8tpj

Top cylinder bound to OCP from 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 20	Orange carotenoid-binding protein × 2 （P74102） Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core × 1 （Q02925） Allophycocyanin alpha chain × 6 （Q01951） Allophycocyanin beta chain × 6 （Q01952） Phycobilisome rod-core linker polypeptide CpcG × 4 （P73093） beta,beta-carotene-4,4'-dione × 1 PHYCOCYANOBILIN × 12 water × 20	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

Synechocystis sp. PCC 6803

UniProt P74102

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 20	Phycobiliprotein ApcE × 1 （Q55544） Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core × 1 （Q02925） Allophycocyanin alpha chain × 6 （Q01951） Allophycocyanin beta chain × 6 （Q01952） Phycobilisome rod-core linker polypeptide CpcG × 4 （P73093） beta,beta-carotene-4,4'-dione × 1 PHYCOCYANOBILIN × 12 water × 20	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 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 20	Phycobiliprotein ApcE × 1 （Q55544） Orange carotenoid-binding protein × 2 （P74102） Allophycocyanin alpha chain × 6 （Q01951） Allophycocyanin beta chain × 6 （Q01952） Phycobilisome rod-core linker polypeptide CpcG × 4 （P73093） beta,beta-carotene-4,4'-dione × 1 PHYCOCYANOBILIN × 12 water × 20	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

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 20	Phycobiliprotein ApcE × 1 （Q55544） Orange carotenoid-binding protein × 2 （P74102） Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core × 1 （Q02925） Allophycocyanin beta chain × 6 （Q01952） Phycobilisome rod-core linker polypeptide CpcG × 4 （P73093） beta,beta-carotene-4,4'-dione × 1 PHYCOCYANOBILIN × 12 water × 20	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

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 20	Phycobiliprotein ApcE × 1 （Q55544） Orange carotenoid-binding protein × 2 （P74102） Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core × 1 （Q02925） Allophycocyanin alpha chain × 6 （Q01951） Phycobilisome rod-core linker polypeptide CpcG × 4 （P73093） beta,beta-carotene-4,4'-dione × 1 PHYCOCYANOBILIN × 12 water × 20	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

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 20	Phycobiliprotein ApcE × 1 （Q55544） Orange carotenoid-binding protein × 2 （P74102） Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core × 1 （Q02925） Allophycocyanin alpha chain × 6 （Q01951） Allophycocyanin beta chain × 6 （Q01952） beta,beta-carotene-4,4'-dione × 1 PHYCOCYANOBILIN × 12 water × 20	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 Author chain Q； PDBConstruct 1–249； UniProt 1–249 Author chain R； PDBConstruct 1–249； UniProt 1–249 Author chain S； 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	8tpj
Deposition date deposition_date	2023-08-04
Last revision last_revision	2024-04-17
Structure title title	Top cylinder bound to OCP from 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.

8tpj__assembly_1__model_1

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

Download this curve (.dat)

8tpj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8tpj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	44.95 Å
Rg (electron density)	44.63 Å
Total Rg	44.91 Å
Atom count	42794
Residues	2720
Excluded volume	382250 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8tpj__assembly_1__model_1`	eicosameric （20）	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 (9)

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	45170

MSVKASGGSSLARPQLYQTVPVSAISQAEQQDRFLEGSELNELTAYFQSGALRLEIAETLTQNADLIVSRAANRIFTGGSPLSYLEKPVERQPALVGASSDSRNGSVTYAESNGSGGLFGGLRSVFSSTGPIPPGFRPINIARYGPSNMQKSLRDMSWFLRYTTYAIVAGDPNIIVVNTRGLKEVIENACSIDATIVAIQEMRAASADYFRNNAQAKEIVLQYFDILLSEFKAPTPANKVRQGPSNDIQGLELPQSYFNAAAKRQKYAMKPGLSALEKNAVIKAAYRQIFERDITKAYSQSISYLESQVRNGDISMKEFVRRLAKSPLYRKQFFEPFINSRALELAFRHILGRGPSSREEVQKYFSIVSSGGLPALVDALVDSQEYADYFGEETVPYLRGLGVEAQECRNWGMQQDLFSYSAPFRKVPQFITTFAQYDRPLPDQHVYGSGNDPLEIQFGAIFPKETRNPSKRPAPFNKDTKRILIHRGPAVNNQVGNPSAVGEFPGSLGAKVFRLNGGLPGAKVGKNTGTSVKFGESSTQALIRAAYRQVFGRDLYEGQRLSVAEIQLENGDISVREFIKRLAKSELFLKLYWAPHYVCKAIEYMHRRLLGRPTYGRQEMNQYFDIASKQGFYAVVEAMIDSKEYSDAFGEDTVPYERYLTPGGLQMRSARVGSLREDIGQRVDKEVTPRFVELGQVSAIRTEPEIAYRSNQGVTRQRQQTKVFKLVSTYDKVAVKNAIRAAYRQVFERDLEPYIINSEFTALESKLSNNEINVKEFIEGLGTSELYMKEFYAPYPNTKVIEMGTKHFLGRAPLNQKEIQQYNQILASQGLKAFIGAMVNGMEYLQTFGEDTVPYRRFPTLPAANFPNTERLYNKLTKQDKELVVPSFTPVVKVGG

Entity 2 Entity 2 polymer

Description description	Orange carotenoid-binding protein
Molecular weight formula_weight	34684.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,b

MPFTIDSARGIFPNTLAADVVPATIARFSQLNAEDQLALIWFAYLEMGKTLTIAAPGAASMQLAENALKEIQAMGPLQQTQAMCDLANRADTPLCRTYASWSPNIKLGFWYRLGELMEQGFVAPIPAGYQLSANANAVLATIQGLESGQQITVLRNAVVDMGFTAGKDGKRIAEPVVPPQDTASRTKVSIEGVTNATVLNYMDNLNANDFDTLIELFTSDGALQPPFQRPIVGKENVLRFFREECQNLKLIPERGVTEPAEDGFTQIKVTGKVQTPWFGGNVGMNIAWRFLLNPEGKIFFVAIDLLASPKELLNFAR

Source Source

Source organism organism	Synechocystis sp. PCC 6803
NCBI taxonomy ID ncbi_taxonomy_id	1148
Host organism host_organism	Escherichia coli BL21(DE3)

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	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	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	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,F,H,J,L,N

MSIVTKSIVNADAEARYLSPGELDRIKAFVTGGAARLRIAETLTGSRETIVKQAGDRLFQKRPDIVSPGGNAYGEEMTATCLRDMDYYLRLVTYGVVSGDVTPIEEIGLVGVREMYRSLGTPIEAVAQSVREMKEVASGLMSSDDAAEASAYFDFVIGKMS

Entity 5 Entity 5 polymer

Description description	Allophycocyanin beta chain
Molecular weight formula_weight	17245.6 kDa
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,G,I,K,M,O

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	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P,Q,R,S

MALPLLNYAPKSQNVRVEGYEIGSEEKPVVFTTENILSSSDMDNLIEAAYRQIFFHAFKWDREKVLESQLRNGQITVRDFVRGLLLSNTFRNSFYEKNSNYRFVEHCVQKILGRDVYSEREKIAWSIVVATKGYQGLIDDLLNSDEYLNNFGYDTVPYQRRRNLPGREAGELPFNIKSPRYDAYHRRQLGFPQIVWQNEVRRFIPQEKKLTAGNPMNFLGMARSINPAANTIPKVSAQNINIEASVPRR

Entity 7 Entity 7 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

Entity 8 Entity 8 non-polymer

Description description	PHYCOCYANOBILIN
Molecular weight formula_weight	588.7 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2376

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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	2.10 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	153576

Top cylinder bound to OCP from 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8tpj__assembly_1__model_1

8tpj__assembly_1__model_1 | I(q)

8tpj__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

7. Citations (1)