SAXSdb — 8io2

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

Ribulose bisphosphate carboxylase large chain

Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1)

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 × 17 PDB declaration: heptadecameric（17） Consistent with protein copy count	Chain A； UniProt 2–472 Chain B； UniProt 2–472 Chain C； UniProt 2–472 Chain D； UniProt 2–472 Chain E； UniProt 2–472 Chain F； UniProt 2–472 Chain G； UniProt 2–472 Chain H； UniProt 2–472	Not recorded	Rubisco accumulation factor 1.2, chloroplastic × 9 （Q9SR19）	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.10 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 8IO2	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 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 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 construct 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 construct 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
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) Deposited 2023-03-03	Different construct Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: nonadecameric	Chain A 1–472（472 aa） Chain B 1–472（472 aa） Chain F 1–472（472 aa） Chain G 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 3.30 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 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 construct 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 1–471； UniProt 2–472 Author chain B； PDBConstruct 1–471； UniProt 2–472 Author chain C； PDBConstruct 1–471； UniProt 2–472 Author chain D； PDBConstruct 1–471； UniProt 2–472 Author chain E； PDBConstruct 1–471； UniProt 2–472 Author chain F； PDBConstruct 1–471； UniProt 2–472 Author chain G； PDBConstruct 1–471； UniProt 2–472 Author chain H； PDBConstruct 1–471； UniProt 2–472

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 × 17 PDB declaration: heptadecameric（17） Consistent with protein copy count	Chain I； UniProt 73–437 Chain J； UniProt 73–437 Chain K； UniProt 73–437 Chain L； UniProt 73–437 Chain M； UniProt 73–437 Chain N； UniProt 73–437 Chain O； UniProt 73–437 Chain P； UniProt 73–437 Chain Q； UniProt 73–437	Not recorded	Ribulose bisphosphate carboxylase large chain × 8 （P00880）	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.10 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 8IO2	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
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) Deposited 2023-03-03	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: nonadecameric	Chain D 62–449（388 aa） Chain E 62–449（388 aa） Chain R 62–449（388 aa） Chain S 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 3.30 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	2
Chains and sequence ranges	Author chain I； PDBConstruct 1–346； UniProt 73–437 Author chain J； PDBConstruct 1–346； UniProt 73–437 Author chain K； PDBConstruct 1–346； UniProt 73–437 Author chain L； PDBConstruct 1–346； UniProt 73–437 Author chain M； PDBConstruct 1–346； UniProt 73–437 Author chain N； PDBConstruct 1–346； UniProt 73–437 Author chain O； PDBConstruct 1–346； UniProt 73–437 Author chain P； PDBConstruct 1–346； UniProt 73–437 Author chain Q； PDBConstruct 1–346； UniProt 73–437

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_id	8io2
Deposition date deposition_date	2023-03-10
Structure title title	The Rubisco assembly intermidate of Arabidopsis thaliana Rubisco accumulation factor 1 (AtRaf1) and Rubisco large subunit (RbcL)
Keywords keywords	Rubisco assembly intermediate, CHAPERONE, LYASE; LYASE
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	57.66 Å
Radius of gyration Rg (electron density) rg_electron	57.99 Å
Forward intensity I(0) i0	3754790000.00
Molecular weight molecular_weight	519280.0 kDa
Excluded volume excluded_volume	651240 Å³
Envelope volume envelope_volume	936460 Å³
Hydration-shell volume shell_volume	130770 Å³
Envelope diameter envelope_diameter	216.8 Å
Shell Rg shell_rg	62.25 Å
Envelope Rg envelope_rg	58.76 Å
Shape Rg shape_rg	57.99 Å
Total Rg total_rg	58.10 Å
Total atoms total_atoms	36624
Residues n_residues	4721
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	191.2 Å
Rg (real space) rg_real	57.64 Å
Rg uncertainty (real space) rg_real_error	1.50 Å
I(0) (real space) i0_real	3.7550e+09
I(0) uncertainty (real space) i0_real_error	6.8250e+07
Rg (reciprocal space) rg_reciprocal	57.65 Å
I(0) (reciprocal space) i0_reciprocal	3755000000.0000
Solution quality estimate total_estimate	0.8756
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	70.8 Å
Skewness Skewness skewness	0.401
Kurtosis Kurtosis kurtosis	-0.080
Angular range angular_range	— – 0.1350 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	324900000.0000
Real-space data points n_real_points	28
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.846; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.846

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Ribulose bisphosphate carboxylase large chain
Molecular weight formula_weight	52385.4 kDa
EC 编号 ec_number	4.1.1.39
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	36624

PKTQSAAGYKAGVKDYKLTYYTPDYTPKDTDLLAAFRFSPQPGVPADEAGAAIAAESSTGTWTTVWTDLLTDMDRYKGKCYHIEPVQGEENSYFAFIAYPLDLFEEGSVTNILTSIVGNVFGFKAIRSLRLEDIRFPVALVKTFQGPPHGIQVERDLLNKYGRPMLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENINSQPFQRWRDRFLFVADAIHKSQAETGEIKGHYLNVTAPTCEEMMKRAEFAKELGMPIIMHDFLTAGFTANTTLAKWCRDNGVLLHIHRAMHAVIDRQRNHGIHFRVLAKCLRLSGGDHLHSGTVVGKLEGDKASTLGFVDLMREDHIEADRSRGVFFTQDWASMPGVLPVASGGIHVWHMPALVEIFGDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQARNEGRDLYREGGDILREAGKWSPELAAALDLWKEIKFEFETMDKL

来源 Source

来源生物 organism	Synechococcus sp. (strain ATCC 27144 / PCC 6301 / SAUG 1402/1)
NCBI Class编号 ncbi_taxonomy_id	269084
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Rubisco accumulation factor 1.2, chloroplastic
Molecular weight formula_weight	38436.7 kDa
Source method src_method	man
Copy count entity_count	9

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,J,K,L,M,N,O,P,Q

SPIPTQFRSLDSAGKIEILAGRMALWFEYAPLISSLYTDGFTPPTIEELTGISSIEQNRLIVGAQVRDSILQSIHEPELISAFDTGGAELLYEIRLLSTTQRVAAATFIIDRNIDSKGAQDLARAIKDYPNRRGDVGWLDFDYNLPGDCLSFLYYRQSRENKNPSDQRTSMLLQALGVAESEKAKNRLNTELYGDRIPVVRLKFGEVAEATSVVVLPVCKAEEGEKKILEAPMEIIAGGDFKVVEAEKGWKRWVVLPSWNPVAAIGKGGVAVSFRDDRKVLPWDGKEEPLLVVADRVRNVVEADDGYYLVVAENGLKLEKGSDLKAREVKESLGMVVLVVRPPRED

来源 Source

来源生物 organism	Arabidopsis thaliana
通用名 common_name	thale cress
NCBI Class编号 ncbi_taxonomy_id	3702
宿主生物 host_organism	Escherichia coli BL21(DE3)

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8. Citations (1)

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Resolution resolution	3.10 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	535498

fit	/app/data/saxs_computation/io/8io2/8io2.fit
pddf	/app/data/pr_computation/io/8io2/8io2.pr.out
profile	/app/data/saxs_computation/io/8io2/8io2.dat

The Rubisco assembly intermidate of Arabidopsis thaliana Rubisco accumulation factor 1 (AtRaf1) and Rubisco large subunit (RbcL)

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

Ribulose bisphosphate carboxylase large chain

State in the Current Structure

Other States of the Same Protein in the Database

Rubisco accumulation factor 1.2, chloroplastic

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)