9V7G | pdb_00009v7g

Phycobilisome Rx rod from Gloeobacter violaceus PCC 7421

PDB DOI: https://doi.org/10.2210/pdb9V7G/pdb
EM Map EMD-64812: EMDB EMDataResource

Classification: PHOTOSYNTHESIS
Organism(s): Gloeobacter violaceus PCC 7421
Mutation(s): No

Deposited: 2025-05-28 Released: 2025-09-24
Deposition Author(s): Burtseva, A.D., Baymukhametov, T.N., Slonimskiy, Y.B., Popov, V.O., Sluchanko, N.N., Boyko, K.M.
Funding Organization(s): Russian Science Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.72 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 and quenching of a bundle-shaped phycobilisome.

Burtseva, A.D., Slonimskiy, Y.B., Baymukhametov, T.N., Sinetova, M.A., Gvozdev, D.A., Tsoraev, G.V., Cherepanov, D.A., Maksimov, E.G., Popov, V.O., Boyko, K.M., Sluchanko, N.N.

(2025) Sci Adv 11: eadz6774-eadz6774

PubMed: 41091862 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1126/sciadv.adz6774
Primary Citation of Related Structures:
9V7G, 9V7H, 9V7I, 9V7J, 9V7K, 9V7L

PubMed Abstract:
Cyanobacteria use soluble antenna megacomplexes, phycobilisomes (PBSs), to maximize light-harvesting efficiency and small photoswitchable orange carotenoid proteins (OCPs) to down-regulate PBSs in high light. Among known PBS morphologies, the one from the basal cyanobacterial genus Gloeobacter still lacks detailed structural characterization. Here, we reconstructed a cryo-electron microscopy structure of the >10-megadalton Gloeobacter violaceus PBS, with diverging, conformationally mobile bundles of rods composed of stacked phycoerythrin and phycocyanin hexamers, stemming from a pentacylindrical allophycocyanin core belted by auxiliary phycocyanin hexamers. We show how two Gloeobacter -specific multidomain linker proteins, Glr1262 and Glr2806, maintain this bundle-shaped architecture and reveal its differential regulation via nonphotochemical quenching by two OCP types of G. violaceus that recognize separate binding sites within the allophycocyanin core, including lateral cylinders absent in tricylindrical cores.

Organizational Affiliation

A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, Moscow 119071, Russia.

Macromolecule Content

Total Structure Weight: 309.09 kDa
Atom Count: 17,599
Modeled Residue Count: 2,207
Deposited Residue Count: 2,733
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glr2806 protein	A [auth X]	729	Gloeobacter violaceus PCC 7421	Mutation(s): 0
UniProt
Find proteins for Q7NGT2 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421)) Explore Q7NGT2 Go to UniProtKB: Q7NGT2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7NGT2
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phycocyanin alpha chain	B [auth A] D [auth C] F [auth E] H [auth G] J [auth I] B [auth A], D [auth C], F [auth E], H [auth G], J [auth I], L [auth K]	162	Gloeobacter violaceus PCC 7421	Mutation(s): 0
UniProt
Find proteins for Q7M7F7 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421)) Explore Q7M7F7 Go to UniProtKB: Q7M7F7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7M7F7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Phycocyanin beta chain	C [auth B] E [auth D] G [auth F] I [auth H] K [auth J] C [auth B], E [auth D], G [auth F], I [auth H], K [auth J], M [auth L]	172	Gloeobacter violaceus PCC 7421	Mutation(s): 0
UniProt
Find proteins for Q7M7C7 (Gloeobacter violaceus (strain ATCC 29082 / PCC 7421)) Explore Q7M7C7 Go to UniProtKB: Q7M7C7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7M7C7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CYC (Subject of Investigation/LOI) Query on CYC Download Ideal Coordinates CCD File SDF format, chain CA [auth K] SDF format, chain DA [auth L] SDF format, chain N [auth A] SDF format, chain Q [auth C] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain Y [auth H] SDF format, chain Z [auth I] SDF format, chain X [auth H] SDF format, chain W [auth G] SDF format, chain V [auth F] SDF format, chain U [auth F] SDF format, chain T [auth E] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain EA [auth L] SDF format, chain BA [auth J] SDF format, chain AA [auth J] MOL2 format, chain CA [auth K] MOL2 format, chain DA [auth L] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain Y [auth H] MOL2 format, chain Z [auth I] MOL2 format, chain X [auth H] MOL2 format, chain W [auth G] MOL2 format, chain V [auth F] MOL2 format, chain U [auth F] MOL2 format, chain T [auth E] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain EA [auth L] MOL2 format, chain BA [auth J] MOL2 format, chain AA [auth J] mmCIF format, chain CA [auth K] mmCIF format, chain DA [auth L] mmCIF format, chain N [auth A] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth D] mmCIF format, chain S [auth D] mmCIF format, chain Y [auth H] mmCIF format, chain Z [auth I] mmCIF format, chain X [auth H] mmCIF format, chain W [auth G] mmCIF format, chain V [auth F] mmCIF format, chain U [auth F] mmCIF format, chain T [auth E] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain EA [auth L] mmCIF format, chain BA [auth J] mmCIF format, chain AA [auth J]	AA [auth J] BA [auth J] CA [auth K] DA [auth L] EA [auth L] AA [auth J], BA [auth J], CA [auth K], DA [auth L], EA [auth L], N [auth A], O [auth B], P [auth B], Q [auth C], R [auth D], S [auth D], T [auth E], U [auth F], V [auth F], W [auth G], X [auth H], Y [auth H], Z [auth I]	PHYCOCYANOBILIN C₃₃ H₄₀ N₄ O₆ VXTXPYZGDQPMHK-GMXXPEQVSA-N		Interactions Focus chain AA [auth J] Focus chain BA [auth J] Focus chain CA [auth K] Focus chain DA [auth L] Focus chain EA [auth L] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth E] Focus chain U [auth F] Focus chain V [auth F] Focus chain W [auth G] Focus chain X [auth H] Focus chain Y [auth H] Focus chain Z [auth I] Interactions & Density Focus chain AA [auth J] Focus chain BA [auth J] Focus chain CA [auth K] Focus chain DA [auth L] Focus chain EA [auth L] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth E] Focus chain U [auth F] Focus chain V [auth F] Focus chain W [auth G] Focus chain X [auth H] Focus chain Y [auth H] Focus chain Z [auth I]