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7jn4

Rubisco in the apo state

Method: ELECTRON MICROSCOPY Dmax: 139.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ribulose bisphosphate carboxylase large chain

OrganismNot specified

UniProt A0A218N8A3

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 16 PDB declaration: hexadecameric（16） Consistent with protein copy count Chain A； UniProt 1–475 Chain C； UniProt 1–475 Chain E； UniProt 1–475 Chain G； UniProt 1–475 Chain I； UniProt 1–475 Chain K； UniProt 1–475 Chain M； UniProt 1–475 Chain O； UniProt 1–475 Non-standard monomer：Yes (specific site not provided by mmCIF) Ribulose bisphosphate carboxylase small chain 2, chloroplastic × 8 （P08475） ELECTRON MICROSCOPY cryo-EM buffer：pH 6.8；200 mM sorbitol, 50 mM HEPES, 50 mM KOAc, 2 mM Mg(OAc)2.4H2O and 1 mM CaCl2 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.68 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 7JN4 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1UZD Chlamydomonas,Spinach Chimeric Rubisco Deposited 2004-03-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain A 1–475（475 aa）
Chain B 1–475（475 aa）
Chain E 1–475（475 aa）
Chain H 1–475（475 aa）
Chain K 1–475（475 aa）
Chain O 1–475（475 aa）
Chain R 1–475（475 aa）
Chain V 1–475（475 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8 EDO 1,2-ETHANEDIOL × 54 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；291 K；50 MM HEPES PH 7.5, 8-12% PEG 4 50 MM NAHCO3, 5 MM MGCL2, 50 UM 2-CABP, 18 DEG C, 10-15 MG PROTEIN
Resolution 2.40 Å R-free 0.230
7JSX EPYC1(106-135) peptide-bound Rubisco Deposited 2020-08-16 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric
Chain A 1–475（475 aa）
Chain C 1–475（475 aa）
Chain E 1–475（475 aa）
Chain G 1–475（475 aa）
Chain I 1–475（475 aa）
Chain K 1–475（475 aa）
Chain M 1–475（475 aa）
Chain O 1–475（475 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8；200 mM sorbitol, 50 mM HEPES, 50 mM KOAc, 2 mM Mg(OAc)2.4H2O and 1 mM CaCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.06 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

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 Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 16 PDB declaration: hexadecameric（16） Consistent with protein copy count Chain B； UniProt 1–185 Chain D； UniProt 1–185 Chain F； UniProt 1–185 Chain H； UniProt 1–185 Chain J； UniProt 1–185 Chain L； UniProt 1–185 Chain N； UniProt 1–185 Chain P； UniProt 1–185 Not recorded Ribulose bisphosphate carboxylase large chain × 8 （A0A218N8A3） ELECTRON MICROSCOPY cryo-EM buffer：pH 6.8；200 mM sorbitol, 50 mM HEPES, 50 mM KOAc, 2 mM Mg(OAc)2.4H2O and 1 mM CaCl2 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 2.68 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 7JN4 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1IR2 Crystal Structure of Activated Ribulose-1,5-bisphosphate Carboxylase/oxygenase (Rubisco) from Green alga, Chlamydomonas reinhardtii Complexed with 2-Carboxyarabinitol-1,5-bisphosphate (2-CABP) Deposited 2001-09-03 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain I 46–185（140 aa）
Chain J 46–185（140 aa）
Chain K 46–185（140 aa）
Chain L 46–185（140 aa）
Chain M 46–185（140 aa）
Chain N 46–185（140 aa）
Chain O 46–185（140 aa）
Chain P 46–185（140 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8 GOL GLYCEROL × 20 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；PEG4000, HEPES-KOH, glycerol, NaHCO3, MgCl2, DTT, 2-carboxyarabinitol-1,5-bisphosphate (2-CABP), EDTA, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.84 Å R-free 0.181
1IR2 Crystal Structure of Activated Ribulose-1,5-bisphosphate Carboxylase/oxygenase (Rubisco) from Green alga, Chlamydomonas reinhardtii Complexed with 2-Carboxyarabinitol-1,5-bisphosphate (2-CABP) Deposited 2001-09-03 Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain 1 46–185（140 aa）
Chain 2 46–185（140 aa）
Chain 3 46–185（140 aa）
Chain 4 46–185（140 aa）
Chain 5 46–185（140 aa）
Chain 6 46–185（140 aa）
Chain 7 46–185（140 aa）
Chain 8 46–185（140 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8 GOL GLYCEROL × 20 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；PEG4000, HEPES-KOH, glycerol, NaHCO3, MgCl2, DTT, 2-carboxyarabinitol-1,5-bisphosphate (2-CABP), EDTA, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.84 Å R-free 0.181
7JFO EPYC1(49-72)-bound Rubisco Deposited 2020-07-17 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric
Chain B 1–185（185 aa）
Chain D 1–185（185 aa）
Chain F 1–185（185 aa）
Chain H 1–185（185 aa）
Chain J 1–185（185 aa）
Chain L 1–185（185 aa）
Chain N 1–185（185 aa）
Chain P 1–185（185 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8；200 mM sorbitol, 50 mM HEPES, 50 mM KOAc, 2 mM Mg(OAc)2.4H2O and 1 mM CaCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.13 Å
7JSX EPYC1(106-135) peptide-bound Rubisco Deposited 2020-08-16 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric
Chain B 1–185（185 aa）
Chain D 1–185（185 aa）
Chain F 1–185（185 aa）
Chain H 1–185（185 aa）
Chain J 1–185（185 aa）
Chain L 1–185（185 aa）
Chain N 1–185（185 aa）
Chain P 1–185（185 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 6.8；200 mM sorbitol, 50 mM HEPES, 50 mM KOAc, 2 mM Mg(OAc)2.4H2O and 1 mM CaCl2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.06 Å

3 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

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

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.

SAXS scattering curve SAXS Profile

SAXS profile for 7jn4

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7jn4
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7jn4
Deposition date deposition_date2020-08-03
Structure title titleRubisco in the apo state
Keywords keywordsRubisco, PLANT PROTEIN, Pyrenoid; PLANT PROTEIN
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier46.90 Å
Radius of gyration Rg (electron density) rg_electron46.00 Å
Forward intensity I(0) i03694030000.00
Molecular weight molecular_weight504780.0 kDa
Excluded volume excluded_volume628950 ų
Envelope volume envelope_volume775110 ų
Hydration-shell volume shell_volume126640 ų
Envelope diameter envelope_diameter138.2 Å
Shell Rg shell_rg59.07 Å
Envelope Rg envelope_rg45.88 Å
Shape Rg shape_rg46.00 Å
Total Rg total_rg46.35 Å
Total atoms total_atoms35472
Residues n_residues4512
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax139.6 Å
Rg (real space) rg_real46.45 Å
Rg uncertainty (real space) rg_real_error0.45 Å
I(0) (real space) i0_real3.6940e+09
I(0) uncertainty (real space) i0_real_error4.5600e+07
Rg (reciprocal space) rg_reciprocal46.90 Å
I(0) (reciprocal space) i0_reciprocal3696000000.0000
Solution quality estimate total_estimate0.8894
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary61.6 Å
Skewness Skewness skewness0.001
Kurtosis Kurtosis kurtosis-0.564
Angular range angular_range— – 0.1700 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha1830000000.0000
Real-space data points n_real_points35
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.949; Smooth: 0.861
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (24 domains)

Domain ID domain_idd7jn4a1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.9 — RuBisCO, large subunit, small (N-terminal) domain
Family Family familyd.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase
Domain ID domain_idd7jn4a2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.14 — RuBisCo, C-terminal domain
Family Family familyc.1.14.1 — RuBisCo, large subunit, C-terminal domain
Domain ID domain_idd7jn4b_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.73 — RuBisCO, small subunit
Superfamily Superfamily superfamilyd.73.1 — RuBisCO, small subunit
Family Family familyd.73.1.1 — RuBisCO, small subunit
Domain ID domain_idd7jn4c1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.9 — RuBisCO, large subunit, small (N-terminal) domain
Family Family familyd.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase
Domain ID domain_idd7jn4c2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.14 — RuBisCo, C-terminal domain
Family Family familyc.1.14.1 — RuBisCo, large subunit, C-terminal domain
Domain ID domain_idd7jn4d_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.73 — RuBisCO, small subunit
Superfamily Superfamily superfamilyd.73.1 — RuBisCO, small subunit
Family Family familyd.73.1.1 — RuBisCO, small subunit
Domain ID domain_idd7jn4e1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.9 — RuBisCO, large subunit, small (N-terminal) domain
Family Family familyd.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase
Domain ID domain_idd7jn4e2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.14 — RuBisCo, C-terminal domain
Family Family familyc.1.14.1 — RuBisCo, large subunit, C-terminal domain
Domain ID domain_idd7jn4f_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.73 — RuBisCO, small subunit
Superfamily Superfamily superfamilyd.73.1 — RuBisCO, small subunit
Family Family familyd.73.1.1 — RuBisCO, small subunit
Domain ID domain_idd7jn4g1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.9 — RuBisCO, large subunit, small (N-terminal) domain
Family Family familyd.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase
Domain ID domain_idd7jn4g2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.14 — RuBisCo, C-terminal domain
Family Family familyc.1.14.1 — RuBisCo, large subunit, C-terminal domain
Domain ID domain_idd7jn4h_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.73 — RuBisCO, small subunit
Superfamily Superfamily superfamilyd.73.1 — RuBisCO, small subunit
Family Family familyd.73.1.1 — RuBisCO, small subunit
Domain ID domain_idd7jn4i1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.9 — RuBisCO, large subunit, small (N-terminal) domain
Family Family familyd.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase
Domain ID domain_idd7jn4i2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.14 — RuBisCo, C-terminal domain
Family Family familyc.1.14.1 — RuBisCo, large subunit, C-terminal domain
Domain ID domain_idd7jn4j_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.73 — RuBisCO, small subunit
Superfamily Superfamily superfamilyd.73.1 — RuBisCO, small subunit
Family Family familyd.73.1.1 — RuBisCO, small subunit
Domain ID domain_idd7jn4k1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.9 — RuBisCO, large subunit, small (N-terminal) domain
Family Family familyd.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase
Domain ID domain_idd7jn4k2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.14 — RuBisCo, C-terminal domain
Family Family familyc.1.14.1 — RuBisCo, large subunit, C-terminal domain
Domain ID domain_idd7jn4l_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.73 — RuBisCO, small subunit
Superfamily Superfamily superfamilyd.73.1 — RuBisCO, small subunit
Family Family familyd.73.1.1 — RuBisCO, small subunit
Domain ID domain_idd7jn4m1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.9 — RuBisCO, large subunit, small (N-terminal) domain
Family Family familyd.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase
Domain ID domain_idd7jn4m2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.14 — RuBisCo, C-terminal domain
Family Family familyc.1.14.1 — RuBisCo, large subunit, C-terminal domain
Domain ID domain_idd7jn4n_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.73 — RuBisCO, small subunit
Superfamily Superfamily superfamilyd.73.1 — RuBisCO, small subunit
Family Family familyd.73.1.1 — RuBisCO, small subunit
Domain ID domain_idd7jn4o1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.9 — RuBisCO, large subunit, small (N-terminal) domain
Family Family familyd.58.9.1 — Ribulose 1,5-bisphosphate carboxylase-oxygenase
Domain ID domain_idd7jn4o2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.14 — RuBisCo, C-terminal domain
Family Family familyc.1.14.1 — RuBisCo, large subunit, C-terminal domain
Domain ID domain_idd7jn4p_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.73 — RuBisCO, small subunit
Superfamily Superfamily superfamilyd.73.1 — RuBisCO, small subunit
Family Family familyd.73.1.1 — RuBisCO, small subunit
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8. Citations (1)

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9. Files and Curves (10)