SAXSdb — 9x6d

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

Phycobilisome rod-core linker polypeptide

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 27	C-phycocyanin alpha subunit × 12 （P13530） C-phycocyanin beta subunit × 12 （P06539） Phycobilisome rod linker polypeptide × 1 （Q31PE0） Phycobilisome rod linker polypeptide × 1 （Q31PD9） PHYCOCYANOBILIN × 34	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q31LK9_SYNE7
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–250； UniProt 1–250

C-phycocyanin alpha subunit

OrganismNot specified

UniProt P13530

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 27	Phycobilisome rod-core linker polypeptide × 1 （Q31LK9） C-phycocyanin beta subunit × 12 （P06539） Phycobilisome rod linker polypeptide × 1 （Q31PE0） Phycobilisome rod linker polypeptide × 1 （Q31PD9） PHYCOCYANOBILIN × 34	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PHCA_SYNE7
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–163； UniProt 1–163 Author chain F； PDBConstruct 1–163； UniProt 1–163 Author chain G； PDBConstruct 1–163； UniProt 1–163 Author chain H； PDBConstruct 1–163； UniProt 1–163 Author chain I； PDBConstruct 1–163； UniProt 1–163 Author chain K； PDBConstruct 1–163； UniProt 1–163 Author chain N； PDBConstruct 1–163； UniProt 1–163 Author chain R； PDBConstruct 1–163； UniProt 1–163 Author chain S； PDBConstruct 1–163； UniProt 1–163 Author chain T； PDBConstruct 1–163； UniProt 1–163 Author chain U； PDBConstruct 1–163； UniProt 1–163 Author chain W； PDBConstruct 1–163； UniProt 1–163

C-phycocyanin beta subunit

OrganismNot specified

UniProt P06539

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 27	Phycobilisome rod-core linker polypeptide × 1 （Q31LK9） C-phycocyanin alpha subunit × 12 （P13530） Phycobilisome rod linker polypeptide × 1 （Q31PE0） Phycobilisome rod linker polypeptide × 1 （Q31PD9） PHYCOCYANOBILIN × 34	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PHCB_SYNE7
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–173； UniProt 1–173 Author chain D； PDBConstruct 1–173； UniProt 1–173 Author chain E； PDBConstruct 1–173； UniProt 1–173 Author chain J； PDBConstruct 1–173； UniProt 1–173 Author chain L； PDBConstruct 1–173； UniProt 1–173 Author chain M； PDBConstruct 1–173； UniProt 1–173 Author chain O； PDBConstruct 1–173； UniProt 1–173 Author chain P； PDBConstruct 1–173； UniProt 1–173 Author chain Q； PDBConstruct 1–173； UniProt 1–173 Author chain V； PDBConstruct 1–173； UniProt 1–173 Author chain X； PDBConstruct 1–173； UniProt 1–173 Author chain a； PDBConstruct 1–173； UniProt 1–173

Phycobilisome rod linker polypeptide

OrganismNot specified

UniProt Q31PE0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 27	Phycobilisome rod-core linker polypeptide × 1 （Q31LK9） C-phycocyanin alpha subunit × 12 （P13530） C-phycocyanin beta subunit × 12 （P06539） Phycobilisome rod linker polypeptide × 1 （Q31PD9） PHYCOCYANOBILIN × 34	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q31PE0_SYNE7
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain Y； PDBConstruct 1–273； UniProt 1–273

Phycobilisome rod linker polypeptide

OrganismNot specified

UniProt Q31PD9

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 27	Phycobilisome rod-core linker polypeptide × 1 （Q31LK9） C-phycocyanin alpha subunit × 12 （P13530） C-phycocyanin beta subunit × 12 （P06539） Phycobilisome rod linker polypeptide × 1 （Q31PE0） PHYCOCYANOBILIN × 34	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q31PD9_SYNE7
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain Z； PDBConstruct 1–289； UniProt 1–289

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	9x6d
Deposition date deposition_date	2025-10-15
Last revision last_revision	2026-04-01
Structure title title	The cryo-EM structure of phycobilisome rod from Synechococcus elongatus PCC 7942
Keywords keywords	phycobilisome PBS, ELECTRON TRANSPORT; ELECTRON TRANSPORT
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.

9x6d__assembly_1__model_1

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

Download this curve (.dat)

9x6d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9x6d__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	48.14 Å
Rg (electron density)	47.27 Å
Total Rg	47.57 Å
Atom count	35641
Residues	4557
Excluded volume	632420 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9x6d__assembly_1__model_1`	27-meric （27）	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 (6)

Entity 1 Entity 1 polymer

Description description	Phycobilisome rod-core linker polypeptide
Molecular weight formula_weight	28372.9 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	35641

MALPLLNYAPTTQNSRVAGFEVPGDEQPKQYNTEDQYSPVQFDEVIQAAYRQIFFHAFKCDRQTVLESQLRNGQITVRDFIRGLLLSATFRSSFYDKNSNYRFVEQVVQRVLGRDVYGEREKIAWSLAVATQGYEGFIDTLLNSDEYLSNFGYDKVPYQRRRVLPGRALGETPFNIKSPRYDSYYRTILGFPKAVFAGGPGKRFPAQYLSAKAGDPGAYLALARSIGARGQALSASADIDYLSKVPYRKR

Entity 2 Entity 2 polymer

Description description	C-phycocyanin alpha subunit
Molecular weight formula_weight	17303.2 kDa
Source method src_method	nat
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,F,G,H,I,K,N,R,S,T,U,W

MSKTPLTEAVAAADSQGRFLSSTELQVAFGRFRQAASGLAAAKALANNADSLVNGAANAVYSKFPYTTSTPGNNFASTPEGKAKCARDIGYYLRIVTYALVAGGTGPIDEYLLAGLDEINKTFDLAPSWYVEALKYIKANHGLSGDSRDEANSYIDYLINALS

Entity 3 Entity 3 polymer

Description description	C-phycocyanin beta subunit
Molecular weight formula_weight	18287.7 kDa
Source method src_method	nat
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D,E,J,L,M,O,P,Q,V,X,a

MTFDAFTKVVAQADARGEFLSDAQLDALSRLVAEGNKRIDTVNRITGNASSIVANAARALFAEQPSLIAPGGNAYTNRRMAACLRDMEIILRYVTYAVFTGDASILDDRCLNGLRETYLALGVPGASVAEGVRKMKDAAVAIVSDRNGITQGDCSAIISELGSYFDKAAAAVA

Entity 4 Entity 4 polymer

Description description	Phycobilisome rod linker polypeptide
Molecular weight formula_weight	30392.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Y

MTSLEAARRLGFSAYSESAPLEWRAGASSDEINAIIRAVYRQVLGNDYVMSTERLTSAESLLRGGEISVRDFVRAVALSELYREKFFHNNAHNRFIELNFKHLLGRAPYDQAEVAAHAATYHSHGYDADINSYIDSAEYTESFGDNVVPYFRGFATIRAQKTVGFNRIFQLYRGYATSDRSATSQRSRLDQEVARNAASPVLIGSTGSALVGTCGGSRDQLFRVQVQQQGVTARTSNRIRRSNATYFVSYEKLNATLQRVHAQGGRIVSITPA

Entity 5 Entity 5 polymer

Description description	Phycobilisome rod linker polypeptide
Molecular weight formula_weight	31734.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Z

MAITVASSRLGTAPFSNAAPVELRPDGDRDQVQAVIRAVYRQVLGNDYIMKSERLTAAESLLVNGSISVRDFVRAVAKSELYKTKFFYNNFQTRVIELHCKHLLGRAPYSEAEVIEHLDRYETQGYDADVDSYIDSSEYLETFGESIVPYYRDIEYHVGQQSVGLPRLFSLYRGYATSDRTSLGGNNSRLAANLAAKSVAPVVAPSVGTNYVASTKGEAPMRALGGSTPFGQTASRIFRVEIAAISKPGFPSVRRSNRSLLVPYEQLNNTLQQVNRSGGRVVSVAPASL

Entity 6 Entity 6 non-polymer

Description description	PHYCOCYANOBILIN
Molecular weight formula_weight	588.7 kDa
Source method src_method	syn
Copy count entity_count	34

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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	—

Resolution resolution	2.920 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	2.92 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	258722

The cryo-EM structure of phycobilisome rod from Synechococcus elongatus PCC 7942

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

Phycobilisome rod-core linker polypeptide

State in the Current Structure

Other States of the Same Protein in the Database

C-phycocyanin alpha subunit

State in the Current Structure

Other States of the Same Protein in the Database

C-phycocyanin beta subunit

State in the Current Structure

Other States of the Same Protein in the Database

Phycobilisome rod linker polypeptide

State in the Current Structure

Other States of the Same Protein in the Database

Phycobilisome rod linker polypeptide

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9x6d__assembly_1__model_1

9x6d__assembly_1__model_1 | I(q)

9x6d__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

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 non-polymer

7. Citations (1)

The cryo-EM structure of phycobilisome rod from Synechococcus elongatus PCC 7942

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

Phycobilisome rod-core linker polypeptide

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 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 rod linker polypeptide

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 linker polypeptide

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

9x6d__assembly_1__model_1

9x6d__assembly_1__model_1 | I(q)

9x6d__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

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 non-polymer

7. Citations (1)