3upf

Crystal structure of murine norovirus RNA-dependent RNA polymerase bound to NF023

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 monomer	Monomer	Protein 1	8-({3-[({3-[(4,6,8-trisulfonaphthalen-1-yl)carbamoyl]phenyl}carbamoyl)amino]benzoyl}amino)naphthalene-1,3,5-trisulfonic acid × 1 SULFATE ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	8-({3-[({3-[(4,6,8-trisulfonaphthalen-1-yl)carbamoyl]phenyl}carbamoyl)amino]benzoyl}amino)naphthalene-1,3,5-trisulfonic acid × 1 SULFATE ION × 2 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	8-({3-[({3-[(4,6,8-trisulfonaphthalen-1-yl)carbamoyl]phenyl}carbamoyl)amino]benzoyl}amino)naphthalene-1,3,5-trisulfonic acid × 1 SULFATE ION × 4 water × 1	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 6	8-({3-[({3-[(4,6,8-trisulfonaphthalen-1-yl)carbamoyl]phenyl}carbamoyl)amino]benzoyl}amino)naphthalene-1,3,5-trisulfonic acid × 6 SULFATE ION × 14 water × 6	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 4–517； UniProt 1174–1687 Author chain B； PDBConstruct 4–517； UniProt 1174–1687 Author chain C； PDBConstruct 4–517； UniProt 1174–1687

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	3upf
Deposition date deposition_date	2011-11-18
Structure title title	Crystal structure of murine norovirus RNA-dependent RNA polymerase bound to NF023
Keywords keywords	murine norovirus, RNA-dependent RNA polymerase, TRANSFERASE-TRANSFERASE INHIBITOR complex; TRANSFERASE/TRANSFERASE INHIBITOR
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.

3upf__assembly_2__model_1

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

Download this curve (.dat)

3upf__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3upf__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	24.54 Å
Rg (electron density)	23.51 Å
Total Rg	24.36 Å
Atom count	3909
Residues	483
Excluded volume	69058 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3upf__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3upf__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3upf__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3upf__assembly_4__model_1`	hexameric （6）	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 (4)

Entity 1 Entity 1 polymer

Description description	RNA-dependent RNA polymerase
Molecular weight formula_weight	59535.7 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	12242

MKALEFQGPPMLPRPSGTYAGLPIADYGDAPPLSTKTMFWRTSPEKLPPGAWEPAYLGSKDERVDGPSLQQVMRDQLKPYSEPRGLLPPQEILDAVCDAIENRLENTLEPQKPWTFKKACESLDKNTSSGYPYHKQKSKDWTGSAFIGDLGDQATHANNMYEMGKSMRPIYTAALKDELVKPDKIYGKIKKRLLWGSDLGTMIRAARAFGPFCDALKETCIFNPIRVGMSMNEDGPFIFARHANFRYHMDADYTRWDSTQQRAILKRAGDIMVRLSPEPDLARVVMDDLLAPSLLDVGDYKIVVEEGLPSGCPCTTQLNSLAHWILTLCAMVEVTRVDPDIVMQESEFSFYGDDEVVSTNLELDMVKYTMALRRYGLLPTRADKEEGPLERRQTLQGISFLRRAIVGDQFGWYGRLDRASIDRQLLWTKGPNHQNPFETLPGHAQRPSQLMALLGEAAMHGEKYYRTVASRVSKEAAQSGIEMVVPRHRSVLRWVRFGTMDAETPQERSAVFVNEDELEHHHHHH

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	8-({3-[({3-[(4,6,8-trisulfonaphthalen-1-yl)carbamoyl]phenyl}carbamoyl)amino]benzoyl}amino)naphthalene-1,3,5-trisulfonic acid
Molecular weight formula_weight	1031.0 kDa
Source method src_method	syn
Copy count entity_count	3

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	7

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	625

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3upfa_
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	d3upfb_
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	d3upfc_
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	3upfA02
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	3upfA03
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	3upfA04
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	3upfB02
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	3upfB03
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	3upfB04
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	3upfC02
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	3upfC03
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	3upfC04
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	120.860 Å
Unit-cell length b length_b	195.950 Å
Unit-cell length c length_c	109.240 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	114.38 °
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	2.600 Å
Low-resolution limit resolution_low	45.000 Å
R factor r_factor	0.2017
R_work r_work	0.1985
R_free r_free	0.2606

Crystal structure of murine norovirus RNA-dependent RNA polymerase bound to NF023

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

3upf__assembly_2__model_1

3upf__assembly_2__model_1 | I(q)

3upf__assembly_2__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (3 domains)

CATH v4.4 (9 domains)

7. Citations (1)

Crystal structure of murine norovirus RNA-dependent RNA polymerase bound to NF023

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

3upf__assembly_2__model_1

3upf__assembly_2__model_1 | I(q)

3upf__assembly_2__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (3 domains)

CATH v4.4 (9 domains)

7. Citations (1)