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9fwv

Rubisco in native beta-carboxysomes

Method: ELECTRON MICROSCOPY Dmax: 146.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Carboxysome assembly protein CcmM

OrganismNot specified

UniProt Q03513

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 × 20 PDB declaration: 20-meric（20） Consistent with protein copy count Chain A； UniProt 225–310 Chain B； UniProt 225–310 Chain F； UniProt 225–310 Chain T； UniProt 225–310 Not recorded Ribulose bisphosphate carboxylase large chain × 8 （Q31NB3） Ribulose bisphosphate carboxylase small subunit × 8 （P04716） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.50 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 9FWV Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6HBA Crystal Structure of the small subunit-like domain 1 of CcmM from Synechococcus elongatus (strain PCC 7942), thiol-oxidized form Deposited 2018-08-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 225–313（89 aa） Fragment：SSUL domain 1
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；277 K；25.5% PEG-3350 and 0.1 M Na-acetate pH 4.5
Resolution 1.65 Å R-free 0.241
6HBA Crystal Structure of the small subunit-like domain 1 of CcmM from Synechococcus elongatus (strain PCC 7942), thiol-oxidized form Deposited 2018-08-10 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 225–313（89 aa） Fragment：SSUL domain 1
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；277 K；25.5% PEG-3350 and 0.1 M Na-acetate pH 4.5
Resolution 1.65 Å R-free 0.241
6HBB Crystal Structure of the small subunit-like domain 1 of CcmM from Synechococcus elongatus (strain PCC 7942) Deposited 2018-08-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 225–313（89 aa） Fragment：SSUL domain 1
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；277 K；1.95 M ammonium sulfate and 0.1 M Na-acetate pH 4.5
Resolution 1.20 Å R-free 0.195
6HBB Crystal Structure of the small subunit-like domain 1 of CcmM from Synechococcus elongatus (strain PCC 7942) Deposited 2018-08-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 225–313（89 aa） Fragment：SSUL domain 1
Not recorded SO4 SULFATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；277 K；1.95 M ammonium sulfate and 0.1 M Na-acetate pH 4.5
Resolution 1.20 Å R-free 0.195
6HBC Structure of the repeat unit in the network formed by CcmM and Rubisco from Synechococcus elongatus Deposited 2018-08-10 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain A 225–313（89 aa） Fragment：SSUL domain 1
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；Solutions were made fresh
cryo-EM vitrification conditions Cryogen ETHANE；blot for 3 seconds before plunging
Resolution 2.78 Å
7D6C Crystal structure of CcmM N-terminal domain in complex with CcmN Deposited 2020-09-30 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain 1 1–209（209 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；287.15 K；PEG 8000, N-(2-acetamido) iminodiacetic acid
Resolution 2.89 Å R-free 0.272
7D6C Crystal structure of CcmM N-terminal domain in complex with CcmN Deposited 2020-09-30 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain 2 1–209（209 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；287.15 K；PEG 8000, N-(2-acetamido) iminodiacetic acid
Resolution 2.89 Å R-free 0.272
7O4Z Crystal structure of the carbonic anhydrase-like domain of CcmM from Synechococcus elongatus (strain PCC 7942) Deposited 2021-04-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 1–181（181 aa）
Not recorded NI NICKEL (II) ION × 3 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；25% PEG-3350 and 0.1 M HEPES pH 7.5
Resolution 1.67 Å R-free 0.200
7O54 Crystal structure of the carbonic anhydrase-like domain of CcmM in complex with the C-terminal 17 residues of CcaA from Synechococcus elongatus (strain PCC 7942) Deposited 2021-04-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–181（181 aa）
Not recorded NI NICKEL (II) ION × 3 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；25% PEG-3350 and 0.1 M HEPES pH 7.5
Resolution 1.63 Å R-free 0.200

6 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CCMM_SYNE7
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–86； UniProt 225–310 Author chain B； PDBConstruct 1–86； UniProt 225–310 Author chain F； PDBConstruct 1–86； UniProt 225–310 Author chain T； PDBConstruct 1–86； UniProt 225–310

Ribulose bisphosphate carboxylase large chain

OrganismNot specified

UniProt Q31NB3

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 × 20 PDB declaration: 20-meric（20） Consistent with protein copy count Chain C； UniProt 17–458 Chain G； UniProt 17–458 Chain H； UniProt 17–458 Chain I； UniProt 17–458 Chain J； UniProt 17–458 Chain Q； UniProt 17–458 Chain R； UniProt 17–458 Chain S； UniProt 17–458 Not recorded Carboxysome assembly protein CcmM × 4 （Q03513） Ribulose bisphosphate carboxylase small subunit × 8 （P04716） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.50 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 9FWV Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6HBC Structure of the repeat unit in the network formed by CcmM and Rubisco from Synechococcus elongatus Deposited 2018-08-10 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain B 1–472（472 aa） Fragment：Rubisco large subunit
Chain C 1–472（472 aa） Fragment：Rubisco large subunit
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8；Solutions were made fresh
cryo-EM vitrification conditions Cryogen ETHANE；blot for 3 seconds before plunging
Resolution 2.78 Å
6SMH Cryo-electron microscopy structure of a RbcL-Raf1 supercomplex from Synechococcus elongatus PCC 7942 Deposited 2019-08-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain A 19–465（447 aa）
Chain B 19–465（447 aa）
Chain C 19–465（447 aa）
Chain D 19–465（447 aa）
Chain E 19–465（447 aa）
Chain F 19–465（447 aa）
Chain G 19–465（447 aa）
Chain H 19–465（447 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 4.30 Å
8BCM Structure of Synechococcus elongatus PCC 7942 Rubisco recombinantly expressed from E.coli Deposited 2022-10-17 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain A 1–472（472 aa） Fragment：Rubisco large subunit
Chain B 1–472（472 aa） Fragment：Rubisco large subunit
Chain C 1–472（472 aa） Fragment：Rubisco large subunit
Chain F 1–472（472 aa） Fragment：Rubisco large subunit
Chain G 1–472（472 aa） Fragment：Rubisco large subunit
Chain H 1–472（472 aa） Fragment：Rubisco large subunit
Chain I 1–472（472 aa） Fragment：Rubisco large subunit
Chain J 1–472（472 aa） Fragment：Rubisco large subunit
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.15 Å
8WPZ Cryo-ET structure of RuBisCO at 3.9 angstroms from Synechococcus elongatus PCC 7942 Deposited 2023-10-10 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain C 1–472（472 aa）
Chain D 1–472（472 aa）
Chain G 1–472（472 aa）
Chain H 1–472（472 aa）
Chain J 1–472（472 aa）
Chain K 1–472（472 aa）
Chain N 1–472（472 aa）
Chain O 1–472（472 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å

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

View Construct and Data Evidence
UniProt name RBL_SYNE7
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 1–442； UniProt 17–458 Author chain G； PDBConstruct 1–442； UniProt 17–458 Author chain H； PDBConstruct 1–442； UniProt 17–458 Author chain I； PDBConstruct 1–442； UniProt 17–458 Author chain J； PDBConstruct 1–442； UniProt 17–458 Author chain Q； PDBConstruct 1–442； UniProt 17–458 Author chain R； PDBConstruct 1–442； UniProt 17–458 Author chain S； PDBConstruct 1–442； UniProt 17–458

Ribulose bisphosphate carboxylase small subunit

OrganismNot specified

UniProt P04716

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 × 20 PDB declaration: 20-meric（20） Consistent with protein copy count Chain D； UniProt 8–108 Chain E； UniProt 8–108 Chain K； UniProt 8–108 Chain L； UniProt 8–108 Chain M； UniProt 8–108 Chain N； UniProt 8–108 Chain O； UniProt 8–108 Chain P； UniProt 8–108 Not recorded Carboxysome assembly protein CcmM × 4 （Q03513） Ribulose bisphosphate carboxylase large chain × 8 （Q31NB3） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.50 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 9FWV Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1RBL STRUCTURE DETERMINATION AND REFINEMENT OF RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE FROM SYNECHOCOCCUS PCC6301 Deposited 1993-05-12 Different construct Different oligomeric state 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 1–109（109 aa）
Chain J 1–109（109 aa）
Chain K 1–109（109 aa）
Chain L 1–109（109 aa）
Chain M 1–109（109 aa）
Chain N 1–109（109 aa）
Chain O 1–109（109 aa）
Chain P 1–109（109 aa）
Not recorded MG MAGNESIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8 FMT FORMIC ACID × 8 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.20 Å
1RSC STRUCTURE OF AN EFFECTOR INDUCED INACTIVATED STATE OF RIBULOSE BISPHOSPHATE CARBOXYLASE(SLASH)OXYGENASE: THE BINARY COMPLEX BETWEEN ENZYME AND XYLULOSE BISPHOSPHATE Deposited 1994-03-29 Different construct Different oligomeric state 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 1–110（110 aa）
Chain J 1–110（110 aa）
Chain K 1–110（110 aa）
Chain L 1–110（110 aa）
Chain M 1–110（110 aa）
Chain N 1–110（110 aa）
Chain O 1–110（110 aa）
Chain P 1–110（110 aa）
Not recorded XBP XYLULOSE-1,5-BISPHOSPHATE × 8 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å
1UZH A CHIMERIC CHLAMYDOMONAS, SYNECHOCOCCUS RUBISCO ENZYME Deposited 2004-03-12 Different construct 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 C 46–52（7 aa）
Chain F 47–53（7 aa）
Chain I 47–53（7 aa）
Chain J 47–53（7 aa）
Chain M 47–53（7 aa）
Chain P 47–53（7 aa）
Chain T 47–53（7 aa）
Chain W 47–53（7 aa）
Not recorded MG MAGNESIUM ION × 8 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 8 EDO 1,2-ETHANEDIOL × 50 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 2.20 Å R-free 0.193

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

View Construct and Data Evidence
UniProt name RBS_SYNP6
Isoform —
PDB entities 3
Chains and sequence ranges Author chain D； PDBConstruct 1–101； UniProt 8–108 Author chain E； PDBConstruct 1–101； UniProt 8–108 Author chain K； PDBConstruct 1–101； UniProt 8–108 Author chain L； PDBConstruct 1–101； UniProt 8–108 Author chain M； PDBConstruct 1–101； UniProt 8–108 Author chain N； PDBConstruct 1–101； UniProt 8–108 Author chain O； PDBConstruct 1–101； UniProt 8–108 Author chain P； PDBConstruct 1–101； UniProt 8–108

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 9fwv

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id9fwv
Deposition date deposition_date2024-07-01
Structure title titleRubisco in native beta-carboxysomes
Keywords keywordsRubisco, CcmM, PHOTOSYNTHESIS; PHOTOSYNTHESIS
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier48.36 Å
Radius of gyration Rg (electron density) rg_electron47.35 Å
Forward intensity I(0) i03830390000.00
Molecular weight molecular_weight515110.0 kDa
Excluded volume excluded_volume641940 ų
Envelope volume envelope_volume819090 ų
Hydration-shell volume shell_volume130070 ų
Envelope diameter envelope_diameter157.6 Å
Shell Rg shell_rg60.78 Å
Envelope Rg envelope_rg47.12 Å
Shape Rg shape_rg47.36 Å
Total Rg total_rg47.66 Å
Total atoms total_atoms36308
Residues n_residues4560
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 dmax146.2 Å
Rg (real space) rg_real47.87 Å
Rg uncertainty (real space) rg_real_error0.90 Å
I(0) (real space) i0_real3.8300e+09
I(0) uncertainty (real space) i0_real_error7.4520e+07
Rg (reciprocal space) rg_reciprocal48.36 Å
I(0) (reciprocal space) i0_reciprocal3833000000.0000
Solution quality estimate total_estimate0.8884
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary62.0 Å
Skewness Skewness skewness0.009
Kurtosis Kurtosis kurtosis-0.543
Angular range angular_range— – 0.1650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1049000000.0000
Real-space data points n_real_points34
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.936; Smooth: 0.916
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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)