SAXSdb — 8wpz

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

Ribulose bisphosphate carboxylase small subunit

OrganismNot specified

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 × 16 PDB declaration: hexadecameric（16） Consistent with protein copy count	Chain A； UniProt 1–111 Chain B； UniProt 1–111 Chain E； UniProt 1–111 Chain F； UniProt 1–111 Chain I； UniProt 1–111 Chain L； UniProt 1–111 Chain M； UniProt 1–111 Chain P； UniProt 1–111	Not recorded	Ribulose bisphosphate carboxylase large chain × 8 （Q31NB3）	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.90 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 8WPZ	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 oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain D 1–111（111 aa） Fragment：Rubisco small subunit Chain E 1–111（111 aa） Fragment：Rubisco small 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
8BCM Structure of Synechococcus elongatus PCC 7942 Rubisco recombinantly expressed from E.coli Deposited 2022-10-17	Different construct 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

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

View Construct and Data Evidence

UniProt name	RBS_SYNE7
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–111； UniProt 1–111 Author chain B； PDBConstruct 1–111； UniProt 1–111 Author chain E； PDBConstruct 1–111； UniProt 1–111 Author chain F； PDBConstruct 1–111； UniProt 1–111 Author chain I； PDBConstruct 1–111； UniProt 1–111 Author chain L； PDBConstruct 1–111； UniProt 1–111 Author chain M； PDBConstruct 1–111； UniProt 1–111 Author chain P； PDBConstruct 1–111； UniProt 1–111

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 × 16 PDB declaration: hexadecameric（16） Consistent with protein copy count	Chain C； UniProt 1–472 Chain D； UniProt 1–472 Chain G； UniProt 1–472 Chain H； UniProt 1–472 Chain J； UniProt 1–472 Chain K； UniProt 1–472 Chain N； UniProt 1–472 Chain O； UniProt 1–472	Not recorded	Ribulose bisphosphate carboxylase small subunit × 8 （Q31NB2）	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.90 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 8WPZ	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 oligomeric state 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 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 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
9FWV Rubisco in native beta-carboxysomes Deposited 2024-07-01	Different construct Different oligomeric state 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 C； PDBConstruct 1–472； UniProt 1–472 Author chain D； 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 J； PDBConstruct 1–472； UniProt 1–472 Author chain K； PDBConstruct 1–472； UniProt 1–472 Author chain N； PDBConstruct 1–472； UniProt 1–472 Author chain O； PDBConstruct 1–472； UniProt 1–472

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	8wpz
Deposition date deposition_date	2023-10-10
Structure title title	Cryo-ET structure of RuBisCO at 3.9 angstroms from Synechococcus elongatus PCC 7942
Keywords keywords	carboxysome, RuBisCO, cryo-et, PHOTOSYNTHESIS; PHOTOSYNTHESIS
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	49.12 Å
Radius of gyration Rg (electron density) rg_electron	48.13 Å
Forward intensity I(0) i0	3649220000.00
Molecular weight molecular_weight	507150.0 kDa
Excluded volume excluded_volume	633570 Å³
Envelope volume envelope_volume	848060 Å³
Hydration-shell volume shell_volume	133050 Å³
Envelope diameter envelope_diameter	145.3 Å
Shell Rg shell_rg	61.53 Å
Envelope Rg envelope_rg	47.54 Å
Shape Rg shape_rg	48.16 Å
Total Rg total_rg	48.40 Å
Total atoms total_atoms	35774
Residues n_residues	4492
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	144.7 Å
Rg (real space) rg_real	48.57 Å
Rg uncertainty (real space) rg_real_error	0.55 Å
I(0) (real space) i0_real	3.6490e+09
I(0) uncertainty (real space) i0_real_error	5.9760e+07
Rg (reciprocal space) rg_reciprocal	49.11 Å
I(0) (reciprocal space) i0_reciprocal	3652000000.0000
Solution quality estimate total_estimate	0.8830
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	67.8 Å
Skewness Skewness skewness	-0.036
Kurtosis Kurtosis kurtosis	-0.576
Angular range angular_range	— – 0.1600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1720000000.0000
Real-space data points n_real_points	33
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.936; Smooth: 0.789

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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 small subunit
Molecular weight formula_weight	13349.2 kDa
Source method src_method	nat
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,E,F,I,L,M,P
Atom count atom_count	35774

MSMKTLPKERRFETFSYLPPLSDRQIAAQIEYMIEQGFHPLIEFNEHSNPEEFYWTMWKLPLFDCKSPQQVLDEVRECRSEYGDCYIRVAGFDNIKQCQTVSFIVHRPGRY

Entity 2 Entity 2 polymer

Description description	Ribulose bisphosphate carboxylase large chain
Molecular weight formula_weight	52516.6 kDa
EC 编号 ec_number	4.1.1.39
Source method src_method	nat
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D,G,H,J,K,N,O

MPKTQSAAGYKAGVKDYKLTYYTPDYTPKDTDLLAAFRFSPQPGVPADEAGAAIAAESSTGTWTTVWTDLLTDMDRYKGKCYHIEPVQGEENSYFAFIAYPLDLFEEGSVTNILTSIVGNVFGFKAIRSLRLEDIRFPVALVKTFQGPPHGIQVERDLLNKYGRPMLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENINSQPFQRWRDRFLFVADAIHKSQAETGEIKGHYLNVTAPTCEEMMKRAEFAKELGMPIIMHDFLTAGFTANTTLAKWCRDNGVLLHIHRAMHAVIDRQRNHGIHFRVLAKCLRLSGGDHLHSGTVVGKLEGDKASTLGFVDLMREDHIEADRSRGVFFTQDWASMPGVLPVASGGIHVWHMPALVEIFGDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQARNEGRDLYREGGDILREAGKWSPELAAALDLWKEIKFEFETMDKL

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.90 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	2700

fit	/app/data/saxs_computation/wp/8wpz/8wpz.fit
pddf	/app/data/pr_computation/wp/8wpz/8wpz.pr.out
profile	/app/data/saxs_computation/wp/8wpz/8wpz.dat

Cryo-ET structure of RuBisCO at 3.9 angstroms from Synechococcus elongatus PCC 7942

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

Ribulose bisphosphate carboxylase small subunit

State in the Current Structure

Other States of the Same Protein in the Database

Ribulose bisphosphate carboxylase large chain

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

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)