3qid

Crystal structures and functional analysis of murine norovirus RNA-dependent RNA polymerase

Method: X-RAY DIFFRACTION

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

RNA dependent RNA polymerase

Murine norovirus 1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 24 MANGANESE (III) ION × 2 GLYCEROL × 6 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 16 MANGANESE (III) ION × 2 GLYCEROL × 7 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q80J95_9CALI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–506； UniProt 1181–1686 Author chain B； PDBConstruct 1–506； UniProt 1181–1686 Author chain C； PDBConstruct 1–506； UniProt 1181–1686

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	3qid
Deposition date deposition_date	2011-01-27
Structure title title	Crystal structures and functional analysis of murine norovirus RNA-dependent RNA polymerase
Keywords keywords	RNA POLYMERASE, VIRAL REPLICATION ENZYME, TRANSFERASE; TRANSFERASE
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.

3qid__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3qid__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3qid__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	34.13 Å
Rg (electron density)	33.56 Å
Total Rg	34.13 Å
Atom count	7926
Residues	984
Excluded volume	140260 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3qid__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3qid__assembly_2__model_1`	dimeric （2）	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 (5)

Entity 1 Entity 1 polymer

Description description	RNA dependent RNA polymerase
Molecular weight formula_weight	58519.5 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	12360

MLPRPSGTYAGLPIADYGDAPPLSTKTMFWRTSPEKLPPGAWEPAYLGSKDERVDGPSLQQVMRDQLKPYSEPRGLLPPQEILDAVCDAIENRLENTLEPQKPWTFKKACESLDKNTSSGYPYHKQKSKDWTGSAFIGDLGDQATHANNMYEMGKSMRPIYTAALKDELVKPDKIYGKIKKRLLWGSDLGTMIRAARAFGPFCDALKETCIFNPIRVGMSMNEDGPFIFARHANFRYHMDADYTRWDSTQQRAILKRAGDIMVRLSPEPDLARVVMDDLLAPSLLDVGDYKIVVEEGLPSGCPCTTQLNSLAHWILTLCAMVEVTRVDPDIVMQESEFSFYGDDEVVSTNLELDMVKYTMALRRYGLLPTRADKEEGPLERRQTLQGISFLRRAIVGDQFGWYGRLDRASIDRQLLWTKGPNHQNPFETLPGHAQRPSQLMALLGEAAMHGEKYYRTVASRVSKEAAQSGIEMVVPRHRSVLRWVRFGTMDAETPQERSAVFVNEDAAALEHHHHHH

Source Source

Source organism organism	Murine norovirus 1
NCBI taxonomy ID ncbi_taxonomy_id	223997
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	28

Entity 3 Entity 3 non-polymer

Description description	MANGANESE (III) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	454

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3qida_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.8 — DNA/RNA polymerases
Superfamily Superfamily superfamily	e.8.1 — DNA/RNA polymerases
Family Family family	e.8.1.4 — RNA-dependent RNA-polymerase

Domain ID domain_id	d3qidb_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.8 — DNA/RNA polymerases
Superfamily Superfamily superfamily	e.8.1 — DNA/RNA polymerases
Family Family family	e.8.1.4 — RNA-dependent RNA-polymerase

Domain ID domain_id	d3qidc_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.8 — DNA/RNA polymerases
Superfamily Superfamily superfamily	e.8.1 — DNA/RNA polymerases
Family Family family	e.8.1.4 — RNA-dependent RNA-polymerase

CATH v4.4 (9 domains)

Domain ID domain_id	3qidA02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	3230 —

Domain ID domain_id	3qidA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	270 — Reverse transcriptase/Diguanylate cyclase domain

Domain ID domain_id	3qidA04
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	960 — Mitochondrial Import Receptor Subunit Tom20; Chain A
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3qidB02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	3230 —

Domain ID domain_id	3qidB03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	270 — Reverse transcriptase/Diguanylate cyclase domain

Domain ID domain_id	3qidB04
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	960 — Mitochondrial Import Receptor Subunit Tom20; Chain A
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	3qidC02
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	3230 —

Domain ID domain_id	3qidC03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	270 — Reverse transcriptase/Diguanylate cyclase domain

Domain ID domain_id	3qidC04
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	960 — Mitochondrial Import Receptor Subunit Tom20; Chain A
Homologous superfamily homologous superfamily	20 —

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Unit-cell length a length_a	120.557 Å
Unit-cell length b length_b	196.262 Å
Unit-cell length c length_c	109.339 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	114.23 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	49.070 Å
R factor r_factor	0.2016
R_work r_work	0.1993
R_free r_free	0.2449

Crystal structures and functional analysis of murine norovirus RNA-dependent RNA polymerase

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

RNA dependent RNA polymerase

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

3qid__assembly_2__model_1

3qid__assembly_2__model_1 | I(q)

3qid__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (3 domains)

CATH v4.4 (9 domains)

7. Citations (1)

Crystal structures and functional analysis of murine norovirus RNA-dependent RNA polymerase

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

RNA dependent RNA polymerase

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

3qid__assembly_2__model_1

3qid__assembly_2__model_1 | I(q)

3qid__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (3 domains)

CATH v4.4 (9 domains)

7. Citations (1)