1upm

ACTIVATED SPINACH RUBISCO COMPLEXED WITH 2-CARBOXYARABINITOL 2 BISPHOSPHAT AND CA2+.

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN

OrganismNot specified

UniProt P00875

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 16 RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN × 8 (Q43832) CALCIUM ION × 8 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8 water × 16 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RBL_SPIOL
Isoform —
PDB entities 1
Chains and sequence ranges Author chain B; PDBConstruct 1–475; UniProt 1–475 Author chain E; PDBConstruct 1–475; UniProt 1–475 Author chain H; PDBConstruct 1–475; UniProt 1–475 Author chain K; PDBConstruct 1–475; UniProt 1–475 Author chain L; PDBConstruct 1–475; UniProt 1–475 Author chain O; PDBConstruct 1–475; UniProt 1–475 Author chain R; PDBConstruct 1–475; UniProt 1–475 Author chain V; PDBConstruct 1–475; UniProt 1–475

RIBULOSE BISPHOSPHATE CARBOXYLASE SMALL CHAIN

OrganismNot specified

UniProt Q43832

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 16 RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN × 8 (P00875) CALCIUM ION × 8 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8 water × 16 Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence
UniProt name RBS2_SPIOL
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 1–123; UniProt 58–180 Author chain F; PDBConstruct 1–123; UniProt 58–180 Author chain I; PDBConstruct 1–123; UniProt 58–180 Author chain M; PDBConstruct 1–123; UniProt 58–180 Author chain P; PDBConstruct 1–123; UniProt 58–180 Author chain S; PDBConstruct 1–123; UniProt 58–180 Author chain T; PDBConstruct 1–123; UniProt 58–180 Author chain W; PDBConstruct 1–123; UniProt 58–180

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_id1upm
Deposition date deposition_date2003-10-08
Structure title titleACTIVATED SPINACH RUBISCO COMPLEXED WITH 2-CARBOXYARABINITOL 2 BISPHOSPHAT AND CA2+.
Keywords keywordsLYASE, CARBON-CARBON, OXIDOREDUCTASE, PHOTOSYNTHESIS, CARBON-DIOXIDE FIXATION LYASE (CARBON-CARBON); LYASE
Experimental Method methodX-RAY DIFFRACTION
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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.

1upm__assembly_1__model_1

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

Download this curve (.dat)

1upm__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

1upm__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg(Guinier)47.33 Å
Rg (electron density)46.63 Å
Total Rg46.99 Å
Atom count37648
Residues4712
Excluded volume667270 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 1upm__assembly_1__model_1 hexadecameric (16) 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 (5)

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6. Fold Classification (SCOP + CATH) 48 domains

SCOP 2.08 (24 domains)

Domain ID domain_idd1upmb1
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_idd1upmb2
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_idd1upmc_
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_idd1upme1
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_idd1upme2
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_idd1upmf_
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_idd1upmh1
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_idd1upmh2
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_idd1upmi_
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_idd1upmk1
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_idd1upmk2
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_idd1upml1
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_idd1upml2
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_idd1upmm_
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_idd1upmo1
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_idd1upmo2
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_idd1upmp_
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_idd1upmr1
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_idd1upmr2
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_idd1upms_
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_idd1upmt_
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_idd1upmv1
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_idd1upmv2
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_idd1upmw_
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

CATH v4.4 (24 domains)

Domain ID domain_id1upmB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily150 — RuBisCO large subunit, N-terminal domain
Domain ID domain_id1upmB02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain
Domain ID domain_id1upmC00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
Homologous superfamily homologous superfamily10 — Ribulose bisphosphate carboxylase, small subunit
Domain ID domain_id1upmE01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily150 — RuBisCO large subunit, N-terminal domain
Domain ID domain_id1upmE02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain
Domain ID domain_id1upmF00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
Homologous superfamily homologous superfamily10 — Ribulose bisphosphate carboxylase, small subunit
Domain ID domain_id1upmH01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily150 — RuBisCO large subunit, N-terminal domain
Domain ID domain_id1upmH02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain
Domain ID domain_id1upmI00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
Homologous superfamily homologous superfamily10 — Ribulose bisphosphate carboxylase, small subunit
Domain ID domain_id1upmK01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily150 — RuBisCO large subunit, N-terminal domain
Domain ID domain_id1upmK02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain
Domain ID domain_id1upmL01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily150 — RuBisCO large subunit, N-terminal domain
Domain ID domain_id1upmL02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain
Domain ID domain_id1upmM00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
Homologous superfamily homologous superfamily10 — Ribulose bisphosphate carboxylase, small subunit
Domain ID domain_id1upmO01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily150 — RuBisCO large subunit, N-terminal domain
Domain ID domain_id1upmO02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain
Domain ID domain_id1upmP00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
Homologous superfamily homologous superfamily10 — Ribulose bisphosphate carboxylase, small subunit
Domain ID domain_id1upmR01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily150 — RuBisCO large subunit, N-terminal domain
Domain ID domain_id1upmR02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain
Domain ID domain_id1upmS00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
Homologous superfamily homologous superfamily10 — Ribulose bisphosphate carboxylase, small subunit
Domain ID domain_id1upmT00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
Homologous superfamily homologous superfamily10 — Ribulose bisphosphate carboxylase, small subunit
Domain ID domain_id1upmV01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily150 — RuBisCO large subunit, N-terminal domain
Domain ID domain_id1upmV02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily110 — Ribulose bisphosphate carboxylase, large subunit, C-terminal domain
Domain ID domain_id1upmW00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
Homologous superfamily homologous superfamily10 — Ribulose bisphosphate carboxylase, small subunit
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7. Citations (1)