6h6y

GI.1 human norovirus protruding domain in complex with Nano-7

Method: X-RAY DIFFRACTION

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

Capsid protein VP1

Norwalk virus (strain GI/Human/United States/Norwalk/1968)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Nanobody (VHH) Nano-7 × 2 SODIUM ION × 4 1,2-ETHANEDIOL × 1 CHLORIDE ION × 2 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Nanobody (VHH) Nano-7 × 2 SODIUM ION × 6 1,2-ETHANEDIOL × 2 CHLORIDE ION × 2 water × 4	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 1–292； UniProt 227–518 Author chain B； PDBConstruct 1–292； UniProt 227–518 Author chain C； PDBConstruct 1–292； UniProt 227–518 Author chain D； PDBConstruct 1–292； UniProt 227–518

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	6h6y
Deposition date deposition_date	2018-07-30
Structure title title	GI.1 human norovirus protruding domain in complex with Nano-7
Keywords keywords	Norovirus, GI.1, P domain, Nano-7, 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.

6h6y__assembly_2__model_1

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

Download this curve (.dat)

6h6y__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6h6y__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	28.33 Å
Rg (electron density)	27.29 Å
Total Rg	27.99 Å
Atom count	11647
Residues	796
Excluded volume	105860 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6h6y__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6h6y__assembly_2__model_1`	tetrameric （4）	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 (6)

Entity 1 Entity 1 polymer

Description description	Capsid protein VP1
Molecular weight formula_weight	31182.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	24368

KTRPFTLPNLPLSSLSNSRAPLPISSIGISPDNVQSVQFQNGRCTLDGRLVGTTPVSLSHVAKIRGTSNGTVINLTELDGTPFHPFEGPAPIGFPDLGGCDWHINMTQFGHSSQTQYDVDTTPDTFVPHLGSIQANGIGSGNYVGVLSWISPPSHPSGSQVDLWKIPNYGSSITEATHLAPSVYPPGFGEVLVFFMSKMPGPGAYNLPCLLPQEYISHLASEQAPTVGEAALLHYVDPDTGRNLGEFKAYPDGFLTCVPNGASSGPQQLPINGVFVFVSWVSRFYQLKPVGT

Source Source

Source organism organism	Norwalk virus (strain GI/Human/United States/Norwalk/1968)
Common name common_name	Hu/NV/NV/1968/US
NCBI taxonomy ID ncbi_taxonomy_id	524364
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Nanobody (VHH) Nano-7
Molecular weight formula_weight	14648.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H

QVQLQESGGGLVQAGGSLRLSCAVSGRTFSNYYSGWFRQAPGKEREFLASIRWSDSTTNYADSVKGRFTISRDTAKNTVYLQMNSLKLEDTAVYHCAARRLATYDYWGQGTQVTVSSGRYPYDVPDYGSGRA

Source Source

Source organism organism	Vicugna pacos
NCBI taxonomy ID ncbi_taxonomy_id	30538
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	10

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	3

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	972

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d6h6ye1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d6h6ye2
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

Domain ID domain_id	d6h6yf1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d6h6yf2
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

Domain ID domain_id	d6h6yg1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d6h6yg2
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

Domain ID domain_id	d6h6yh1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d6h6yh2
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 (8 domains)

Domain ID domain_id	6h6yA01
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	6h6yA02
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	6h6yB01
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	6h6yB02
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	6h6yC01
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	6h6yC02
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	6h6yD01
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	6h6yD02
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	59.170 Å
Unit-cell length b length_b	140.900 Å
Unit-cell length c length_c	92.150 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.81 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	1.580 Å
Low-resolution limit resolution_low	47.535 Å
R factor r_factor	0.1556
R_work r_work	0.1546
R_free r_free	0.1748

GI.1 human norovirus protruding domain in complex with Nano-7

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

6h6y__assembly_2__model_1

6h6y__assembly_2__model_1 | I(q)

6h6y__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

GI.1 human norovirus protruding domain in complex with Nano-7

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

6h6y__assembly_2__model_1

6h6y__assembly_2__model_1 | I(q)

6h6y__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)