SAXSdb — 5n7m

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

Capsid protein VP1

Norwalk virus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Homooligomer	Protein 2 其他Polymer 2	alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose × 2 SODIUM ION × 2 1,2-ETHANEDIOL × 9 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CAPSD_NVN68
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–295； UniProt 225–519 Author chain B； PDBConstruct 1–295； UniProt 225–519

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	5n7m
Deposition date deposition_date	2017-02-20
Structure title title	Protruding domain of GI.1 norovirus in complex with 2-fucosyllactose (2FL)
Keywords keywords	Norovirus, Protruding domain, human milk oligosaccharides, 2FL, viral protein; VIRAL PROTEIN
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.

5n7m__assembly_1__model_1

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

Download this curve (.dat)

5n7m__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5n7m__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.63 Å
Rg (electron density)	23.39 Å
Total Rg	24.24 Å
Atom count	4402
Residues	575
Excluded volume	78229 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5n7m__assembly_1__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	Capsid protein VP1
Molecular weight formula_weight	31511.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5048

EQKTRPFTLPNLPLSSLSNSRAPLPISSIGISPDNVQSVQFQNGRCTLDGRLVGTTPVSLSHVAKIRGTSNGTVINLTELDGTPFHPFEGPAPIGFPDLGGCDWHINMTQFGHSSQTQYDVDTTPDTFVPHLGSIQANGIGSGNYVGVLSWISPPSHPSGSQVDLWKIPNYGSSITEATHLAPSVYPPGFGEVLVFFMSKMPGPGAYNLPCLLPQEYISHLASEQAPTVGEAALLHYVDPDTGRNLGEFKAYPDGFLTCVPNGASSGPQQLPINGVFVFVSWVSRFYQLKPVGTA

Source Source

Source organism organism	Norwalk virus
Common name common_name	Hu/NV/NV/1968/US
NCBI taxonomy ID ncbi_taxonomy_id	524364
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 branched

Description description	alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose
Molecular weight formula_weight	488.4 kDa
Source method src_method	man
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	man
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	527

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	5n7mA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	510 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Homologous superfamily homologous superfamily	10 — Positive stranded ssRNA viruses

Domain ID domain_id	5n7mA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	120 — Positive stranded ssRNA viruses

Domain ID domain_id	5n7mB01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	510 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Homologous superfamily homologous superfamily	10 — Positive stranded ssRNA viruses

Domain ID domain_id	5n7mB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily	120 — Positive stranded ssRNA viruses

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Unit-cell length a length_a	84.070 Å
Unit-cell length b length_b	84.070 Å
Unit-cell length c length_c	165.120 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 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	1.730 Å
Low-resolution limit resolution_low	43.906 Å
R factor r_factor	0.1619
R_work r_work	0.1604
R_free r_free	0.1913

Protruding domain of GI.1 norovirus in complex with 2-fucosyllactose (2FL)

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

Capsid protein VP1

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

5n7m__assembly_1__model_1

5n7m__assembly_1__model_1 | I(q)

5n7m__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Protruding domain of GI.1 norovirus in complex with 2-fucosyllactose (2FL)

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

Capsid protein VP1

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

5n7m__assembly_1__model_1

5n7m__assembly_1__model_1 | I(q)

5n7m__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)