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9i28

Form II Rubisco inside EPYC1-formed liquid-liquid phase separated condensates with bound Magnesium and CABP

Method: ELECTRON MICROSCOPY Dmax: 100.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ribulose bisphosphate carboxylase

Rhodospirillum rubrum ATCC 11170

UniProt Q2RRP5

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–466 Chain B； UniProt 1–466 Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 2 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 2 ELECTRON MICROSCOPY cryo-EM buffer：pH 8.5 cryo-EM vitrification conditions：Cryogen ETHANE；sample was blotted for 3 s with blot force 20 Resolution 2.93 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 9I28 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7VWX CryoEM structure of football-shaped GroEL:ES2 with RuBisCO Deposited 2021-11-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 29 PDB declaration: 29-meric
Chain a 1–466（466 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
8BAA CryoEM structure of GroEL-GroES-ADP.AlF3-Rubisco, class II. Deposited 2022-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 22 PDB declaration: 22-meric
Chain Z 1–466（466 aa）
Not recorded AF3 ALUMINUM FLUORIDE × 7 MG MAGNESIUM ION × 14 ADP ADENOSINE-5'-DIPHOSPHATE × 14 K POTASSIUM ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；The grid was prepared using a chameleon (SPT Labtech).
Resolution 4.20 Å
9I26 inactive Form II Rubisco from Rhodospirillum rubrum Deposited 2025-01-20 Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–466（466 aa）
Chain B 1–466（466 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；289 K；Inactive CbbM in 20 mM Tris buffer (pH 8.5), containing 100 mM NaCl was mixed with condition comprised of 1.2 M ammonium chloride, 100 mM MES (pH 6), 20 %(w/v) PEG6000 in a 1:1 ratio with a final drop volume of 1 micro liter. The mother liquor was supplemented with 30% (v/v) PEG200, before the crystals were plunge frozen in liquid nitrogen
Resolution 2.30 Å R-free 0.226
9I27 activated Form II Rubisco from Rhodospirillum rubrum with bound Magnesium and CABP Deposited 2025-01-20 Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–466（466 aa）
Chain B 1–466（466 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 2 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.3；289 K；Crystallization of activated CbbM in buffer containing 20 mM Tris (pH 8.5), 100 mM NaCl, 0.2 mM CABP, and 10 mM sodium bicarbonate was mixed with a condition containing 200 mM Bis-Tris propane (pH 7.3) and 20 % (w/v) PEG4000. Prior to plung freezing the crystals in liquid nitrogen the mother liquor was supplemented with 33 % (v/v) PEG200.
Resolution 2.30 Å R-free 0.217

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

View Construct and Data Evidence
UniProt name RBL2_RHORT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–466； UniProt 1–466 Author chain B； PDBConstruct 1–466； UniProt 1–466

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 9i28

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9i28
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9i28
Deposition date deposition_date2025-01-20
Structure title titleForm II Rubisco inside EPYC1-formed liquid-liquid phase separated condensates with bound Magnesium and CABP
Keywords keywordsribulose-1, 5-bisphosphate carboxylase/oxygenase, Rubisco, LYASE; LYASE
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier28.44 Å
Radius of gyration Rg (electron density) rg_electron27.54 Å
Forward intensity I(0) i0158933000.00
Molecular weight molecular_weight98133.0 kDa
Excluded volume excluded_volume121720 ų
Envelope volume envelope_volume138620 ų
Hydration-shell volume shell_volume40608 ų
Envelope diameter envelope_diameter103.8 Å
Shell Rg shell_rg36.12 Å
Envelope Rg envelope_rg27.84 Å
Shape Rg shape_rg27.58 Å
Total Rg total_rg28.15 Å
Total atoms total_atoms6908
Residues n_residues896
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 dmax100.0 Å
Rg (real space) rg_real28.39 Å
Rg uncertainty (real space) rg_real_error0.68 Å
I(0) (real space) i0_real1.5890e+08
I(0) uncertainty (real space) i0_real_error2.1740e+06
Rg (reciprocal space) rg_reciprocal28.40 Å
I(0) (reciprocal space) i0_reciprocal158900000.0000
Solution quality estimate total_estimate0.8537
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary33.9 Å
Skewness Skewness skewness0.384
Kurtosis Kurtosis kurtosis-0.154
Angular range angular_range— – 0.2800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha58280000.0000
Real-space data points n_real_points57
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.706; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.994
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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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8. Citations (1)

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9. Files and Curves (10)