SAXSdb — 2rqb

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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 896–1025	Fragment：UNP residues 896-1025	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

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 2RQB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3B6E Crystal structure of human DECH-box RNA Helicase MDA5 (Melanoma differentiation-associated protein 5), DECH-domain Deposited 2007-10-29	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 277–490（214 aa） Fragment：DECH domain: Residues 277-490	Not recorded	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
3GA3 Crystal structure of the C-terminal domain of human MDA5 Deposited 2009-02-16	Different construct Different experimental method 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 method 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 method 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 6–135； UniProt 896–1025

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	2rqb
Deposition date deposition_date	2009-03-17
Structure title title	Solution structure of MDA5 CTD
Keywords keywords	;RNA binding protein, HYDROLASE, Alternative splicing, Antiviral defense, ATP-binding, Cytoplasm, Diabetes mellitus, Helicase, Host-virus interaction, Immune response, Innate immunity, Nucleotide-binding, Nucleus, Phosphoprotein, Polymorphism, RNA-binding ;; HYDROLASE
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	16.07 Å
Radius of gyration Rg (electron density) rg_electron	15.78 Å
Forward intensity I(0) i0	1310330000.00
Molecular weight molecular_weight	310650.0 kDa
Excluded volume excluded_volume	389710 Å³
Envelope volume envelope_volume	34746 Å³
Hydration-shell volume shell_volume	16349 Å³
Envelope diameter envelope_diameter	71.6 Å
Shell Rg shell_rg	24.74 Å
Envelope Rg envelope_rg	19.61 Å
Shape Rg shape_rg	15.75 Å
Total Rg total_rg	16.05 Å
Total atoms total_atoms	43180
Residues n_residues	2700
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	67.8 Å
Rg (real space) rg_real	16.13 Å
Rg uncertainty (real space) rg_real_error	0.65 Å
I(0) (real space) i0_real	1.3100e+09
I(0) uncertainty (real space) i0_real_error	1.7250e+07
Rg (reciprocal space) rg_reciprocal	16.13 Å
I(0) (reciprocal space) i0_reciprocal	1310000000.0000
Solution quality estimate total_estimate	0.7190
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	18.0 Å
Skewness Skewness skewness	0.520
Kurtosis Kurtosis kurtosis	0.255
Angular range angular_range	— – 0.4950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	454900.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.317; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.401; Smooth: 0.992

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2rqba1
Class class	b — All beta proteins
Fold Fold fold	b.88 — Mss4-like
Superfamily Superfamily superfamily	b.88.2 — RIG-I C-terminal-like
Family Family family	b.88.2.1 — RIG-I C-terminal domain-like

Domain ID domain_id	d2rqba2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	2rqbA00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	150 — Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A
Homologous superfamily homologous superfamily	30 — RIG-I-like receptor, C-terminal regulatory domain

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8. Citations (1)

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Description description	Interferon-induced helicase C domain-containing protein 1
Molecular weight formula_weight	15503.1 kDa
EC 编号 ec_number	3.6.1.-
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	43180

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

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

fit	/app/data/saxs_computation/rq/2rqb/2rqb.fit
pddf	/app/data/pr_computation/rq/2rqb/2rqb.pr.out
profile	/app/data/saxs_computation/rq/2rqb/2rqb.dat

Solution structure of MDA5 CTD

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)