SAXSdb — 6smh

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

Ribulose bisphosphate carboxylase large chain

Synechococcus elongatus (strain PCC 7942 / FACHB-805)

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 19–465 Chain B； UniProt 19–465 Chain C； UniProt 19–465 Chain D； UniProt 19–465 Chain E； UniProt 19–465 Chain F； UniProt 19–465 Chain G； UniProt 19–465 Chain H； UniProt 19–465	Not recorded	Rubisco accumulation factor 1 (RAF1) peptide × 8 （Q31Q05）	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen NITROGEN	Resolution 4.30 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 6SMH	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
8BCM Structure of Synechococcus elongatus PCC 7942 Rubisco recombinantly expressed from E.coli Deposited 2022-10-17	Different construct 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 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 oligomeric state 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	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–447； UniProt 19–465 Author chain B； PDBConstruct 1–447； UniProt 19–465 Author chain C； PDBConstruct 1–447； UniProt 19–465 Author chain D； PDBConstruct 1–447； UniProt 19–465 Author chain E； PDBConstruct 1–447； UniProt 19–465 Author chain F； PDBConstruct 1–447； UniProt 19–465 Author chain G； PDBConstruct 1–447； UniProt 19–465 Author chain H； PDBConstruct 1–447； UniProt 19–465

Rubisco accumulation factor 1 (RAF1) peptide

Synechococcus elongatus (strain PCC 7942 / FACHB-805)

UniProt Q31Q05

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 I； UniProt 13–200 Chain J； UniProt 13–200 Chain K； UniProt 13–200 Chain L； UniProt 13–200 Chain M； UniProt 13–200 Chain N； UniProt 13–200 Chain O； UniProt 13–200 Chain P； UniProt 13–200	Not recorded	Ribulose bisphosphate carboxylase large chain × 8 （Q31NB3）	ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen NITROGEN	Resolution 4.30 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q31Q05_SYNE7
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain I； PDBConstruct 1–188； UniProt 13–200 Author chain J； PDBConstruct 1–188； UniProt 13–200 Author chain K； PDBConstruct 1–188； UniProt 13–200 Author chain L； PDBConstruct 1–188； UniProt 13–200 Author chain M； PDBConstruct 1–188； UniProt 13–200 Author chain N； PDBConstruct 1–188； UniProt 13–200 Author chain O； PDBConstruct 1–188； UniProt 13–200 Author chain P； PDBConstruct 1–188； UniProt 13–200

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	6smh
Deposition date deposition_date	2019-08-21
Structure title title	Cryo-electron microscopy structure of a RbcL-Raf1 supercomplex from Synechococcus elongatus PCC 7942
Keywords keywords	Rubisco, Rubisco accumulation factor1, Raf1, Synechococcus elongatus 7942, Cyanobacteria, 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	51.51 Å
Radius of gyration Rg (electron density) rg_electron	50.76 Å
Forward intensity I(0) i0	4600710000.00
Molecular weight molecular_weight	563740.0 kDa
Excluded volume excluded_volume	702280 Å³
Envelope volume envelope_volume	978250 Å³
Hydration-shell volume shell_volume	144460 Å³
Envelope diameter envelope_diameter	159.2 Å
Shell Rg shell_rg	64.60 Å
Envelope Rg envelope_rg	50.64 Å
Shape Rg shape_rg	50.78 Å
Total Rg total_rg	51.01 Å
Total atoms total_atoms	39744
Residues n_residues	5025
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	155.8 Å
Rg (real space) rg_real	51.20 Å
Rg uncertainty (real space) rg_real_error	0.71 Å
I(0) (real space) i0_real	4.6010e+09
I(0) uncertainty (real space) i0_real_error	7.1730e+07
Rg (reciprocal space) rg_reciprocal	51.77 Å
I(0) (reciprocal space) i0_reciprocal	4604000000.0000
Solution quality estimate total_estimate	0.8848
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	70.3 Å
Skewness Skewness skewness	0.025
Kurtosis Kurtosis kurtosis	-0.550
Angular range angular_range	— – 0.1550 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	2479000000.0000
Real-space data points n_real_points	32
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.945; Smooth: 0.816

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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	49641.2 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	39744

LTYYTPDYTPKDTDLLAAFRFSPQPGVPAPEAGAAIAAESSTGTWTTVWTDLLTDMDRYDGKCYHIEPVQGEENSYFAFIADPLDLFEEGSVTNILTSIVGNVFGFKAIRSLRLEDIRFPVALVKTFQGPPHGIQVERDLLNKYGRPMLGCTIKPKLGLSAKNYGRAVYECLRGGLDFTKDDENINSQPFQRWRDRFLFVADAIHKSQAETGEIKGHYLNVTAPTCEEMMKRAEFAKELGMPIIMHDFLTAGFTANTTLAKWCRDNGVLLHIHRAMHAVIDRQRNHGIHFRVLAKCLRLSGGDHLHSGTVVGKLEGDKASTLGFVDLMREDHIEADRSRGVFFTQDWASMPGVLPVASGGIHVWHMPALVEIFGDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQARNEGRDLYREGGDILREAGKWSPELAAALDLWKEIKFE

来源 Source

来源生物 organism	Synechococcus elongatus (strain PCC 7942 / FACHB-805)
NCBI Class编号 ncbi_taxonomy_id	1140
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Rubisco accumulation factor 1 (RAF1) peptide
Molecular weight formula_weight	21676.6 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

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

ERQELLGQLRRKEGRWLAWARACQTLLKNGLNPQTLFEATGFEPIQQNQITVAMQVYDSILRQDPPAHVRETYQEWGSDLLYELRELDQEQRSLCAQLALERKLDADQIREVAKATKDFCRLPKQPENFDRHPGDAVAHQCWRLAQERTDLTERSRLIARGLQFAQSAGARALIEALLLDLSGVPSRK

来源 Source

来源生物 organism	Synechococcus elongatus (strain PCC 7942 / FACHB-805)
NCBI Class编号 ncbi_taxonomy_id	1140
宿主生物 host_organism	Escherichia coli

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8. Citations (1)

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Resolution resolution	4.30 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	16022

fit	/app/data/saxs_computation/sm/6smh/6smh.fit
pddf	/app/data/pr_computation/sm/6smh/6smh.pr.out
profile	/app/data/saxs_computation/sm/6smh/6smh.dat

Cryo-electron microscopy structure of a RbcL-Raf1 supercomplex from Synechococcus elongatus PCC 7942

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 (RAF1) peptide

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)