PDB-9v7g: Phycobilisome Rx rod from Gloeobacter violaceus PCC 7421

ID or keywords:

Entry

Database: PDB / ID: 9v7g

Title

Phycobilisome Rx rod from Gloeobacter violaceus PCC 7421

Components

Glr2806 protein
Phycocyanin alpha chain
Phycocyanin beta chain

Keywords

PHOTOSYNTHESIS / Phycobilisome

Function / homology

Function and homology information

phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis
Similarity search - Function

Biological species

Gloeobacter violaceus PCC 7421 (bacteria)

Method

ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.72 Å

Authors

Burtseva, A.D. / Baymukhametov, T.N. / Slonimskiy, Y.B. / Popov, V.O. / Sluchanko, N.N. / Boyko, K.M.

Funding support

Russian Federation, 1items

Citation

Journal: To Be Published
Title: Structure and quenching of a bundle-shaped phycobilisome
Authors: Burtseva, A.D. / Slonimskiy, Y.B. / Baymukhametov, T.N. / Sinetova, M.A. / Maksimov, E.G. / Popov, V.O. / Boyko, K.M. / Sluchanko, N.N.

History

Deposition	May 28, 2025	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Sep 24, 2025	Provider: repository / Type: Initial release
Revision 1.0	Sep 24, 2025	Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0	Sep 24, 2025	Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0	Sep 24, 2025	Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0	Sep 24, 2025	Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0	Sep 24, 2025	Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9v7g.cif.gz	444.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9v7g.ent.gz	354.9 KB	Display	PDB format
PDBx/mmJSON format	9v7g.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9v7g_validation.pdf.gz	2.3 MB	Display	wwPDB validaton report
Full document	9v7g_full_validation.pdf.gz	2.3 MB	Display
Data in XML	9v7g_validation.xml.gz	72.1 KB	Display
Data in CIF	9v7g_validation.cif.gz	104.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/v7/9v7g ftp://data.pdbj.org/pub/pdb/validation_reports/v7/9v7g	HTTPS FTP

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Related structure data

Related structure data	64812MC 64813C 64814C 64815C 64816C 64817C 64828C 64851C 64852C 64868C 9v7hC 9v7iC 9v7jC 9v7kC 9v7lC M: map data used to model this data C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

X: Glr2806 protein

A: Phycocyanin alpha chain

B: Phycocyanin beta chain

C: Phycocyanin alpha chain

D: Phycocyanin beta chain

E: Phycocyanin alpha chain

F: Phycocyanin beta chain

G: Phycocyanin alpha chain

H: Phycocyanin beta chain

I: Phycocyanin alpha chain

J: Phycocyanin beta chain

K: Phycocyanin alpha chain

L: Phycocyanin beta chain

hetero molecules

309 kDa, 13 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: electron microscopy, not applicable

Noncrystallographic symmetry (NCS)

NCS domain:
NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30
16	Local NCS retraints between domains: 31 32
17	Local NCS retraints between domains: 33 34
18	Local NCS retraints between domains: 35 36
19	Local NCS retraints between domains: 37 38
20	Local NCS retraints between domains: 39 40
21	Local NCS retraints between domains: 41 42
22	Local NCS retraints between domains: 43 44
23	Local NCS retraints between domains: 45 46
24	Local NCS retraints between domains: 47 48
25	Local NCS retraints between domains: 49 50
26	Local NCS retraints between domains: 51 52
27	Local NCS retraints between domains: 53 54
28	Local NCS retraints between domains: 55 56
29	Local NCS retraints between domains: 57 58
30	Local NCS retraints between domains: 59 60

#1: Protein	Glr2806 protein Mass: 81544.312 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gloeobacter violaceus PCC 7421 (bacteria) / References: UniProt: Q7NGT2
#2: Protein	Phycocyanin alpha chain Mass: 17679.852 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Gloeobacter violaceus PCC 7421 (bacteria) / References: UniProt: Q7M7F7
#3: Protein	Phycocyanin beta chain Mass: 18478.953 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Gloeobacter violaceus PCC 7421 (bacteria) / References: UniProt: Q7M7C7
#4: Chemical	ChemComp-CYC / PHYCOCYANOBILIN Mass: 588.694 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C₃₃H₄₀N₄O₆ / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: ELECTRON MICROSCOPY
EM experiment	Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component	Name: Bundle-shaped phycobilisome / Type: COMPLEX / Entity ID: #1-#3 / Source: NATURAL
Source (natural)	Organism: Gloeobacter violaceus PCC 7421 (bacteria)
Buffer solution	pH: 7
Buffer component	Conc.: 50 mM / Name: Tris(hydroxymethyl)aminomethane hydrochloride / Formula: Tris-HCl
Specimen	Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Vitrification	Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment	Model: Titan Krios / Image courtesy: FEI Company
Microscopy	Model: TFS KRIOS / Details: Preliminary grid screening was performed manually.
Electron gun	Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lens	Mode: BRIGHT FIELD / Nominal magnification: 85000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm / Cs: 0.01 mm / C2 aperture diameter: 100 µm / Alignment procedure: ZEMLIN TABLEAU
Specimen holder	Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recording	Average exposure time: 3.9 sec. / Electron dose: 66 e/Å² / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)
EM imaging optics	Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV Spherical aberration corrector: Microscope was modified with a Cs corrector (CEOS GmbH, Germany).
Image scans	Width: 5760 / Height: 4092

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Processing

EM software

ID	Name	Version	Category
2	SerialEM	4.04	image acquisition
4	Warp	1.0.9	CTF correction
11	cryoSPARC	4.7	final Euler assignment
13	cryoSPARC	4.7	3D reconstruction

CTF correction

Type: NONE

Symmetry

Point symmetry: C₁ (asymmetric)

3D reconstruction

Resolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 746972 / Symmetry type: POINT

Refinement

Resolution: 2.72→2.72 Å / Cor.coef. F_o:F_c: 0.931 / WR_factor R_work: 0.302 / SU B: 14.328 / SU ML: 0.272 / Average fsc free: 0 / Average fsc overall: 0.8222 / Average fsc work: 0.8222 / ESU R: 0.408
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_work	0.3017	147013	-
all	0.302	-	-
R_free	-	-	0 %
obs	-	-	100 %

Solvent computation

Solvent model: NONE

Displacement parameters

B_iso mean: 41.041 Å²

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
ELECTRON MICROSCOPY	r_bond_refined_d	0.009	0.012	17919
ELECTRON MICROSCOPY	r_bond_other_d	0.001	0.016	16992
ELECTRON MICROSCOPY	r_angle_refined_deg	1.581	1.814	24384
ELECTRON MICROSCOPY	r_angle_other_deg	0.661	1.749	38864
ELECTRON MICROSCOPY	r_dihedral_angle_1_deg	4.844	5	2194
ELECTRON MICROSCOPY	r_dihedral_angle_2_deg	17.139	8.568	454
ELECTRON MICROSCOPY	r_dihedral_angle_3_deg	17.008	10	2856
ELECTRON MICROSCOPY	r_dihedral_angle_6_deg	15.188	10	777
ELECTRON MICROSCOPY	r_chiral_restr	0.097	0.2	2699
ELECTRON MICROSCOPY	r_gen_planes_refined	0.008	0.02	22219
ELECTRON MICROSCOPY	r_gen_planes_other	0.004	0.02	4145
ELECTRON MICROSCOPY	r_nbd_refined	0.219	0.2	4555
ELECTRON MICROSCOPY	r_symmetry_nbd_other	0.211	0.2	15915
ELECTRON MICROSCOPY	r_nbtor_refined	0.187	0.2	9267
ELECTRON MICROSCOPY	r_symmetry_nbtor_other	0.077	0.2	10801
ELECTRON MICROSCOPY	r_xyhbond_nbd_refined	0.167	0.2	252
ELECTRON MICROSCOPY	r_symmetry_xyhbond_nbd_other	0.061	0.2	1
ELECTRON MICROSCOPY	r_mcbond_it	2.164	3.944	8815
ELECTRON MICROSCOPY	r_mcbond_other	2.164	3.944	8815
ELECTRON MICROSCOPY	r_mcangle_it	3.391	7.078	10996
ELECTRON MICROSCOPY	r_mcangle_other	3.391	7.078	10997
ELECTRON MICROSCOPY	r_scbond_it	2.502	4.267	9104
ELECTRON MICROSCOPY	r_scbond_other	2.502	4.267	9103
ELECTRON MICROSCOPY	r_scangle_it	4.283	7.675	13388
ELECTRON MICROSCOPY	r_scangle_other	4.283	7.675	13389
ELECTRON MICROSCOPY	r_lrange_it	5.671	36.29	21006
ELECTRON MICROSCOPY	r_lrange_other	5.671	36.289	21007
ELECTRON MICROSCOPY	r_ncsr_local_group_1	0.084	0.05	5389
ELECTRON MICROSCOPY	r_ncsr_local_group_2	0.096	0.05	5387
ELECTRON MICROSCOPY	r_ncsr_local_group_3	0.087	0.05	5463
ELECTRON MICROSCOPY	r_ncsr_local_group_4	0.091	0.05	5420
ELECTRON MICROSCOPY	r_ncsr_local_group_5	0.081	0.05	5477
ELECTRON MICROSCOPY	r_ncsr_local_group_6	0.089	0.05	5706
ELECTRON MICROSCOPY	r_ncsr_local_group_7	0.111	0.05	5621
ELECTRON MICROSCOPY	r_ncsr_local_group_8	0.109	0.05	5711
ELECTRON MICROSCOPY	r_ncsr_local_group_9	0.101	0.05	5712
ELECTRON MICROSCOPY	r_ncsr_local_group_10	0.1	0.05	5651
ELECTRON MICROSCOPY	r_ncsr_local_group_11	0.089	0.05	5386
ELECTRON MICROSCOPY	r_ncsr_local_group_12	0.079	0.05	5451
ELECTRON MICROSCOPY	r_ncsr_local_group_13	0.088	0.05	5424
ELECTRON MICROSCOPY	r_ncsr_local_group_14	0.084	0.05	5399
ELECTRON MICROSCOPY	r_ncsr_local_group_15	0.102	0.05	5629
ELECTRON MICROSCOPY	r_ncsr_local_group_16	0.102	0.05	5668
ELECTRON MICROSCOPY	r_ncsr_local_group_17	0.098	0.05	5654
ELECTRON MICROSCOPY	r_ncsr_local_group_18	0.096	0.05	5619
ELECTRON MICROSCOPY	r_ncsr_local_group_19	0.077	0.05	5442
ELECTRON MICROSCOPY	r_ncsr_local_group_20	0.083	0.05	5393
ELECTRON MICROSCOPY	r_ncsr_local_group_21	0.088	0.05	5417
ELECTRON MICROSCOPY	r_ncsr_local_group_22	0.112	0.05	5658
ELECTRON MICROSCOPY	r_ncsr_local_group_23	0.103	0.05	5662
ELECTRON MICROSCOPY	r_ncsr_local_group_24	0.099	0.05	5613
ELECTRON MICROSCOPY	r_ncsr_local_group_25	0.075	0.05	5461
ELECTRON MICROSCOPY	r_ncsr_local_group_26	0.082	0.05	5465
ELECTRON MICROSCOPY	r_ncsr_local_group_27	0.108	0.05	5710
ELECTRON MICROSCOPY	r_ncsr_local_group_28	0.102	0.05	5655
ELECTRON MICROSCOPY	r_ncsr_local_group_29	0.087	0.05	5436
ELECTRON MICROSCOPY	r_ncsr_local_group_30	0.088	0.05	5691

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	X	ELECTRON MICROSCOPY	Local ncs	0.08398	0.05009
1	2	X	ELECTRON MICROSCOPY	Local ncs	0.08398	0.05009
2	3	X	ELECTRON MICROSCOPY	Local ncs	0.09588	0.05008
2	4	X	ELECTRON MICROSCOPY	Local ncs	0.09588	0.05008
3	5	X	ELECTRON MICROSCOPY	Local ncs	0.08699	0.05009
3	6	X	ELECTRON MICROSCOPY	Local ncs	0.08699	0.05009
4	7	X	ELECTRON MICROSCOPY	Local ncs	0.09141	0.05009
4	8	X	ELECTRON MICROSCOPY	Local ncs	0.09141	0.05009
5	9	X	ELECTRON MICROSCOPY	Local ncs	0.08074	0.05009
5	10	X	ELECTRON MICROSCOPY	Local ncs	0.08074	0.05009
6	11	X	ELECTRON MICROSCOPY	Local ncs	0.08893	0.05008
6	12	X	ELECTRON MICROSCOPY	Local ncs	0.08893	0.05008
7	13	X	ELECTRON MICROSCOPY	Local ncs	0.11098	0.05008
7	14	X	ELECTRON MICROSCOPY	Local ncs	0.11098	0.05008
8	15	X	ELECTRON MICROSCOPY	Local ncs	0.10854	0.05008
8	16	X	ELECTRON MICROSCOPY	Local ncs	0.10854	0.05008
9	17	X	ELECTRON MICROSCOPY	Local ncs	0.10078	0.05009
9	18	X	ELECTRON MICROSCOPY	Local ncs	0.10078	0.05009
10	19	X	ELECTRON MICROSCOPY	Local ncs	0.10033	0.05008
10	20	X	ELECTRON MICROSCOPY	Local ncs	0.10033	0.05008
11	21	X	ELECTRON MICROSCOPY	Local ncs	0.0889	0.05008
11	22	X	ELECTRON MICROSCOPY	Local ncs	0.0889	0.05008
12	23	X	ELECTRON MICROSCOPY	Local ncs	0.07942	0.05009
12	24	X	ELECTRON MICROSCOPY	Local ncs	0.07942	0.05009
13	25	X	ELECTRON MICROSCOPY	Local ncs	0.08755	0.05009
13	26	X	ELECTRON MICROSCOPY	Local ncs	0.08755	0.05009
14	27	X	ELECTRON MICROSCOPY	Local ncs	0.08431	0.05009
14	28	X	ELECTRON MICROSCOPY	Local ncs	0.08431	0.05009
15	29	X	ELECTRON MICROSCOPY	Local ncs	0.10238	0.05008
15	30	X	ELECTRON MICROSCOPY	Local ncs	0.10238	0.05008
16	31	X	ELECTRON MICROSCOPY	Local ncs	0.10169	0.05008
16	32	X	ELECTRON MICROSCOPY	Local ncs	0.10169	0.05008
17	33	X	ELECTRON MICROSCOPY	Local ncs	0.09785	0.05008
17	34	X	ELECTRON MICROSCOPY	Local ncs	0.09785	0.05008
18	35	X	ELECTRON MICROSCOPY	Local ncs	0.09568	0.05008
18	36	X	ELECTRON MICROSCOPY	Local ncs	0.09568	0.05008
19	37	X	ELECTRON MICROSCOPY	Local ncs	0.07712	0.05009
19	38	X	ELECTRON MICROSCOPY	Local ncs	0.07712	0.05009
20	39	X	ELECTRON MICROSCOPY	Local ncs	0.08323	0.05008
20	40	X	ELECTRON MICROSCOPY	Local ncs	0.08323	0.05008
21	41	X	ELECTRON MICROSCOPY	Local ncs	0.08774	0.05009
21	42	X	ELECTRON MICROSCOPY	Local ncs	0.08774	0.05009
22	43	X	ELECTRON MICROSCOPY	Local ncs	0.1124	0.05008
22	44	X	ELECTRON MICROSCOPY	Local ncs	0.1124	0.05008
23	45	X	ELECTRON MICROSCOPY	Local ncs	0.10258	0.05008
23	46	X	ELECTRON MICROSCOPY	Local ncs	0.10258	0.05008
24	47	X	ELECTRON MICROSCOPY	Local ncs	0.09932	0.05008
24	48	X	ELECTRON MICROSCOPY	Local ncs	0.09932	0.05008
25	49	X	ELECTRON MICROSCOPY	Local ncs	0.07515	0.05009
25	50	X	ELECTRON MICROSCOPY	Local ncs	0.07515	0.05009
26	51	X	ELECTRON MICROSCOPY	Local ncs	0.0824	0.05009
26	52	X	ELECTRON MICROSCOPY	Local ncs	0.0824	0.05009
27	53	X	ELECTRON MICROSCOPY	Local ncs	0.10837	0.05008
27	54	X	ELECTRON MICROSCOPY	Local ncs	0.10837	0.05008
28	55	X	ELECTRON MICROSCOPY	Local ncs	0.10191	0.05008
28	56	X	ELECTRON MICROSCOPY	Local ncs	0.10191	0.05008
29	57	X	ELECTRON MICROSCOPY	Local ncs	0.08684	0.05009
29	58	X	ELECTRON MICROSCOPY	Local ncs	0.08684	0.05009
30	59	X	ELECTRON MICROSCOPY	Local ncs	0.08799	0.05009
30	60	X	ELECTRON MICROSCOPY	Local ncs	0.08799	0.05009

LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection R_free: _ / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc work	WR_factor R_work
2.82-2.893	0.748	10856	0.748	10856	0.549	0.748
2.893-2.973	0.455	10573	0.455	10573	0.645	0.455
2.973-3.059	0.42	10385	0.42	10385	0.696	0.42
3.059-3.153	0.379	10011	0.379	10011	0.751	0.379
3.153-3.256	0.356	9613	0.356	9613	0.796	0.356
3.256-3.37	0.322	9397	0.322	9397	0.839	0.322
3.37-3.497	0.305	9135	0.305	9135	0.864	0.305
3.497-3.64	0.293	8693	0.293	8693	0.879	0.293
3.64-3.802	0.277	8307	0.277	8307	0.9	0.277
3.802-3.987	0.275	8041	0.275	8041	0.91	0.275
3.987-4.203	0.266	7543	0.266	7543	0.921	0.266
4.203-4.457	0.267	7253	0.267	7253	0.925	0.267
4.457-4.765	0.26	6720	0.26	6720	0.925	0.26
4.765-5.146	0.257	6239	0.257	6239	0.919	0.257
5.146-5.636	0.28	5822	0.28	5822	0.899	0.28
5.636-6.3	0.341	5273	0.341	5273	0.877	0.341
6.3-7.272	0.332	4572	0.332	4572	0.871	0.332
7.272-8.9	0.268	3922	0.268	3922	0.906	0.268
8.9-12.558	0.216	2993	0.216	2993	0.948	0.216
12.558-132.349	0.287	1663	0.287	1663	0.975	0.287

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Yorodumi