SAXSdb — 3ng2

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

RING finger protein 4

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 124–194 Chain B； UniProt 124–194	Fragment：RING domain	ZN ZINC ION × 4 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.2；291 K；0.2M lithium sulfate, 0.1M bis-Tris, 22% PEG 3350, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.80 Å R-free 0.242

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 3NG2	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4AP4 Rnf4 - ubch5a - ubiquitin heterotrimeric complex Deposited 2012-03-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 131–194（64 aa） Fragment：RESIDUES 131-195,131-195	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.2；pH 7.2	Resolution 2.21 Å R-free 0.242
5AIT A complex of of RNF4-RING domain, UbeV2, Ubc13-Ub (isopeptide crosslink) Deposited 2015-02-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 131–194（64 aa） Fragment：RING DOMAIN, UNP RESIDUES 131-194,131-194	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.40 Å R-free 0.286
5AIU A complex of RNF4-RING domain, Ubc13-Ub (isopeptide crosslink) Deposited 2015-02-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 131–194（64 aa） Fragment：RING DOMAIN, UNP RESIDUES 131-194,131-194	Mutation：YES	ZN ZINC ION × 4 EDO 1,2-ETHANEDIOL × 6	X-RAY DIFFRACTION X-ray crystallization conditions 1,2-ETHANEDIOL	Resolution 2.21 Å R-free 0.255

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RNF4_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–71； UniProt 124–194 Author chain B； PDBConstruct 1–71； UniProt 124–194

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	3ng2
Deposition date deposition_date	2010-06-10
Structure title title	Crystal structure of the RNF4 ring domain dimer
Keywords keywords	RING domain, E3 ligase, Ubiquitylation, Sumoylation, Zinc-finger, METAL BINDING PROTEIN; METAL BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	18.35 Å
Radius of gyration Rg (electron density) rg_electron	17.95 Å
Forward intensity I(0) i0	5406300.00
Molecular weight molecular_weight	15334.0 kDa
Excluded volume excluded_volume	18610 Å³
Envelope volume envelope_volume	25746 Å³
Hydration-shell volume shell_volume	12817 Å³
Envelope diameter envelope_diameter	65.1 Å
Shell Rg shell_rg	22.85 Å
Envelope Rg envelope_rg	18.13 Å
Shape Rg shape_rg	18.05 Å
Total Rg total_rg	18.57 Å
Total atoms total_atoms	1047
Residues n_residues	133
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	64.5 Å
Rg (real space) rg_real	18.32 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	5.4060e+06
I(0) uncertainty (real space) i0_real_error	7.2180e+04
Rg (reciprocal space) rg_reciprocal	18.33 Å
I(0) (reciprocal space) i0_reciprocal	5406000.0000
Solution quality estimate total_estimate	0.8717
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.5 Å
Skewness Skewness skewness	0.251
Kurtosis Kurtosis kurtosis	-0.203
Angular range angular_range	— – 0.4350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	358000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.793; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.975

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	RING finger protein 4
Molecular weight formula_weight	7885.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1090

GTTGLRPSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPIYI

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 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	43

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3ng2A00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	3ng2B00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

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8. Citations (1)

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Unit-cell length a length_a	58.487 Å
Unit-cell length b length_b	85.922 Å
Unit-cell length c length_c	22.277 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	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	18.730 Å
R factor r_factor	0.1900
R_work r_work	0.1873
R_free r_free	0.2420

fit	/app/data/saxs_computation/ng/3ng2/3ng2.fit
pddf	/app/data/pr_computation/ng/3ng2/3ng2.pr.out
profile	/app/data/saxs_computation/ng/3ng2/3ng2.dat

Crystal structure of the RNF4 ring domain dimer

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

RING finger protein 4

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

Refinement Refinement

Diffraction experiment Diffraction