SAXSdb — 2lgy

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

RanBP-type and C3HC4-type zinc finger-containing protein 1

Homo sapiens

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 51–139	Fragment：sequence database residues 51-139	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 61；Pressure ambient NMR sample composition：10 mM potassium phosphate, 1 mM EDTA, 50 mM potassium chloride, 30 uM DSS, 0.2 mM [U-15N] HOIL-1 Ubl, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：10 mM potassium phosphate, 1 mM EDTA, 50 mM potassium chloride, 30 uM DSS, 0.2 mM [U-13C; U-15N] HOIL-1 Ubl, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition：10 mM potassium phosphate, 1 mM EDTA, 50 mM potassium chloride, 30 uM DSS, 0.2 mM [U-13C; U-15N] HOIL-1 Ubl, 100% D2O \| 100% 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 2LGY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2CRC Solution structure of the zf-RanBP domain of the protein HBV associated factor Deposited 2005-05-20	Different construct Different ligand/ion Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 184–222（39 aa） Fragment：zf-RanBP domain	Not recorded	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 2.17mM 13C, 15N-labeled protein; 20mM d-Tris-HCl (pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3, 0.05mM ZnCl2, 0.1mM NTA \| 90% H2O/10% D2O	Resolution not provided
4DBG Crystal structure of HOIL-1L-UBL complexed with a HOIP-UBA derivative Deposited 2012-01-15	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 37–137（101 aa） Fragment：Ub-like domain, residues 37-137	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；15%(w/v) PEG6000, 0.1M KCl, 0.1M HEPES-Na buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.71 Å R-free 0.253
7V8E Crystal structure of IpaH1.4 LRR domain bound to HOIL-1L UBL domain. Deposited 2021-08-22	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 53–135（83 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.5；289 K；0.2 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.5), and 25% (w/v) PEG3350	Resolution 1.90 Å R-free 0.246
7V8E Crystal structure of IpaH1.4 LRR domain bound to HOIL-1L UBL domain. Deposited 2021-08-22	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 53–135（83 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.5；289 K；0.2 M (NH4)2SO4, 0.1 M Tris-HCl (pH 8.5), and 25% (w/v) PEG3350	Resolution 1.90 Å R-free 0.246
7YUI Crystal structure of HOIL-1L(195-423) in complex with the linear tetra-ubiquitin Deposited 2022-08-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 195–424（230 aa）	Not recorded	ZN ZINC ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2 M Lithium chloride, 0.1 M Tris(pH 8), 20 %(w/v)PEG 8000	Resolution 2.60 Å R-free 0.258
7YUJ Crystal structure of HOIL-1L(365-510) Deposited 2022-08-17	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 365–510（146 aa） Chain B 365–510（146 aa）	Not recorded	ZN ZINC ION × 10 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；22 % w/v Poly(acrylic acid sodium salt) 5,100, 100 mM HEPES(pH 7.5), 20 mM Magnesium chloride	Resolution 1.86 Å R-free 0.187
8BVL Crystal structure of the IBR-RING2 domain of HOIL-1 Deposited 2022-12-04	Different construct 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 368–510（143 aa）	Not recorded	ZN ZINC ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；200 mM magnesium chloride hexahydrate 100mM Tris-HCl pH 7.0 10% PEG 8000	Resolution 2.24 Å R-free 0.296
8BVL Crystal structure of the IBR-RING2 domain of HOIL-1 Deposited 2022-12-04	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 368–510（143 aa）	Not recorded	ZN ZINC ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；200 mM magnesium chloride hexahydrate 100mM Tris-HCl pH 7.0 10% PEG 8000	Resolution 2.24 Å R-free 0.296
8EAZ HOIL-1/E2-Ub/Ub transthiolation complex Deposited 2022-08-30	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 × 4 PDB declaration: tetrameric	Chain A 232–510（279 aa）	Mutation：C460A	ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；298 K；28% PEG smear broad, 0.2 M sodium chloride, 0.1 M sodium phosphate, pH 6.2	Resolution 3.08 Å R-free 0.266
8EAZ HOIL-1/E2-Ub/Ub transthiolation complex Deposited 2022-08-30	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 × 4 PDB declaration: tetrameric	Chain B 232–510（279 aa）	Mutation：C460A	ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；298 K；28% PEG smear broad, 0.2 M sodium chloride, 0.1 M sodium phosphate, pH 6.2	Resolution 3.08 Å R-free 0.266
8K6Q Crystal structure of HOIL-1L LTM domain Deposited 2023-07-25	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 B 1–51（51 aa） Fragment：LTM domain Chain D 1–51（51 aa） Fragment：LTM domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；100 mM sodium acetate, 1 M di-ammonium hydrogen phosphate (pH 4.5).	Resolution 1.59 Å R-free 0.206
8K6Q Crystal structure of HOIL-1L LTM domain Deposited 2023-07-25	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–51（51 aa） Fragment：LTM domain Chain C 1–51（51 aa） Fragment：LTM domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289.15 K；100 mM sodium acetate, 1 M di-ammonium hydrogen phosphate (pH 4.5).	Resolution 1.59 Å R-free 0.206
9EGV HOIL-1 RING2 domain bound to ubiquitin Deposited 2024-11-21	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 × 3 PDB declaration: trimeric	Chain A 425–510（86 aa） Chain B 425–510（86 aa）	Mutation：C460A Mutation：C460A	ZN ZINC ION × 6 CL CHLORIDE ION × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；293 K；0.01 M magnesium chloride hexahydrate, 0.05 M MES monohydrate pH 6.2, 1.8 M lithium sulfate monohydrate	Resolution 2.00 Å R-free 0.208
9EGV HOIL-1 RING2 domain bound to ubiquitin Deposited 2024-11-21	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 × 3 PDB declaration: dimeric	Chain A 425–510（86 aa） Chain B 425–510（86 aa）	Mutation：C460A Mutation：C460A	ZN ZINC ION × 6 CL CHLORIDE ION × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；293 K；0.01 M magnesium chloride hexahydrate, 0.05 M MES monohydrate pH 6.2, 1.8 M lithium sulfate monohydrate	Resolution 2.00 Å R-free 0.208
9EGW HOIL-1 RING2 domain bound to ubiquitin-maltose (maltose not modelled) Deposited 2024-11-21	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 × 3 PDB declaration: trimeric	Chain A 425–510（86 aa） Chain B 425–510（86 aa）	Mutation：C460A Mutation：C460A	ZN ZINC ION × 6 CL CHLORIDE ION × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.02 M MgCl2, 0.05 M MES pH6 and 1.8 M LiSO4	Resolution 1.78 Å R-free 0.182
9EGW HOIL-1 RING2 domain bound to ubiquitin-maltose (maltose not modelled) Deposited 2024-11-21	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 × 2 PDB declaration: dimeric	Chain A 425–510（86 aa）	Mutation：C460A	ZN ZINC ION × 3 CL CHLORIDE ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.02 M MgCl2, 0.05 M MES pH6 and 1.8 M LiSO4	Resolution 1.78 Å R-free 0.182
9EGW HOIL-1 RING2 domain bound to ubiquitin-maltose (maltose not modelled) Deposited 2024-11-21	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 425–510（86 aa）	Mutation：C460A	ZN ZINC ION × 3 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.02 M MgCl2, 0.05 M MES pH6 and 1.8 M LiSO4	Resolution 1.78 Å R-free 0.182

10 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HOIL1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–90； UniProt 51–139

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	2lgy
Deposition date deposition_date	2011-08-03
Structure title title	Ubiquitin-like domain from HOIL-1
Keywords keywords	ubiquitin, HOIP, E3 ligase, UBLD, LIGASE; LIGASE
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	13.63 Å
Radius of gyration Rg (electron density) rg_electron	13.23 Å
Forward intensity I(0) i0	600914000.00
Molecular weight molecular_weight	206840.0 kDa
Excluded volume excluded_volume	258430 Å³
Envelope volume envelope_volume	25853 Å³
Hydration-shell volume shell_volume	13889 Å³
Envelope diameter envelope_diameter	54.4 Å
Shell Rg shell_rg	21.70 Å
Envelope Rg envelope_rg	16.65 Å
Shape Rg shape_rg	13.17 Å
Total Rg total_rg	13.62 Å
Total atoms total_atoms	28980
Residues n_residues	1800
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	47.4 Å
Rg (real space) rg_real	13.64 Å
Rg uncertainty (real space) rg_real_error	0.41 Å
I(0) (real space) i0_real	6.0090e+08
I(0) uncertainty (real space) i0_real_error	6.8340e+06
Rg (reciprocal space) rg_reciprocal	13.64 Å
I(0) (reciprocal space) i0_reciprocal	600900000.0000
Solution quality estimate total_estimate	0.7642
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	16.2 Å
Skewness Skewness skewness	0.366
Kurtosis Kurtosis kurtosis	-0.108
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	152900.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.656; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2lgyA00
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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Description description	RanBP-type and C3HC4-type zinc finger-containing protein 1
Molecular weight formula_weight	10353.8 kDa
EC 编号 ec_number	6.3.2.-
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	28980

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/lg/2lgy/2lgy.fit
pddf	/app/data/pr_computation/lg/2lgy/2lgy.pr.out
profile	/app/data/saxs_computation/lg/2lgy/2lgy.dat

Ubiquitin-like domain from HOIL-1

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

RanBP-type and C3HC4-type zinc finger-containing protein 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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)