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6hbc

Structure of the repeat unit in the network formed by CcmM and Rubisco from Synechococcus elongatus

Method: ELECTRON MICROSCOPY Dmax: 117.6 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Carbon dioxide concentrating mechanism protein CcmM

Synechococcus elongatus (strain PCC 7942)

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: eicosameric（20） Consistent with protein copy count Chain A； UniProt 225–313 Fragment：SSUL domain 1 Ribulose bisphosphate carboxylase large chain × 8 （Q31NB3） Ribulose 1,5-bisphosphate carboxylase small subunit × 8 （Q31NB2） 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

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 6HBC 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 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 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 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 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
7D6C Crystal structure of CcmM N-terminal domain in complex with CcmN Deposited 2020-09-30 Different construct 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 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 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 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
9FWV Rubisco in native beta-carboxysomes Deposited 2024-07-01 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: 20-meric
Chain A 225–310（86 aa）
Chain B 225–310（86 aa）
Chain F 225–310（86 aa）
Chain T 225–310（86 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å

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 4–92； UniProt 225–313

Ribulose bisphosphate carboxylase large chain

Synechococcus elongatus (strain PCC 7942)

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: eicosameric（20） Consistent with protein copy count Chain B； UniProt 1–472 Chain C； UniProt 1–472 Fragment：Rubisco large subunit Carbon dioxide concentrating mechanism protein CcmM × 4 （Q03513） Ribulose 1,5-bisphosphate carboxylase small subunit × 8 （Q31NB2） 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

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 6HBC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6SMH Cryo-electron microscopy structure of a RbcL-Raf1 supercomplex from Synechococcus elongatus PCC 7942 Deposited 2019-08-21 Different construct Different mutation/modification 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 mutation/modification Different oligomeric state Different experimental conditions 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 mutation/modification Different oligomeric state Different experimental conditions 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
9FWV Rubisco in native beta-carboxysomes Deposited 2024-07-01 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: 20-meric
Chain C 17–458（442 aa）
Chain G 17–458（442 aa）
Chain H 17–458（442 aa）
Chain I 17–458（442 aa）
Chain J 17–458（442 aa）
Chain Q 17–458（442 aa）
Chain R 17–458（442 aa）
Chain S 17–458（442 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 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 B； PDBConstruct 1–472； UniProt 1–472 Author chain C； PDBConstruct 1–472； UniProt 1–472

Ribulose 1,5-bisphosphate carboxylase small subunit

Synechococcus elongatus (strain PCC 7942)

UniProt Q31NB2

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: eicosameric（20） Consistent with protein copy count Chain D； UniProt 1–111 Chain E； UniProt 1–111 Fragment：Rubisco small subunit Carbon dioxide concentrating mechanism protein CcmM × 4 （Q03513） Ribulose bisphosphate carboxylase large chain × 8 （Q31NB3） 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

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 6HBC Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8BCM Structure of Synechococcus elongatus PCC 7942 Rubisco recombinantly expressed from E.coli Deposited 2022-10-17 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain D 1–111（111 aa） Fragment：Rubisco small subunit
Chain E 1–111（111 aa） Fragment：Rubisco small subunit
Chain K 1–111（111 aa） Fragment：Rubisco small subunit
Chain L 1–111（111 aa） Fragment：Rubisco small subunit
Chain M 1–111（111 aa） Fragment：Rubisco small subunit
Chain N 1–111（111 aa） Fragment：Rubisco small subunit
Chain O 1–111（111 aa） Fragment：Rubisco small subunit
Chain P 1–111（111 aa） Fragment：Rubisco small 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 mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain A 1–111（111 aa）
Chain B 1–111（111 aa）
Chain E 1–111（111 aa）
Chain F 1–111（111 aa）
Chain I 1–111（111 aa）
Chain L 1–111（111 aa）
Chain M 1–111（111 aa）
Chain P 1–111（111 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

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

View Construct and Data Evidence
UniProt name Q31NB2_SYNE7
Isoform —
PDB entities 3
Chains and sequence ranges Author chain D； PDBConstruct 1–111； UniProt 1–111 Author chain E； PDBConstruct 1–111； UniProt 1–111

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 6hbc

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6hbc
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6hbc
Deposition date deposition_date2018-08-10
Structure title titleStructure of the repeat unit in the network formed by CcmM and Rubisco from Synechococcus elongatus
Keywords keywordsCcmM, M58, M35, SSUL domain, Rubisco, Carboxysome, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier35.92 Å
Radius of gyration Rg (electron density) rg_electron35.36 Å
Forward intensity I(0) i0272419000.00
Molecular weight molecular_weight132640.0 kDa
Excluded volume excluded_volume165590 ų
Envelope volume envelope_volume211060 ų
Hydration-shell volume shell_volume49266 ų
Envelope diameter envelope_diameter120.0 Å
Shell Rg shell_rg41.92 Å
Envelope Rg envelope_rg35.06 Å
Shape Rg shape_rg35.36 Å
Total Rg total_rg35.81 Å
Total atoms total_atoms9353
Residues n_residues1178
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 dmax117.6 Å
Rg (real space) rg_real35.89 Å
Rg uncertainty (real space) rg_real_error0.79 Å
I(0) (real space) i0_real2.7240e+08
I(0) uncertainty (real space) i0_real_error4.4260e+06
Rg (reciprocal space) rg_reciprocal35.91 Å
I(0) (reciprocal space) i0_reciprocal272400000.0000
Solution quality estimate total_estimate0.6847
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary42.8 Å
Skewness Skewness skewness0.299
Kurtosis Kurtosis kurtosis-0.428
Angular range angular_range— – 0.2200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha44070000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.909; Stabil: 1.000; Sysdev: 0.101; Positv: 1.000; Valcen: 0.993; Smooth: 0.876
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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) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd6hbcb1
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_idd6hbcb2
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_idd6hbcc1
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_idd6hbcc2
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_idd6hbcd_
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_idd6hbce_
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 (6 domains)

Domain ID domain_id6hbcB01
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_id6hbcB02
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_id6hbcC01
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_id6hbcC02
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_id6hbcD00
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_id6hbcE00
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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8. Citations (1)

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9. Files and Curves (10)