7jsx

EPYC1(106-135) peptide-bound Rubisco

Method: ELECTRON MICROSCOPY

▼

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

Ribulose bisphosphate carboxylase large chain

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 24	Ribulose bisphosphate carboxylase small chain 2, chloroplastic × 8 （P08475） EPYC1 × 8 （A0A2K3DA85） water × 16	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A218N8A3_CHLRE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–475； UniProt 1–475 Author chain C； PDBConstruct 1–475； UniProt 1–475 Author chain E； PDBConstruct 1–475； UniProt 1–475 Author chain G； PDBConstruct 1–475； UniProt 1–475 Author chain I； PDBConstruct 1–475； UniProt 1–475 Author chain K； PDBConstruct 1–475； UniProt 1–475 Author chain M； PDBConstruct 1–475； UniProt 1–475 Author chain O； PDBConstruct 1–475； UniProt 1–475

Ribulose bisphosphate carboxylase small chain 2, chloroplastic

OrganismNot specified

UniProt P08475

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 24	Ribulose bisphosphate carboxylase large chain × 8 （A0A218N8A3） EPYC1 × 8 （A0A2K3DA85） water × 16	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RBS2_CHLRE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–185； UniProt 1–185 Author chain D； PDBConstruct 1–185； UniProt 1–185 Author chain F； PDBConstruct 1–185； UniProt 1–185 Author chain H； PDBConstruct 1–185； UniProt 1–185 Author chain J； PDBConstruct 1–185； UniProt 1–185 Author chain L； PDBConstruct 1–185； UniProt 1–185 Author chain N； PDBConstruct 1–185； UniProt 1–185 Author chain P； PDBConstruct 1–185； UniProt 1–185

EPYC1

OrganismNot specified

UniProt A0A2K3DA85

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 24	Ribulose bisphosphate carboxylase large chain × 8 （A0A218N8A3） Ribulose bisphosphate carboxylase small chain 2, chloroplastic × 8 （P08475） water × 16	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A2K3DA85_CHLRE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain q； PDBConstruct 1–30； UniProt 106–135 Author chain r； PDBConstruct 1–30； UniProt 106–135 Author chain s； PDBConstruct 1–30； UniProt 106–135 Author chain t； PDBConstruct 1–30； UniProt 106–135 Author chain u； PDBConstruct 1–30； UniProt 106–135 Author chain v； PDBConstruct 1–30； UniProt 106–135 Author chain w； PDBConstruct 1–30； UniProt 106–135 Author chain x； PDBConstruct 1–30； UniProt 106–135

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	7jsx
Deposition date deposition_date	2020-08-16
Structure title title	EPYC1(106-135) peptide-bound Rubisco
Keywords keywords	Rubisco, Pyrenoid, PLANT PROTEIN, Lyase; PLANT PROTEIN, Lyase
Experimental Method method	ELECTRON MICROSCOPY

▼

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.

7jsx__assembly_1__model_1

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

Download this curve (.dat)

7jsx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7jsx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	47.80 Å
Rg (electron density)	46.87 Å
Total Rg	47.19 Å
Atom count	37672
Residues	4824
Excluded volume	667170 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7jsx__assembly_1__model_1`	24-meric （24）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Ribulose bisphosphate carboxylase large chain
Molecular weight formula_weight	52607.8 kDa
EC 编号 ec_number	4.1.1.39
Source method src_method	nat
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K,M,O
Atom count atom_count	38813

MVPQTETKAGAGFKAGVKDYRLTYYTPDYVVRDTDILAAFRMTPQPGVPPEECGAAVAAESSTGTWTTVWTDGLTSLDRYKGRCYDIEPVPGEDNQYIAYVAYPIDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFVGPPHGIQVERDKLNKYGRGLLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKGHYLNATAGTCEEMMKRAVCAKELGVPIIMHDYLTGGFTANTSLAIYCRDNGLLLHIHRAMHAVIDRQRNHGIHFRVLAKALRMSGGDHLHSGTVVGKLEGEREVTLGFVDLMRDDYVEKDRSRGIYFTQDWCSMPGVMPVASGGIHVWHMPALVEIFGDDACLQFGGGTLGHPWGNAPGAAANRVALEACTQARNEGRDLAREGGDVIRSACKWSPELAAACEVWKEIKFEFDTIDKL

Entity 2 Entity 2 polymer

Description description	Ribulose bisphosphate carboxylase small chain 2, chloroplastic
Molecular weight formula_weight	20668.0 kDa
EC 编号 ec_number	4.1.1.39
Source method src_method	nat
Copy count entity_count	8

Polymer Polymer

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

MAAVIAKSSVSAAVARPARSSVRPMAALKPAVKAAPVAAPAQANQMMVWTPVNNKMFETFSYLPPLSDEQIAAQVDYIVANGWIPCLEFAESDKAYVSNESAIRFGSVSCLYYDNRYWTMWKLPMFGCRDPMQVLREIVACTKAFPDAYVRLVAFDNQKQVQIMGFLVQRPKSARDWQPANKRSV

Entity 3 Entity 3 polymer

Description description	EPYC1
Molecular weight formula_weight	3294.7 kDa
Source method src_method	nat
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	q,r,s,t,u,v,w,x

RSSSASKKAVTPSRSALPSNWKQELESLRS

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1141

▼

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (24 domains)

Domain ID domain_id	d7jsxa1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.9 — RuBisCO, large subunit, small (N-terminal) domain
Family Family family	d.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase

Domain ID domain_id	d7jsxa2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.14 — RuBisCo, C-terminal domain
Family Family family	c.1.14.1 — RuBisCo, large subunit, C-terminal domain

Domain ID domain_id	d7jsxb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.73 — RuBisCO, small subunit
Superfamily Superfamily superfamily	d.73.1 — RuBisCO, small subunit
Family Family family	d.73.1.1 — RuBisCO, small subunit

Domain ID domain_id	d7jsxc1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.9 — RuBisCO, large subunit, small (N-terminal) domain
Family Family family	d.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase

Domain ID domain_id	d7jsxc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.14 — RuBisCo, C-terminal domain
Family Family family	c.1.14.1 — RuBisCo, large subunit, C-terminal domain

Domain ID domain_id	d7jsxd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.73 — RuBisCO, small subunit
Superfamily Superfamily superfamily	d.73.1 — RuBisCO, small subunit
Family Family family	d.73.1.1 — RuBisCO, small subunit

Domain ID domain_id	d7jsxe1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.9 — RuBisCO, large subunit, small (N-terminal) domain
Family Family family	d.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase

Domain ID domain_id	d7jsxe2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.14 — RuBisCo, C-terminal domain
Family Family family	c.1.14.1 — RuBisCo, large subunit, C-terminal domain

Domain ID domain_id	d7jsxf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.73 — RuBisCO, small subunit
Superfamily Superfamily superfamily	d.73.1 — RuBisCO, small subunit
Family Family family	d.73.1.1 — RuBisCO, small subunit

Domain ID domain_id	d7jsxg1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.9 — RuBisCO, large subunit, small (N-terminal) domain
Family Family family	d.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase

Domain ID domain_id	d7jsxg2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.14 — RuBisCo, C-terminal domain
Family Family family	c.1.14.1 — RuBisCo, large subunit, C-terminal domain

Domain ID domain_id	d7jsxh_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.73 — RuBisCO, small subunit
Superfamily Superfamily superfamily	d.73.1 — RuBisCO, small subunit
Family Family family	d.73.1.1 — RuBisCO, small subunit

Domain ID domain_id	d7jsxi1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.9 — RuBisCO, large subunit, small (N-terminal) domain
Family Family family	d.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase

Domain ID domain_id	d7jsxi2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.14 — RuBisCo, C-terminal domain
Family Family family	c.1.14.1 — RuBisCo, large subunit, C-terminal domain

Domain ID domain_id	d7jsxj_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.73 — RuBisCO, small subunit
Superfamily Superfamily superfamily	d.73.1 — RuBisCO, small subunit
Family Family family	d.73.1.1 — RuBisCO, small subunit

Domain ID domain_id	d7jsxk1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.9 — RuBisCO, large subunit, small (N-terminal) domain
Family Family family	d.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase

Domain ID domain_id	d7jsxk2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.14 — RuBisCo, C-terminal domain
Family Family family	c.1.14.1 — RuBisCo, large subunit, C-terminal domain

Domain ID domain_id	d7jsxl_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.73 — RuBisCO, small subunit
Superfamily Superfamily superfamily	d.73.1 — RuBisCO, small subunit
Family Family family	d.73.1.1 — RuBisCO, small subunit

Domain ID domain_id	d7jsxm1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.9 — RuBisCO, large subunit, small (N-terminal) domain
Family Family family	d.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase

Domain ID domain_id	d7jsxm2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.14 — RuBisCo, C-terminal domain
Family Family family	c.1.14.1 — RuBisCo, large subunit, C-terminal domain

Domain ID domain_id	d7jsxn_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.73 — RuBisCO, small subunit
Superfamily Superfamily superfamily	d.73.1 — RuBisCO, small subunit
Family Family family	d.73.1.1 — RuBisCO, small subunit

Domain ID domain_id	d7jsxo1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.9 — RuBisCO, large subunit, small (N-terminal) domain
Family Family family	d.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase

Domain ID domain_id	d7jsxo2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.14 — RuBisCo, C-terminal domain
Family Family family	c.1.14.1 — RuBisCo, large subunit, C-terminal domain

Domain ID domain_id	d7jsxp_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.73 — RuBisCO, small subunit
Superfamily Superfamily superfamily	d.73.1 — RuBisCO, small subunit
Family Family family	d.73.1.1 — RuBisCO, small subunit

▶

Resolution resolution	2.06 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	152839

EPYC1(106-135) peptide-bound Rubisco

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

Ribulose bisphosphate carboxylase large chain

State in the Current Structure

Other States of the Same Protein in the Database

Ribulose bisphosphate carboxylase small chain 2, chloroplastic

State in the Current Structure

Other States of the Same Protein in the Database

EPYC1

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

7jsx__assembly_1__model_1

7jsx__assembly_1__model_1 | I(q)

7jsx__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (24 domains)

7. Citations (1)

EPYC1(106-135) peptide-bound Rubisco

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

Ribulose bisphosphate carboxylase large 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

Ribulose bisphosphate carboxylase small chain 2, chloroplastic

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

EPYC1

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

7jsx__assembly_1__model_1

7jsx__assembly_1__model_1 | I(q)

7jsx__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (24 domains)

7. Citations (1)