8to2

Bottom cylinder of high-resolution phycobilisome quenched by OCP (local refinement)

Method: ELECTRON MICROSCOPY

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

Phycobiliprotein ApcE

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 29	Orange carotenoid-binding protein × 1 （P74102） Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core × 2 （Q02925） Allophycocyanin alpha chain × 10 （Q01951） Allophycocyanin beta chain × 11 （Q01952） Phycobilisome rod-core linker polypeptide CpcG × 1 （P73093） Allophycocyanin subunit alpha-B × 1 （P72870） Allophycocyanin subunit beta-18 × 1 （P74551） Translation initiation factor IF-2 × 1 （A0A6P1VGS4） PHYCOCYANOBILIN × 24 beta,beta-carotene-4,4'-dione × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	APCE_SYNY3
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–896； UniProt 1–896

Orange carotenoid-binding protein

OrganismNot specified

UniProt P74102

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 29	Phycobiliprotein ApcE × 1 （Q55544） Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core × 2 （Q02925） Allophycocyanin alpha chain × 10 （Q01951） Allophycocyanin beta chain × 11 （Q01952） Phycobilisome rod-core linker polypeptide CpcG × 1 （P73093） Allophycocyanin subunit alpha-B × 1 （P72870） Allophycocyanin subunit beta-18 × 1 （P74551） Translation initiation factor IF-2 × 1 （A0A6P1VGS4） PHYCOCYANOBILIN × 24 beta,beta-carotene-4,4'-dione × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	OCP_SYNY3
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–317； UniProt 1–317

Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core

OrganismNot specified

UniProt Q02925

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 29	Phycobiliprotein ApcE × 1 （Q55544） Orange carotenoid-binding protein × 1 （P74102） Allophycocyanin alpha chain × 10 （Q01951） Allophycocyanin beta chain × 11 （Q01952） Phycobilisome rod-core linker polypeptide CpcG × 1 （P73093） Allophycocyanin subunit alpha-B × 1 （P72870） Allophycocyanin subunit beta-18 × 1 （P74551） Translation initiation factor IF-2 × 1 （A0A6P1VGS4） PHYCOCYANOBILIN × 24 beta,beta-carotene-4,4'-dione × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PYC1_SYNY4
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–67； UniProt 1–67 Author chain c； PDBConstruct 1–67； UniProt 1–67

Allophycocyanin alpha chain

OrganismNot specified

UniProt Q01951

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 29	Phycobiliprotein ApcE × 1 （Q55544） Orange carotenoid-binding protein × 1 （P74102） Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core × 2 （Q02925） Allophycocyanin beta chain × 11 （Q01952） Phycobilisome rod-core linker polypeptide CpcG × 1 （P73093） Allophycocyanin subunit alpha-B × 1 （P72870） Allophycocyanin subunit beta-18 × 1 （P74551） Translation initiation factor IF-2 × 1 （A0A6P1VGS4） PHYCOCYANOBILIN × 24 beta,beta-carotene-4,4'-dione × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PHAA_SYNY3
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–161； UniProt 1–161 Author chain F； PDBConstruct 1–161； UniProt 1–161 Author chain H； PDBConstruct 1–161； UniProt 1–161 Author chain J； PDBConstruct 1–161； UniProt 1–161 Author chain L； PDBConstruct 1–161； UniProt 1–161 Author chain N； PDBConstruct 1–161； UniProt 1–161 Author chain f； PDBConstruct 1–161； UniProt 1–161 Author chain h； PDBConstruct 1–161； UniProt 1–161 Author chain j； PDBConstruct 1–161； UniProt 1–161 Author chain l； PDBConstruct 1–161； UniProt 1–161

Allophycocyanin beta chain

OrganismNot specified

UniProt Q01952

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 29	Phycobiliprotein ApcE × 1 （Q55544） Orange carotenoid-binding protein × 1 （P74102） Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core × 2 （Q02925） Allophycocyanin alpha chain × 10 （Q01951） Phycobilisome rod-core linker polypeptide CpcG × 1 （P73093） Allophycocyanin subunit alpha-B × 1 （P72870） Allophycocyanin subunit beta-18 × 1 （P74551） Translation initiation factor IF-2 × 1 （A0A6P1VGS4） PHYCOCYANOBILIN × 24 beta,beta-carotene-4,4'-dione × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	APCB_SYNY3
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–161； UniProt 1–161 Author chain G； PDBConstruct 1–161； UniProt 1–161 Author chain I； PDBConstruct 1–161； UniProt 1–161 Author chain K； PDBConstruct 1–161； UniProt 1–161 Author chain M； PDBConstruct 1–161； UniProt 1–161 Author chain O； PDBConstruct 1–161； UniProt 1–161 Author chain e； PDBConstruct 1–161； UniProt 1–161 Author chain g； PDBConstruct 1–161； UniProt 1–161 Author chain i； PDBConstruct 1–161； UniProt 1–161 Author chain k； PDBConstruct 1–161； UniProt 1–161 Author chain m； PDBConstruct 1–161； UniProt 1–161

Phycobilisome rod-core linker polypeptide CpcG

OrganismNot specified

UniProt P73093

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 29	Phycobiliprotein ApcE × 1 （Q55544） Orange carotenoid-binding protein × 1 （P74102） Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core × 2 （Q02925） Allophycocyanin alpha chain × 10 （Q01951） Allophycocyanin beta chain × 11 （Q01952） Allophycocyanin subunit alpha-B × 1 （P72870） Allophycocyanin subunit beta-18 × 1 （P74551） Translation initiation factor IF-2 × 1 （A0A6P1VGS4） PHYCOCYANOBILIN × 24 beta,beta-carotene-4,4'-dione × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PYG_SYNY3
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain P； PDBConstruct 1–249； UniProt 1–249

Allophycocyanin subunit alpha-B

OrganismNot specified

UniProt P72870

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 29	Phycobiliprotein ApcE × 1 （Q55544） Orange carotenoid-binding protein × 1 （P74102） Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core × 2 （Q02925） Allophycocyanin alpha chain × 10 （Q01951） Allophycocyanin beta chain × 11 （Q01952） Phycobilisome rod-core linker polypeptide CpcG × 1 （P73093） Allophycocyanin subunit beta-18 × 1 （P74551） Translation initiation factor IF-2 × 1 （A0A6P1VGS4） PHYCOCYANOBILIN × 24 beta,beta-carotene-4,4'-dione × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	APCD_SYNY3
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain d； PDBConstruct 1–161； UniProt 1–161

Allophycocyanin subunit beta-18

OrganismNot specified

UniProt P74551

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 29	Phycobiliprotein ApcE × 1 （Q55544） Orange carotenoid-binding protein × 1 （P74102） Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core × 2 （Q02925） Allophycocyanin alpha chain × 10 （Q01951） Allophycocyanin beta chain × 11 （Q01952） Phycobilisome rod-core linker polypeptide CpcG × 1 （P73093） Allophycocyanin subunit alpha-B × 1 （P72870） Translation initiation factor IF-2 × 1 （A0A6P1VGS4） PHYCOCYANOBILIN × 24 beta,beta-carotene-4,4'-dione × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	APCF_SYNY3
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain o； PDBConstruct 1–169； UniProt 1–169

Translation initiation factor IF-2

OrganismNot specified

UniProt A0A6P1VGS4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 29	Phycobiliprotein ApcE × 1 （Q55544） Orange carotenoid-binding protein × 1 （P74102） Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core × 2 （Q02925） Allophycocyanin alpha chain × 10 （Q01951） Allophycocyanin beta chain × 11 （Q01952） Phycobilisome rod-core linker polypeptide CpcG × 1 （P73093） Allophycocyanin subunit alpha-B × 1 （P72870） Allophycocyanin subunit beta-18 × 1 （P74551） PHYCOCYANOBILIN × 24 beta,beta-carotene-4,4'-dione × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A6P1VGS4_9SYNC
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain p； PDBConstruct 1–121； UniProt 1–121

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	8to2
Deposition date deposition_date	2023-08-02
Structure title title	Bottom cylinder of high-resolution phycobilisome quenched by OCP (local refinement)
Keywords keywords	Complex, light harvesting, pigment, 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.

8to2__assembly_1__model_1

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

Download this curve (.dat)

8to2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8to2__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	49.51 Å
Rg (electron density)	48.72 Å
Total Rg	49.10 Å
Atom count	74379
Residues	4737
Excluded volume	664410 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8to2__assembly_1__model_1`	29-meric （29）	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 (11)

Entity 1 Entity 1 polymer

Description description	Phycobiliprotein ApcE
Molecular weight formula_weight	100412.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	74379

MSVKASGGSSLARPQLYQTVPVSAISQAEQQDRFLEGSELNELTAYFQSGALRLEIAETLTQNADLIVSRAANRIFTGGSPLSYLEKPVERQPALVGASSDSRNGSVTYAESNGSGGLFGGLRSVFSSTGPIPPGFRPINIARYGPSNMQKSLRDMSWFLRYTTYAIVAGDPNIIVVNTRGLKEVIENACSIDATIVAIQEMRAASADYFRNNAQAKEIVLQYFDILLSEFKAPTPANKVRQGPSNDIQGLELPQSYFNAAAKRQKYAMKPGLSALEKNAVIKAAYRQIFERDITKAYSQSISYLESQVRNGDISMKEFVRRLAKSPLYRKQFFEPFINSRALELAFRHILGRGPSSREEVQKYFSIVSSGGLPALVDALVDSQEYADYFGEETVPYLRGLGVEAQECRNWGMQQDLFSYSAPFRKVPQFITTFAQYDRPLPDQHVYGSGNDPLEIQFGAIFPKETRNPSKRPAPFNKDTKRILIHRGPAVNNQVGNPSAVGEFPGSLGAKVFRLNGGLPGAKVGKNTGTSVKFGESSTQALIRAAYRQVFGRDLYEGQRLSVAEIQLENGDISVREFIKRLAKSELFLKLYWAPHYVCKAIEYMHRRLLGRPTYGRQEMNQYFDIASKQGFYAVVEAMIDSKEYSDAFGEDTVPYERYLTPGGLQMRSARVGSLREDIGQRVDKEVTPRFVELGQVSAIRTEPEIAYRSNQGVTRQRQQTKVFKLVSTYDKVAVKNAIRAAYRQVFERDLEPYIINSEFTALESKLSNNEINVKEFIEGLGTSELYMKEFYAPYPNTKVIEMGTKHFLGRAPLNQKEIQQYNQILASQGLKAFIGAMVNGMEYLQTFGEDTVPYRRFPTLPAANFPNTERLYNKLTKQDKELVVPSFTPVVKVGG

Entity 2 Entity 2 polymer

Description description	Orange carotenoid-binding protein
Molecular weight formula_weight	34684.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MPFTIDSARGIFPNTLAADVVPATIARFSQLNAEDQLALIWFAYLEMGKTLTIAAPGAASMQLAENALKEIQAMGPLQQTQAMCDLANRADTPLCRTYASWSPNIKLGFWYRLGELMEQGFVAPIPAGYQLSANANAVLATIQGLESGQQITVLRNAVVDMGFTAGKDGKRIAEPVVPPQDTASRTKVSIEGVTNATVLNYMDNLNANDFDTLIELFTSDGALQPPFQRPIVGKENVLRFFREECQNLKLIPERGVTEPAEDGFTQIKVTGKVQTPWFGGNVGMNIAWRFLLNPEGKIFFVAIDLLASPKELLNFAR

Entity 3 Entity 3 polymer

Description description	Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
Molecular weight formula_weight	7817.2 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,c

MRMFRITACVPSQTRIRTQRELQNTYFTKLVPYDNWFREQQRIMKMGGKIVKVELATGRPGTNAGLA

Entity 4 Entity 4 polymer

Description description	Allophycocyanin alpha chain
Molecular weight formula_weight	17429.8 kDa
Source method src_method	nat
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,F,H,J,L,N,f,h,j,l

MSIVTKSIVNADAEARYLSPGELDRIKAFVTGGAARLRIAETLTGSRETIVKQAGDRLFQKRPDIVSPGGNAYGEEMTATCLRDMDYYLRLVTYGVVSGDVTPIEEIGLVGVREMYRSLGTPIEAVAQSVREMKEVASGLMSSDDAAEASAYFDFVIGKMS

Entity 5 Entity 5 polymer

Description description	Allophycocyanin beta chain
Molecular weight formula_weight	17231.6 kDa
Source method src_method	nat
Copy count entity_count	11

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,G,I,K,M,O,e,g,i,k,m

MQDAITAVINSADVQGKYLDGAAMDKLKSYFASGELRVRAASVISANAATIVKEAVAKSLLYSDVTRPGGNMYTTRRYAACIRDLDYYLRYATYAMLAGDASILDERVLNGLKETYNSLGVPISSTVQAIQAIKEVTASLVGADAGKEMGVYLDYICSGLS

Entity 6 Entity 6 polymer

Description description	Phycobilisome rod-core linker polypeptide CpcG
Molecular weight formula_weight	28938.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

MALPLLNYAPKSQNVRVEGYEIGSEEKPVVFTTENILSSSDMDNLIEAAYRQIFFHAFKWDREKVLESQLRNGQITVRDFVRGLLLSNTFRNSFYEKNSNYRFVEHCVQKILGRDVYSEREKIAWSIVVATKGYQGLIDDLLNSDEYLNNFGYDTVPYQRRRNLPGREAGELPFNIKSPRYDAYHRRQLGFPQIVWQNEVRRFIPQEKKLTAGNPMNFLGMARSINPAANTIPKVSAQNINIEASVPRR

Entity 7 Entity 7 polymer

Description description	Allophycocyanin subunit alpha-B
Molecular weight formula_weight	17940.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	d

MSVVSQVILQADDQLRYPTSGELKGIQAFLTTGAQRIRIAETLAENEKKIVDQAQKQLFKKHPEYRAPGGNAYGQRQYNQCLRDYGWYLRLVTYGVLAGNKEPIETTGLIGVKEMYNSLNVPVPGMVDAVTVLKDAALGLLSAEDANETAPYFDYIIQFMS

Entity 8 Entity 8 polymer

Description description	Allophycocyanin subunit beta-18
Molecular weight formula_weight	18911.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	o

MRDAVTTLIKNYDLTGRYLDRNAMDELKAYFESGSARIAAAAMINANSATIVKRAAAQLFEEIPELIRPSGNAYTTRRFSACLRDMDYYLRYASYALIAADNNVLDERVLQGLRETYNSLGVPIGPTVRGIQIMKEMIEAMAEDSSLNSTDFIASPFDHMTRELSELSV

Entity 9 Entity 9 polymer

Description description	Translation initiation factor IF-2
Molecular weight formula_weight	12928.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	p

MLKKLFGAKKEFYVQLDESQAPAQVEEADVAIVKSEVAPVEKPAPTTSKKTSIKKKSATKAAAPVETPASAPVAPAPKAKVDPSQVAFASGDPIPQNVARRTPGPSLNRFKEMARQVKVKR

Entity 10 Entity 10 non-polymer

Description description	PHYCOCYANOBILIN
Molecular weight formula_weight	588.7 kDa
Source method src_method	syn
Copy count entity_count	24

Entity 11 Entity 11 non-polymer

Description description	beta,beta-carotene-4,4'-dione
Molecular weight formula_weight	564.8 kDa
Source method src_method	syn
Copy count entity_count	1

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	2.00 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	153576

Bottom cylinder of high-resolution phycobilisome quenched by OCP (local refinement)

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

Phycobiliprotein ApcE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Orange carotenoid-binding protein

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 7.8 kDa linker polypeptide, allophycocyanin-associated, core

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Allophycocyanin alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Allophycocyanin beta chain

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 rod-core linker polypeptide CpcG

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Allophycocyanin subunit alpha-B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Allophycocyanin subunit beta-18

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Translation initiation factor IF-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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8to2__assembly_1__model_1

8to2__assembly_1__model_1 | I(q)

8to2__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment