8hfq

Cryo-EM structure of CpcL-PBS from cyanobacterium Synechocystis sp. PCC 6803

Method: ELECTRON MICROSCOPY

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1. Protein Identity and Related Structures Protein Identity & Related Structures

C-phycocyanin alpha subunit

Synechocystis sp. (strain PCC 6803 / Kazusa)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 40	C-phycocyanin beta subunit × 18 （Q54714） Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 1 × 1 （P73203） Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 2 × 1 （P73204） Ferredoxin--NADP reductase × 1 （Q55318） Photosystem I-associated linker protein CpcL × 1 （P74625） PHYCOCYANOBILIN × 54	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PHCA_SYNY3
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–162； UniProt 1–162 Author chain C； PDBConstruct 1–162； UniProt 1–162 Author chain E； PDBConstruct 1–162； UniProt 1–162 Author chain G； PDBConstruct 1–162； UniProt 1–162 Author chain I； PDBConstruct 1–162； UniProt 1–162 Author chain K； PDBConstruct 1–162； UniProt 1–162 Author chain M； PDBConstruct 1–162； UniProt 1–162 Author chain O； PDBConstruct 1–162； UniProt 1–162 Author chain Q； PDBConstruct 1–162； UniProt 1–162 Author chain S； PDBConstruct 1–162； UniProt 1–162 Author chain U； PDBConstruct 1–162； UniProt 1–162 Author chain W； PDBConstruct 1–162； UniProt 1–162 Author chain Y； PDBConstruct 1–162； UniProt 1–162 Author chain a； PDBConstruct 1–162； UniProt 1–162 Author chain c； PDBConstruct 1–162； UniProt 1–162 Author chain e； PDBConstruct 1–162； UniProt 1–162 Author chain g； PDBConstruct 1–162； UniProt 1–162 Author chain i； PDBConstruct 1–162； UniProt 1–162

C-phycocyanin beta subunit

Synechocystis sp. (strain PCC 6803 / Kazusa)

UniProt Q54714

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 40	C-phycocyanin alpha subunit × 18 （Q54715） Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 1 × 1 （P73203） Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 2 × 1 （P73204） Ferredoxin--NADP reductase × 1 （Q55318） Photosystem I-associated linker protein CpcL × 1 （P74625） PHYCOCYANOBILIN × 54	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PHCB_SYNY3
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–172； UniProt 1–172 Author chain D； PDBConstruct 1–172； UniProt 1–172 Author chain F； PDBConstruct 1–172； UniProt 1–172 Author chain H； PDBConstruct 1–172； UniProt 1–172 Author chain J； PDBConstruct 1–172； UniProt 1–172 Author chain L； PDBConstruct 1–172； UniProt 1–172 Author chain N； PDBConstruct 1–172； UniProt 1–172 Author chain P； PDBConstruct 1–172； UniProt 1–172 Author chain R； PDBConstruct 1–172； UniProt 1–172 Author chain T； PDBConstruct 1–172； UniProt 1–172 Author chain V； PDBConstruct 1–172； UniProt 1–172 Author chain X； PDBConstruct 1–172； UniProt 1–172 Author chain Z； PDBConstruct 1–172； UniProt 1–172 Author chain b； PDBConstruct 1–172； UniProt 1–172 Author chain d； PDBConstruct 1–172； UniProt 1–172 Author chain f； PDBConstruct 1–172； UniProt 1–172 Author chain h； PDBConstruct 1–172； UniProt 1–172 Author chain j； PDBConstruct 1–172； UniProt 1–172

Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 1

Synechocystis sp. (strain PCC 6803 / Kazusa)

UniProt P73203

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 40	C-phycocyanin alpha subunit × 18 （Q54715） C-phycocyanin beta subunit × 18 （Q54714） Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 2 × 1 （P73204） Ferredoxin--NADP reductase × 1 （Q55318） Photosystem I-associated linker protein CpcL × 1 （P74625） PHYCOCYANOBILIN × 54	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PYR1_SYNY3
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain k； PDBConstruct 1–291； UniProt 1–291

Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 2

Synechocystis sp. (strain PCC 6803 / Kazusa)

UniProt P73204

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 40	C-phycocyanin alpha subunit × 18 （Q54715） C-phycocyanin beta subunit × 18 （Q54714） Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 1 × 1 （P73203） Ferredoxin--NADP reductase × 1 （Q55318） Photosystem I-associated linker protein CpcL × 1 （P74625） PHYCOCYANOBILIN × 54	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PYR2_SYNY3
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain l； PDBConstruct 1–273； UniProt 1–273

Ferredoxin--NADP reductase

Synechocystis sp. (strain PCC 6803 / Kazusa)

UniProt Q55318

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 40	C-phycocyanin alpha subunit × 18 （Q54715） C-phycocyanin beta subunit × 18 （Q54714） Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 1 × 1 （P73203） Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 2 × 1 （P73204） Photosystem I-associated linker protein CpcL × 1 （P74625） PHYCOCYANOBILIN × 54	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FENR_SYNY3
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain m； PDBConstruct 1–413； UniProt 1–413

Photosystem I-associated linker protein CpcL

Synechocystis sp. (strain PCC 6803 / Kazusa)

UniProt P74625

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 40	C-phycocyanin alpha subunit × 18 （Q54715） C-phycocyanin beta subunit × 18 （Q54714） Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 1 × 1 （P73203） Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 2 × 1 （P73204） Ferredoxin--NADP reductase × 1 （Q55318） PHYCOCYANOBILIN × 54	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CPCL_SYNY3
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain n； PDBConstruct 1–249； UniProt 1–249

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8hfq
Deposition date deposition_date	2022-11-11
Structure title title	Cryo-EM structure of CpcL-PBS from cyanobacterium Synechocystis sp. PCC 6803
Keywords keywords	CpcL-phycobilisome, energy transfer, ferredoxin:NADP+ oxidoreductase, ultrafast spectroscopy, PHOTOSYNTHESIS; PHOTOSYNTHESIS
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

8hfq__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

8hfq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8hfq__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	59.59 Å
Rg (electron density)	59.36 Å
Total Rg	59.46 Å
Atom count	54193
Residues	6851
Excluded volume	958290 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8hfq__assembly_1__model_1`	40-meric （40）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	C-phycocyanin alpha subunit
Molecular weight formula_weight	17602.5 kDa
Source method src_method	man
Copy count entity_count	18

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K,M,O,Q,S,U,W,Y,a,c,e,g,i
Atom count atom_count	54193

MKTPLTEAVSTADSQGRFLSSTELQIAFGRLRQANAGLQAAKALTDNAQSLVNGAAQAVYNKFPYTTQTQGNNFAADQRGKDKCARDIGYYLRIVTYCLVAGGTGPLDEYLIAGIDEINRTFDLSPSWYVEALKYIKANHGLSGDARDEANSYLDYAINALS

Source Source

Source organism organism	Synechocystis sp. (strain PCC 6803 / Kazusa)
NCBI taxonomy ID ncbi_taxonomy_id	1111708
Host organism host_organism	Synechocystis sp. PCC 6803

Entity 2 Entity 2 polymer

Description description	C-phycocyanin beta subunit
Molecular weight formula_weight	18142.4 kDa
Source method src_method	man
Copy count entity_count	18

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H,J,L,N,P,R,T,V,X,Z,b,d,f,h,j

MFDVFTRVVSQADARGEYLSGSQLDALSATVAEGNKRIDSVNRITGNASAIVSNAARALFAEQPQLIQPGGNAYTSRRMAACLRDMEIILRYVTYATFTGDASVLEDRCLNGLRETYVALGVPGASVAAGVQKMKEAALDIVNDPNGITRGDCSAIVAEIAGYFDRAAAAVA

Source Source

Source organism organism	Synechocystis sp. (strain PCC 6803 / Kazusa)
NCBI taxonomy ID ncbi_taxonomy_id	1111708
Host organism host_organism	Synechocystis sp. PCC 6803

Entity 3 Entity 3 polymer

Description description	Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 1
Molecular weight formula_weight	32558.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	k

MAITTAASRLGVAPYNESRPVELRPDFSLDDAKMVIRAVYRQVLGNDYIMDSERLKGAESLLTNGSISVREFVRTVAKSELYKKKFLYNNFQTRVIELNYKHLLGRAPFSEDEVIFHLDLYENQGFDADIDSYIDSVEYQENFGENIVPYYRFNNQVGDRTVGFTRMFRLYRGYANSDRSQLERSSSRLATELGQNTVSAIVGPSGSNAGWAYRPSRAGNTPAKALGGTVPFGQASKLFRVEITAISAPGYPKVRRSNKAVIVPFEQLNQTLQQINRLGGKVASITPASLS

Source Source

Source organism organism	Synechocystis sp. (strain PCC 6803 / Kazusa)
NCBI taxonomy ID ncbi_taxonomy_id	1111708
Host organism host_organism	Synechocystis sp. PCC 6803

Entity 4 Entity 4 polymer

Description description	Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 2
Molecular weight formula_weight	30836.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	l

MTSLVSAQRLGIVAVDEAIPLELRSRSTEEEVDAVILAVYRQVLGNDHLMSQERLTSAESLLRGREISVRDFVRAVALSEVYRQKFFHSNPQNRFIELNYKHLLGRAPYDQSEIAFHTDLYHQGGYEAEINSYIDSVEYTENFGDWVVPYFRGFATQRNQKTVGFSRSFQVYRGYATSDRSQGNGSRSRLTRELARNTASPVYAGSTAESLRGTSAGSRNQMYRLQVIQGAAPGRGTRVRRGKAEYLVSYDNLSAKLQQINRQGDTVTMISLA

Source Source

Source organism organism	Synechocystis sp. (strain PCC 6803 / Kazusa)
NCBI taxonomy ID ncbi_taxonomy_id	1111708
Host organism host_organism	Synechocystis sp. PCC 6803

Entity 5 Entity 5 polymer

Description description	Ferredoxin--NADP reductase
Molecular weight formula_weight	46417.5 kDa
EC 编号 ec_number	1.18.1.2
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	m

MYSPGYVATSSRQSDAGNRLFVYEVIGLSQSTMTDGLDYPIRRSGSTFITVPLKRMNQEMRRITRMGGKIVSIKPLEGDSPLPHTEGIAKPSQSEGSGSEAVANPAPESNKTMTTTPKEKKADDIPVNIYRPKTPYIGKVLENYPLVREGAIGTVQHLTFDLSAGDLRYLEGQSIGIIPPGEDDKGKPHKLRLYSIASTRHGDFGDDKTVSLCVRQLEYQNEAGETVQGVCSTYLCNIKEGDDIAITGPVGKEMLLPPDEDANIVMLATGTGIAPFRAFLWRMFKEQHEDYKFKGLAWLIFGIPKSENILYKDDLEKMAAEFPDNFRLTYAISREQQNAEGGRMYIQHRVAENAEELWNLMQNPKTHTYMCGLKGMEPGIDEAFTALAEQNGKEWTTFQREMKKEHRWHVETY

Source Source

Source organism organism	Synechocystis sp. (strain PCC 6803 / Kazusa)
NCBI taxonomy ID ncbi_taxonomy_id	1111708
Host organism host_organism	Synechocystis sp. PCC 6803

Entity 6 Entity 6 polymer

Description description	Photosystem I-associated linker protein CpcL
Molecular weight formula_weight	28551.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	n

MTLPLIAYAPVSQNQRVTNYEVSGDEHARIFTTEGTLSPSAMDNLIAAAYRQVFNEQQMIQSNRQIALESQFKNQQITVRDFIRGLALSDSFRRRNFEVNNNYRFVQMCIQRLLGRDVYSEEEKIAWSIVIATKGLPGFINELLNSQEYLENFGYDTVPYQRRRILPQRISGELPFARMPRYGADHREKLEAIGYFRNQAPLTYRWEWQKQPYPAGVYLAGKVVLYVGGALVSLGIIAVALSAWGIIGL

Source Source

Source organism organism	Synechocystis sp. (strain PCC 6803 / Kazusa)
NCBI taxonomy ID ncbi_taxonomy_id	1111708
Host organism host_organism	Synechocystis sp. PCC 6803

Entity 7 Entity 7 non-polymer

Description description	PHYCOCYANOBILIN
Molecular weight formula_weight	588.7 kDa
Source method src_method	syn
Copy count entity_count	54

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Resolution resolution	2.64 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	124441

Cryo-EM structure of CpcL-PBS from cyanobacterium Synechocystis sp. PCC 6803

1. Protein Identity and Related Structures Protein Identity & Related Structures

C-phycocyanin alpha subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

C-phycocyanin beta subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Ferredoxin--NADP reductase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Photosystem I-associated linker protein CpcL

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8hfq__assembly_1__model_1

8hfq__assembly_1__model_1 | I(q)

8hfq__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 non-polymer

7. Citations (1)