← Back to search
8ilm

The cryo-EM structure of eight Rubisco large subunits (RbcL), two Arabidopsis thaliana Rubisco accumulation factors 1 (AtRaf1), and seven Arabidopsis thaliana Bundle Sheath Defective 2 (AtBSD2)

Method: ELECTRON MICROSCOPY Dmax: 169.9 Å Quality: GOOD
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Ribulose bisphosphate carboxylase large chain

Synechococcus elongatus PCC 6301

UniProt P00880

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 × 19 PDB declaration: nonadecameric（19） Consistent with protein copy count Chain A； UniProt 1–472 Chain B； UniProt 1–472 Chain F； UniProt 1–472 Chain G； UniProt 1–472 Chain H； UniProt 1–472 Chain I； UniProt 1–472 Chain J； UniProt 1–472 Chain K； UniProt 1–472 Not recorded Protein BUNDLE SHEATH DEFECTIVE 2, chloroplastic × 7 （Q9SN73） Rubisco accumulation factor 1.2, chloroplastic × 4 （Q9SR19） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.30 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 8ILM 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 A 6–472（467 aa）
Chain B 6–472（467 aa）
Chain C 6–472（467 aa）
Chain D 6–472（467 aa）
Chain E 6–472（467 aa）
Chain F 6–472（467 aa）
Chain G 6–472（467 aa）
Chain H 6–472（467 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 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 A 1–472（472 aa）
Chain B 1–472（472 aa）
Chain C 1–472（472 aa）
Chain D 1–472（472 aa）
Chain E 1–472（472 aa）
Chain F 1–472（472 aa）
Chain G 1–472（472 aa）
Chain H 1–472（472 aa）
Not recorded XBP XYLULOSE-1,5-BISPHOSPHATE × 8 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.30 Å
2WVW Cryo-EM structure of the RbcL-RbcX complex Deposited 2009-10-20 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric
Chain A 1–472（472 aa）
Chain B 1–472（472 aa）
Chain C 1–472（472 aa）
Chain D 1–472（472 aa）
Chain E 1–472（472 aa）
Chain F 1–472（472 aa）
Chain G 1–472（472 aa）
Chain H 1–472（472 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 20 MM TRIS-HCL, PH 8.7；pH 8.7；20 MM TRIS-HCL, PH 8.7
cryo-EM vitrification conditions Cryogen ETHANE；VITROBOT USED, LIQUID ETHANE
Resolution 9.00 Å
3RG6 Crystal structure of a chaperone-bound assembly intermediate of form I Rubisco Deposited 2011-04-07 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric
Chain A 1–472（472 aa）
Chain B 1–472（472 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.7；277 K；15-17 % 2-methyl-2,4-pentanediol, 0.1 M KCl, 0.1 M Tris-HCl, pH 8.7, vapor diffusion, temperature 277K
Resolution 3.20 Å R-free 0.245
8ILB The complexes of RbcL, AtRaf1 and AtBSD2 (LFB) Deposited 2023-03-03 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain A 1–472（472 aa）
Chain B 1–472（472 aa）
Chain C 1–472（472 aa）
Chain D 1–472（472 aa）
Chain J 1–472（472 aa）
Chain K 1–472（472 aa）
Chain L 1–472（472 aa）
Chain M 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 3.00 Å
8IO2 The Rubisco assembly intermidate of Arabidopsis thaliana Rubisco accumulation factor 1 (AtRaf1) and Rubisco large subunit (RbcL) Deposited 2023-03-10 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain A 2–472（471 aa）
Chain B 2–472（471 aa）
Chain C 2–472（471 aa）
Chain D 2–472（471 aa）
Chain E 2–472（471 aa）
Chain F 2–472（471 aa）
Chain G 2–472（471 aa）
Chain H 2–472（471 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8IOJ The Rubisco assembly intermidiate of Rubisco large subunit (RbcL) and Arabidopsis thaliana Rubisco accumulation factor 1 (AtRaf1) Deposited 2023-03-11 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain A 1–472（472 aa）
Chain B 1–472（472 aa）
Chain C 1–472（472 aa）
Chain D 1–472（472 aa）
Chain H 1–472（472 aa）
Chain I 1–472（472 aa）
Chain J 1–472（472 aa）
Chain K 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 4.10 Å
8IOL The complex of Rubisco large subunit (RbcL) Deposited 2023-03-11 Different oligomeric state Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1–472（472 aa）
Chain B 1–472（472 aa）
Chain C 1–472（472 aa）
Chain D 1–472（472 aa）
Chain E 1–472（472 aa）
Chain F 1–472（472 aa）
Chain G 1–472（472 aa）
Chain H 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 2.90 Å

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RBL_SYNP6
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–472； UniProt 1–472 Author chain B； PDBConstruct 1–472； UniProt 1–472 Author chain F； PDBConstruct 1–472； UniProt 1–472 Author chain G； PDBConstruct 1–472； UniProt 1–472 Author chain H； PDBConstruct 1–472； UniProt 1–472 Author chain I； PDBConstruct 1–472； UniProt 1–472 Author chain J； PDBConstruct 1–472； UniProt 1–472 Author chain K； PDBConstruct 1–472； UniProt 1–472

Protein BUNDLE SHEATH DEFECTIVE 2, chloroplastic

Arabidopsis thaliana

UniProt Q9SN73

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 × 19 PDB declaration: nonadecameric（19） Consistent with protein copy count Chain C； UniProt 57–136 Chain L； UniProt 57–136 Chain M； UniProt 57–136 Chain N； UniProt 57–136 Chain O； UniProt 57–136 Chain P； UniProt 57–136 Chain Q； UniProt 57–136 Not recorded Ribulose bisphosphate carboxylase large chain × 8 （P00880） Rubisco accumulation factor 1.2, chloroplastic × 4 （Q9SR19） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.30 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 8ILM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6EKB Crystal structure of the BSD2 homolog of Arabidopsis thaliana Deposited 2017-09-26 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 57–136（80 aa）
Mutation：K56M ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；20 % PEG 10,000, 8 % ethylene glycol and 0.1 M HEPES-NaOH pH 7.5
Resolution 1.90 Å R-free 0.216
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus Deposited 2017-09-26 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 × 16 PDB declaration: hexadecameric
Chain B1 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain B2 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain B3 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain B4 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain B5 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain B6 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain B7 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain B8 57–136（80 aa） Fragment：mature protein, residues 53-136
Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M ZN ZINC ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0
Resolution 2.63 Å R-free 0.274
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus Deposited 2017-09-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 10 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain T1 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain T2 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain T3 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain T4 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain T5 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain T6 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain T7 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain T8 57–136（80 aa） Fragment：mature protein, residues 53-136
Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M ZN ZINC ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0
Resolution 2.63 Å R-free 0.274
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus Deposited 2017-09-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain D1 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain D2 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain D3 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain D4 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain D5 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain D6 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain D7 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain D8 57–136（80 aa） Fragment：mature protein, residues 53-136
Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M ZN ZINC ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0
Resolution 2.63 Å R-free 0.274
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus Deposited 2017-09-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain F1 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain F2 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain F3 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain F4 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain F5 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain F6 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain F7 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain F8 57–136（80 aa） Fragment：mature protein, residues 53-136
Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M ZN ZINC ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0
Resolution 2.63 Å R-free 0.274
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus Deposited 2017-09-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain H1 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain H2 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain H3 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain H4 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain H5 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain H6 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain H7 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain H8 57–136（80 aa） Fragment：mature protein, residues 53-136
Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M ZN ZINC ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0
Resolution 2.63 Å R-free 0.274
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus Deposited 2017-09-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain J1 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain J2 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain J3 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain J4 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain J5 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain J6 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain J7 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain J8 57–136（80 aa） Fragment：mature protein, residues 53-136
Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M ZN ZINC ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0
Resolution 2.63 Å R-free 0.274
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus Deposited 2017-09-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain L1 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain L2 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain L3 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain L4 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain L5 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain L6 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain L7 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain L8 57–136（80 aa） Fragment：mature protein, residues 53-136
Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M ZN ZINC ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0
Resolution 2.63 Å R-free 0.274
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus Deposited 2017-09-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain N1 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain N2 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain N3 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain N4 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain N5 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain N6 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain N7 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain N8 57–136（80 aa） Fragment：mature protein, residues 53-136
Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M ZN ZINC ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0
Resolution 2.63 Å R-free 0.274
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus Deposited 2017-09-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain P1 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain P2 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain P3 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain P4 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain P5 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain P6 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain P7 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain P8 57–136（80 aa） Fragment：mature protein, residues 53-136
Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M ZN ZINC ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0
Resolution 2.63 Å R-free 0.274
6EKC Crystal structure of the BSD2 homolog of Arabidopsis thaliana bound to the octameric assembly of RbcL from Thermosynechococcus elongatus Deposited 2017-09-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 9 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain R1 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain R2 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain R3 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain R4 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain R5 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain R6 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain R7 57–136（80 aa） Fragment：mature protein, residues 53-136
Chain R8 57–136（80 aa） Fragment：mature protein, residues 53-136
Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M Mutation：K56M ZN ZINC ION × 16 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；21 % PEG 3350 and 0.12M DL-malic acid pH 7.0
Resolution 2.63 Å R-free 0.274
8ILB The complexes of RbcL, AtRaf1 and AtBSD2 (LFB) Deposited 2023-03-03 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain F 57–136（80 aa）
Chain G 57–136（80 aa）
Chain H 57–136（80 aa）
Chain I 57–136（80 aa）
Chain O 57–136（80 aa）
Chain P 57–136（80 aa）
Chain Q 57–136（80 aa）
Chain R 57–136（80 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9CI2 Anthoceros agrestis Rubisco octamer core complexed with small subunits and Arabidopsis thaliana BSD2 Deposited 2024-07-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: 16-meric
Chain 1 1–136（136 aa）
Chain 2 1–136（136 aa）
Chain 3 1–136（136 aa）
Chain 4 1–136（136 aa）
Not recorded MG MAGNESIUM ION × 4 CAP 2-CARBOXYARABINITOL-1,5-DIPHOSPHATE × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；20 mM Tris pH 8.0 50 mM NaCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å

4 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BSD2_ARATH
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 2–81； UniProt 57–136 Author chain L； PDBConstruct 2–81； UniProt 57–136 Author chain M； PDBConstruct 2–81； UniProt 57–136 Author chain N； PDBConstruct 2–81； UniProt 57–136 Author chain O； PDBConstruct 2–81； UniProt 57–136 Author chain P； PDBConstruct 2–81； UniProt 57–136 Author chain Q； PDBConstruct 2–81； UniProt 57–136

Rubisco accumulation factor 1.2, chloroplastic

Arabidopsis thaliana

UniProt Q9SR19

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 × 19 PDB declaration: nonadecameric（19） Consistent with protein copy count Chain D； UniProt 62–449 Chain E； UniProt 62–449 Chain R； UniProt 62–449 Chain S； UniProt 62–449 Not recorded Ribulose bisphosphate carboxylase large chain × 8 （P00880） Protein BUNDLE SHEATH DEFECTIVE 2, chloroplastic × 7 （Q9SN73） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.30 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 8ILM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4WT3 The N-terminal domain of Rubisco Accumulation Factor 1 from Arabidopsis thaliana Deposited 2014-10-29 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 62–274（213 aa） Fragment：Raf1 alpha-domain, UNP residues 62-274
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1 M MES-NaOH pH 6.0 and 26% (w/v) PEG-6000
Resolution 1.95 Å R-free 0.246
4WT4 The C-terminal domain of Rubisco Accumulation Factor 1 from Arabidopsis thaliana, crystal form I Deposited 2014-10-29 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 × 2 PDB declaration: dimeric
Chain A 281–449（169 aa） Fragment：Raf1 beta-domain, UNP residues 281-449
Chain C 281–449（169 aa） Fragment：Raf1 beta-domain, UNP residues 281-449
Not recorded PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；10% PEG 3350
Resolution 2.81 Å R-free 0.289
4WT4 The C-terminal domain of Rubisco Accumulation Factor 1 from Arabidopsis thaliana, crystal form I Deposited 2014-10-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 281–449（169 aa） Fragment：Raf1 beta-domain, UNP residues 281-449
Chain D 281–449（169 aa） Fragment：Raf1 beta-domain, UNP residues 281-449
Not recorded PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；10% PEG 3350
Resolution 2.81 Å R-free 0.289
4WT5 The C-terminal domain of Rubisco Accumulation Factor 1 from Arabidopsis thaliana, crystal form II Deposited 2014-10-29 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: Dimeric
Chain A 281–449（169 aa） Fragment：Raf1 beta-domain, UNP residues 281-449
Chain B 281–449（169 aa） Fragment：Raf1 beta-domain, UNP residues 281-449
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；200 mM KH2PO4 and 20% (w/v) PEG-5000MME
Resolution 2.57 Å R-free 0.279
8ILB The complexes of RbcL, AtRaf1 and AtBSD2 (LFB) Deposited 2023-03-03 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain E 62–449（388 aa）
Chain N 62–449（388 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8IO2 The Rubisco assembly intermidate of Arabidopsis thaliana Rubisco accumulation factor 1 (AtRaf1) and Rubisco large subunit (RbcL) Deposited 2023-03-10 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric
Chain I 73–437（365 aa）
Chain J 73–437（365 aa）
Chain K 73–437（365 aa）
Chain L 73–437（365 aa）
Chain M 73–437（365 aa）
Chain N 73–437（365 aa）
Chain O 73–437（365 aa）
Chain P 73–437（365 aa）
Chain Q 73–437（365 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8IOJ The Rubisco assembly intermidiate of Rubisco large subunit (RbcL) and Arabidopsis thaliana Rubisco accumulation factor 1 (AtRaf1) Deposited 2023-03-11 Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric
Chain E 62–264（203 aa）
Chain F 62–264（203 aa）
Chain G 62–264（203 aa）
Chain L 287–437（151 aa）
Chain M 287–437（151 aa）
Chain N 287–437（151 aa）
Chain O 287–437（151 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å

6 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RAF2_ARATH
Isoform —
PDB entities 3
Chains and sequence ranges Author chain D； PDBConstruct 2–389； UniProt 62–449 Author chain E； PDBConstruct 2–389； UniProt 62–449 Author chain R； PDBConstruct 2–389； UniProt 62–449 Author chain S； PDBConstruct 2–389； UniProt 62–449

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 8ilm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8ilm
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id8ilm
Deposition date deposition_date2023-03-03
Structure title titleThe cryo-EM structure of eight Rubisco large subunits (RbcL), two Arabidopsis thaliana Rubisco accumulation factors 1 (AtRaf1), and seven Arabidopsis thaliana Bundle Sheath Defective 2 (AtBSD2)
Keywords keywordsComplex, BIOSYNTHETIC PROTEIN, LYASE-CHAPERONE complex; LYASE/CHAPERONE
Experimental Method methodELECTRON MICROSCOPY
▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier53.47 Å
Radius of gyration Rg (electron density) rg_electron52.97 Å
Forward intensity I(0) i04141600000.00
Molecular weight molecular_weight538300.0 kDa
Excluded volume excluded_volume671790 ų
Envelope volume envelope_volume940260 ų
Hydration-shell volume shell_volume137580 ų
Envelope diameter envelope_diameter181.9 Å
Shell Rg shell_rg63.11 Å
Envelope Rg envelope_rg52.78 Å
Shape Rg shape_rg52.97 Å
Total Rg total_rg53.20 Å
Total atoms total_atoms37908
Residues n_residues4886
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
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax169.9 Å
Rg (real space) rg_real53.22 Å
Rg uncertainty (real space) rg_real_error1.04 Å
I(0) (real space) i0_real4.1420e+09
I(0) uncertainty (real space) i0_real_error7.4990e+07
Rg (reciprocal space) rg_reciprocal53.66 Å
I(0) (reciprocal space) i0_reciprocal4144000000.0000
Solution quality estimate total_estimate0.8671
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary70.3 Å
Skewness Skewness skewness0.180
Kurtosis Kurtosis kurtosis-0.293
Angular range angular_range— – 0.1450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha827700000.0000
Real-space data points n_real_points30
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.857; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.945; Smooth: 0.751
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

▶

8. Citations (1)

▶

9. Files and Curves (10)