chain AB [auth 5] Focus chain BB [auth 5] Focus chain CB [auth 5] Focus chain DB [auth 5] Focus chain EB [auth 5] Focus chain F [auth 6] Focus chain G [auth 6] Focus chain H [auth 6] Focus chain I [auth 6] Focus chain JA [auth 9] Focus chain KA [auth 9] Focus chain LA [auth 9] Focus chain MA [auth 9] Focus chain NA [auth 9] Focus chain OA [auth 9] Focus chain PA [auth 9] Focus chain RB [auth 5] Focus chain SB [auth 7] Focus chain T [auth 8] Focus chain TB [auth 7] Focus chain U [auth 8] Focus chain UB [auth 7] Focus chain V [auth 8] Focus chain VB [auth 7] Focus chain W [auth 8] Focus chain WB [auth 7] Focus chain X [auth 8] Focus chain XB [auth 7] Focus chain Y [auth 8] Focus chain YB [auth 7]
KC1 (Subject of Investigation/LOI) Query on KC1 Download:Ideal Coordinates CCD File SDF format, chain EC [auth 7] SDF format, chain GC [auth 7] SDF format, chain KB [auth 5] SDF format, chain XA [auth 9] SDF format, chain Q [auth 6] SDF format, chain O [auth 6] SDF format, chain MB [auth 5] SDF format, chain FA [auth 8] SDF format, chain DA [auth 8] MOL2 format, chain EC [auth 7] MOL2 format, chain GC [auth 7] MOL2 format, chain KB [auth 5] MOL2 format, chain XA [auth 9] MOL2 format, chain Q [auth 6] MOL2 format, chain O [auth 6] MOL2 format, chain MB [auth 5] MOL2 format, chain FA [auth 8] MOL2 format, chain DA [auth 8] mmCIF format, chain EC [auth 7] mmCIF format, chain GC [auth 7] mmCIF format, chain KB [auth 5] mmCIF format, chain XA [auth 9] mmCIF format, chain Q [auth 6] mmCIF format, chain O [auth 6] mmCIF format, chain MB [auth 5] mmCIF format, chain FA [auth 8] mmCIF format, chain DA [auth 8]	DA [auth 8] EC [auth 7] FA [auth 8] GC [auth 7] KB [auth 5] DA [auth 8], EC [auth 7], FA [auth 8], GC [auth 7], KB [auth 5], MB [auth 5], O [auth 6], Q [auth 6], XA [auth 9]	Chlorophyll c1 C₃₅ H₃₀ Mg N₄ O₅ DGNIJJSSARBJSH-QIEHNWLWSA-L		Interactions Focus chain DA [auth 8] Focus chain EC [auth 7] Focus chain FA [auth 8] Focus chain GC [auth 7] Focus chain KB [auth 5] Focus chain MB [auth 5] Focus chain O [auth 6] Focus chain Q [auth 6] Focus chain XA [auth 9] Interactions & Density Focus chain DA [auth 8] Focus chain EC [auth 7] Focus chain FA [auth 8] Focus chain GC [auth 7] Focus chain KB [auth 5] Focus chain MB [auth 5] Focus chain O [auth 6] Focus chain Q [auth 6] Focus chain XA [auth 9]
KC2 (Subject of Investigation/LOI) Query on KC2 Download:Ideal Coordinates CCD File SDF format, chain AA [auth 8] SDF format, chain DC [auth 7] SDF format, chain SA [auth 9] SDF format, chain N [auth 6] SDF format, chain L [auth 6] SDF format, chain JB [auth 5] SDF format, chain HB [auth 5] SDF format, chain CA [auth 8] SDF format, chain BC [auth 7] MOL2 format, chain AA [auth 8] MOL2 format, chain DC [auth 7] MOL2 format, chain SA [auth 9] MOL2 format, chain N [auth 6] MOL2 format, chain L [auth 6] MOL2 format, chain JB [auth 5] MOL2 format, chain HB [auth 5] MOL2 format, chain CA [auth 8] MOL2 format, chain BC [auth 7] mmCIF format, chain AA [auth 8] mmCIF format, chain DC [auth 7] mmCIF format, chain SA [auth 9] mmCIF format, chain N [auth 6] mmCIF format, chain L [auth 6] mmCIF format, chain JB [auth 5] mmCIF format, chain HB [auth 5] mmCIF format, chain CA [auth 8] mmCIF format, chain BC [auth 7]	AA [auth 8] BC [auth 7] CA [auth 8] DC [auth 7] HB [auth 5] AA [auth 8], BC [auth 7], CA [auth 8], DC [auth 7], HB [auth 5], JB [auth 5], L [auth 6], N [auth 6], SA [auth 9]	Chlorophyll c2 C₃₅ H₂₈ Mg N₄ O₅ QDRBYWCRXZZVLY-QIEHNWLWSA-L		Interactions Focus chain AA [auth 8] Focus chain BC [auth 7] Focus chain CA [auth 8] Focus chain DC [auth 7] Focus chain HB [auth 5] Focus chain JB [auth 5] Focus chain L [auth 6] Focus chain N [auth 6] Focus chain SA [auth 9] Interactions & Density Focus chain AA [auth 8] Focus chain BC [auth 7] Focus chain CA [auth 8] Focus chain DC [auth 7] Focus chain HB [auth 5] Focus chain JB [auth 5] Focus chain L [auth 6] Focus chain N [auth 6] Focus chain SA [auth 9]
LMT (Subject of Investigation/LOI) Query on LMT Download:Ideal Coordinates CCD File SDF format, chain QB [auth 5] SDF format, chain PB [auth 5] SDF format, chain KC [auth 7] SDF format, chain JC [auth 7] SDF format, chain IA [auth 8] MOL2 format, chain QB [auth 5] MOL2 format, chain PB [auth 5] MOL2 format, chain KC [auth 7] MOL2 format, chain JC [auth 7] MOL2 format, chain IA [auth 8] mmCIF format, chain QB [auth 5] mmCIF format, chain PB [auth 5] mmCIF format, chain KC [auth 7] mmCIF format, chain JC [auth 7] mmCIF format, chain IA [auth 8]	IA [auth 8], JC [auth 7], KC [auth 7], PB [auth 5], QB [auth 5]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain IA [auth 8] Focus chain JC [auth 7] Focus chain KC [auth 7] Focus chain PB [auth 5] Focus chain QB [auth 5] Interactions & Density Focus chain IA [auth 8] Focus chain JC [auth 7] Focus chain KC [auth 7] Focus chain PB [auth 5] Focus chain QB [auth 5]