SAXSdb — 3b6e

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

Interferon-induced helicase C domain-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 277–490	Fragment：DECH domain: Residues 277-490	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；1.2M Sodium citrate, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.60 Å R-free 0.204

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 3B6E	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2RQB Solution structure of MDA5 CTD Deposited 2009-03-17	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 896–1025（130 aa） Fragment：UNP residues 896-1025	Not recorded	ZN ZINC ION × 1	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.25；Pressure ambient NMR sample composition 1mM [U-100% 13C; U-100% 15N] MDA5, 20mM Bis-Tris-2, 250mM sodium chloride-3, 10mM DTT-4, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3GA3 Crystal structure of the C-terminal domain of human MDA5 Deposited 2009-02-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 893–1017（125 aa） Fragment：C-terminal domain, residues 893-1017	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 8.5；277 K；0.1 M Tris, 14 to 18% ethanol, pH 8.5, EVAPORATION, temperature 277K	Resolution 1.45 Å R-free 0.204
4GL2 Structural Basis for dsRNA duplex backbone recognition by MDA5 Deposited 2012-08-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 306–1017（712 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.56 Å R-free 0.320
4GL2 Structural Basis for dsRNA duplex backbone recognition by MDA5 Deposited 2012-08-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 306–1017（712 aa）	Not recorded	ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.56 Å R-free 0.320
7DNI MDA5 CARDs-MAVS CARD polyUb complex Deposited 2020-12-09	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 × 16 PDB declaration: hexadecameric	Chain A 1–208（208 aa） Chain B 1–208（208 aa） Chain C 1–208（208 aa） Chain D 1–208（208 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5	Resolution 3.20 Å
7DNJ K63-polyUb MDA5CARDs complex Deposited 2020-12-09	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 × 12 PDB declaration: dodecameric	Chain A 1–208（208 aa） Chain B 1–208（208 aa） Chain C 1–208（208 aa） Chain D 1–208（208 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen OTHER	Resolution 3.30 Å
7JL0 Cryo-EM structure of MDA5-dsRNA in complex with TRIM65 PSpry domain (Monomer) Deposited 2020-07-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 287–1025（739 aa） Fragment：UNP residues 287-1025	Not recorded	ZN ZINC ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ALF TETRAFLUOROALUMINATE ION × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.30 Å
7JL2 Cryo-EM structure of MDA5-dsRNA filament in complex with TRIM65 PSpry domain (Trimer) Deposited 2020-07-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 6 PDB declaration: octameric	Chain A 287–1025（739 aa） Fragment：UNP residues 287-1025 Chain C 287–1025（739 aa） Fragment：UNP residues 287-1025 Chain E 287–1025（739 aa） Fragment：UNP residues 287-1025	Not recorded	ZN ZINC ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 3 ALF TETRAFLUOROALUMINATE ION × 3 MG MAGNESIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.30 Å
9LOV LGP2:MDA5:dsRNA filament Deposited 2025-01-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: pentameric	Chain B 287–1025（739 aa） Chain C 287–1025（739 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 3 ZN ZINC ION × 3 MG MAGNESIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.07 Å

8 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IFIH1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–216； UniProt 277–490

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	3b6e
Deposition date deposition_date	2007-10-29
Structure title title	Crystal structure of human DECH-box RNA Helicase MDA5 (Melanoma differentiation-associated protein 5), DECH-domain
Keywords keywords	;DECH, DExD/H RNA-binding helicase, innate immunity, IFIH1, Structural Genomics, Structural Genomics Consortium, SGC, Antiviral defense, ATP-binding, Diabetes mellitus, Host-virus interaction, Hydrolase, Immune response, Nucleotide-binding, Nucleus, Phosphorylation ;; HYDROLASE
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	19.06 Å
Radius of gyration Rg (electron density) rg_electron	17.69 Å
Forward intensity I(0) i0	7041880.00
Molecular weight molecular_weight	20522.0 kDa
Excluded volume excluded_volume	26375 Å³
Envelope volume envelope_volume	31898 Å³
Hydration-shell volume shell_volume	15782 Å³
Envelope diameter envelope_diameter	72.9 Å
Shell Rg shell_rg	23.25 Å
Envelope Rg envelope_rg	18.58 Å
Shape Rg shape_rg	17.66 Å
Total Rg total_rg	18.84 Å
Total atoms total_atoms	1442
Residues n_residues	182
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	72.8 Å
Rg (real space) rg_real	19.13 Å
Rg uncertainty (real space) rg_real_error	0.74 Å
I(0) (real space) i0_real	7.0420e+06
I(0) uncertainty (real space) i0_real_error	1.0810e+05
Rg (reciprocal space) rg_reciprocal	19.12 Å
I(0) (reciprocal space) i0_reciprocal	7042000.0000
Solution quality estimate total_estimate	0.7877
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.3 Å
Skewness Skewness skewness	0.583
Kurtosis Kurtosis kurtosis	0.499
Angular range angular_range	— – 0.4150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1259000.0000
Real-space data points n_real_points	73
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.468; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.850; Smooth: 0.983

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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	Interferon-induced helicase C domain-containing protein 1
Molecular weight formula_weight	24104.9 kDa
EC 编号 ec_number	3.6.1.-
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	1664

SMNSNMGSDSGTMGSDSDEENVAARASPEPELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLKKWYRVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKEAVYNNIMRHYLMQKLKNNRLKKENKPVIPLPQILGLTAS

来源 Source

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

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	174

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3b6eA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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8. Citations (1)

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Unit-cell length a length_a	72.830 Å
Unit-cell length b length_b	72.830 Å
Unit-cell length c length_c	182.780 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	19.970 Å
R factor r_factor	0.1806
R_work r_work	0.1794
R_free r_free	0.2037

fit	/app/data/saxs_computation/b6/3b6e/3b6e.fit
pddf	/app/data/pr_computation/b6/3b6e/3b6e.pr.out
profile	/app/data/saxs_computation/b6/3b6e/3b6e.dat

Crystal structure of human DECH-box RNA Helicase MDA5 (Melanoma differentiation-associated protein 5), DECH-domain

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

Interferon-induced helicase C domain-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

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction