SAXSdb — 2ktr

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

Sequestosome-1

Rattus norvegicus

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 3–100 Chain B； UniProt 3–100	Fragment：PB1 domain, OPR domain, residues 3-100 Mutation：C42S, D67A, D69R Fragment：PB1 domain, OPR domain, residues 3-100 Mutation：K207E, C226S, C242S, R294A	TB TERBIUM(III) ION × 1	SOLUTION NMR NMR measurement conditions：pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.05；Pressure ambient NMR sample composition：0.5mM [U-99% 13C; U-99% 15N] p62_1; 0.5mM p62_2; 20mM MES; 50mM sodium chloride; 0.5mM TERBIUM(III) ION; 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：0.5 mM p62_1; 0.5mM [U-99% 13C; U-99% 15N] p62_2; 20mM MES; 50mM sodium chloride; 0.5mM TERBIUM(III) ION; 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

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 2KTR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2K6Q LC3 p62 complex structure Deposited 2008-07-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 331–346（16 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.125；Pressure ambient NMR sample composition 0.8 mM [U-99% 13C; U-99% 15N] LC3, 1.2 mM p62 peptide, 25 mM sodium phosphate, 100 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.8 mM [U-99% 13C; U-99% 15N] p62 peptide, 1.2 mM LC3, 25 mM sodium phosphate, 100 mM sodium chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2KKC NMR structure of the p62 PB1 domain Deposited 2009-06-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 3–100（98 aa） Fragment：PB1 domain, OPR domain, residues 3-100	Mutation：D67A, D69R	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient NMR sample composition 1mM [U-99% 13C; U-99% 15N] p62 PB1-1, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

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

View Construct and Data Evidence

UniProt name	SQSTM_RAT
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 20–117； UniProt 3–100 Author chain B； PDBConstruct 3–100； UniProt 3–100

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	2ktr
Deposition date deposition_date	2010-02-05
Structure title title	NMR structure of p62 PB1 dimer determined based on PCS
Keywords keywords	Autophagy, NF-kB signaling, homo-oligomer, PB1 dimer, Signaling Protein, Transport Protein; Signaling Protein, Transport Protein
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	19.41 Å
Radius of gyration Rg (electron density) rg_electron	18.80 Å
Forward intensity I(0) i0	679956000.00
Molecular weight molecular_weight	220980.0 kDa
Excluded volume excluded_volume	276020 Å³
Envelope volume envelope_volume	39400 Å³
Hydration-shell volume shell_volume	17560 Å³
Envelope diameter envelope_diameter	66.6 Å
Shell Rg shell_rg	24.86 Å
Envelope Rg envelope_rg	19.42 Å
Shape Rg shape_rg	18.68 Å
Total Rg total_rg	19.33 Å
Total atoms total_atoms	30690
Residues n_residues	1970
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	61.1 Å
Rg (real space) rg_real	19.39 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	6.8000e+08
I(0) uncertainty (real space) i0_real_error	7.7200e+06
Rg (reciprocal space) rg_reciprocal	19.39 Å
I(0) (reciprocal space) i0_reciprocal	680000000.0000
Solution quality estimate total_estimate	0.8991
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.7 Å
Skewness Skewness skewness	0.269
Kurtosis Kurtosis kurtosis	-0.519
Angular range angular_range	— – 0.4100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1493000.0000
Real-space data points n_real_points	72
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.900; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.991

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Sequestosome-1
Molecular weight formula_weight	13074.7 kDa
Mutation mutation	C42S, D67A, D69R
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	30690

CYVDTNNDGAYEGDELHMGSLTVKAYLLGKEEAAREIRRFSFCFSPEPEAEAAAGPGPSERLLSRVAVLFPALRPGGFQAHYRAERGDLVAFSSDEELTMAMSYVKDDIFRIYIKEK

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Sequestosome-1
Molecular weight formula_weight	11157.5 kDa
Mutation mutation	K207E, C226S, C242S, R294A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

HMSLTVEAYLLGKEEAAREIRRFSFSFSPEPEAEAAAGPGPSERLLSRVAVLFPALRPGGFQAHYRDEDGDLVAFSSDEELTMAMSYVKDDIFAIYIKEK

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	TERBIUM(III) ION
Molecular weight formula_weight	158.9 kDa
Source method src_method	syn
Copy count entity_count	1

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2ktrA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Domain ID domain_id	2ktrB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

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8. Citations (1)

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fit	/app/data/saxs_computation/kt/2ktr/2ktr.fit
pddf	/app/data/pr_computation/kt/2ktr/2ktr.pr.out
profile	/app/data/saxs_computation/kt/2ktr/2ktr.dat

NMR structure of p62 PB1 dimer determined based on PCS

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

Sequestosome-1

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)