2qfd

Crystal structure of the regulatory domain of human RIG-I with bound Hg

Method: X-RAY DIFFRACTION

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

Probable ATP-dependent RNA helicase DDX58

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	MERCURY (II) ION × 1 water × 1	Consistent with protein count
10	Protein monomer	Monomer	Protein 1	MERCURY (II) ION × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	MERCURY (II) ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	MERCURY (II) ION × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	MERCURY (II) ION × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	MERCURY (II) ION × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	MERCURY (II) ION × 1 water × 1	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	MERCURY (II) ION × 1 water × 1	Consistent with protein count
8	Protein monomer	Monomer	Protein 1	MERCURY (II) ION × 1 water × 1	Consistent with protein count
9	Protein monomer	Monomer	Protein 1	MERCURY (II) ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DDX58_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–145； UniProt 802–925 Author chain B； PDBConstruct 22–145； UniProt 802–925 Author chain C； PDBConstruct 22–145； UniProt 802–925 Author chain D； PDBConstruct 22–145； UniProt 802–925 Author chain E； PDBConstruct 22–145； UniProt 802–925 Author chain F； PDBConstruct 22–145； UniProt 802–925 Author chain G； PDBConstruct 22–145； UniProt 802–925 Author chain H； PDBConstruct 22–145； UniProt 802–925 Author chain I； PDBConstruct 22–145； UniProt 802–925 Author chain J； PDBConstruct 22–145； UniProt 802–925

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	2qfd
Deposition date deposition_date	2007-06-27
Structure title title	Crystal structure of the regulatory domain of human RIG-I with bound Hg
Keywords keywords	;Zinc Finger, Alternative splicing, Antiviral defense, ATP-binding, Helicase, Hydrolase, Immune response, Innate immunity, Interferon induction, Nucleotide-binding, Polymorphism, RNA-binding, Ubl conjugation ;; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

2qfd__assembly_5__model_1

Assembly 5 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2qfd__assembly_5__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2qfd__assembly_5__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	15.39 Å
Rg (electron density)	14.12 Å
Total Rg	15.40 Å
Atom count	999
Residues	121
Excluded volume	18010 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2qfd__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2qfd__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2qfd__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2qfd__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2qfd__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`2qfd__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`2qfd__assembly_7__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`2qfd__assembly_8__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`2qfd__assembly_9__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`2qfd__assembly_10__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Probable ATP-dependent RNA helicase DDX58
Molecular weight formula_weight	16853.5 kDa
EC 编号 ec_number	3.6.1.-
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J
Atom count atom_count	10092

MGSSHHHHHHSSGLVPRGSHMDKENKKLLCRKCKALACYTADVRVIEECHYTVLGDAFKECFVSRPHPKPKQFSSFEKRAKIFCARQNCSHDWGIHVKYKTFEIPVIKIESFVVEDIATGVQTLYSKWKDFHFEKIPFDPAEMSK

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MERCURY (II) ION
Molecular weight formula_weight	200.6 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	102

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d2qfda_
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	d2qfdb_
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	d2qfdc_
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	d2qfdd_
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	d2qfde_
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	d2qfdf_
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	d2qfdg_
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	d2qfdh_
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	d2qfdi_
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	d2qfdj_
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

CATH v4.4 (10 domains)

Domain ID domain_id	2qfdA00
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

Domain ID domain_id	2qfdB00
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

Domain ID domain_id	2qfdC00
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

Domain ID domain_id	2qfdD00
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

Domain ID domain_id	2qfdE00
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

Domain ID domain_id	2qfdF00
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

Domain ID domain_id	2qfdG00
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

Domain ID domain_id	2qfdH00
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

Domain ID domain_id	2qfdI00
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

Domain ID domain_id	2qfdJ00
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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Unit-cell length a length_a	97.150 Å
Unit-cell length b length_b	76.540 Å
Unit-cell length c length_c	137.900 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.07 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	20

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2530
R_work r_work	0.2410
R_free r_free	0.2760

Crystal structure of the regulatory domain of human RIG-I with bound Hg

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

Probable ATP-dependent RNA helicase DDX58

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2qfd__assembly_5__model_1

2qfd__assembly_5__model_1 | I(q)

2qfd__assembly_5__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

CATH v4.4 (10 domains)

7. Citations (1)

Crystal structure of the regulatory domain of human RIG-I with bound Hg

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

Probable ATP-dependent RNA helicase DDX58

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2qfd__assembly_5__model_1

2qfd__assembly_5__model_1 | I(q)

2qfd__assembly_5__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (10 domains)

CATH v4.4 (10 domains)

7. Citations (1)