SAXSdb — 1v9u

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

Coat protein VP1

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 300	LDL-receptor class A 3 × 60 （P98155） LAURIC ACID × 60 CALCIUM ION × 60	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	LDL-receptor class A 3 × 1 （P98155） LAURIC ACID × 1 CALCIUM ION × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 25	LDL-receptor class A 3 × 5 （P98155） LAURIC ACID × 5 CALCIUM ION × 5	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 30	LDL-receptor class A 3 × 6 （P98155） LAURIC ACID × 6 CALCIUM ION × 6	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 5	LDL-receptor class A 3 × 1 （P98155） LAURIC ACID × 1 CALCIUM ION × 1	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 150	LDL-receptor class A 3 × 30 （P98155） LAURIC ACID × 30 CALCIUM ION × 30	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POLG_HRV2
Isoform	—
PDB entities	1, 2, 3, 4
Chains and sequence ranges	Author chain 1； PDBConstruct 1–289； UniProt 568–856 Author chain 2； PDBConstruct 1–261； UniProt 70–330 Author chain 3； PDBConstruct 1–237； UniProt 331–567 Author chain 4； PDBConstruct 1–68； UniProt 2–69

LDL-receptor class A 3

Homo sapiens

UniProt P98155

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 300	Coat protein VP1 × 60 （P04936） Coat protein VP2 × 60 （P04936） Coat protein VP3 × 60 （P04936） Coat protein VP4 × 60 （P04936） LAURIC ACID × 60 CALCIUM ION × 60	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Coat protein VP1 × 1 （P04936） Coat protein VP2 × 1 （P04936） Coat protein VP3 × 1 （P04936） Coat protein VP4 × 1 （P04936） LAURIC ACID × 1 CALCIUM ION × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 25	Coat protein VP1 × 5 （P04936） Coat protein VP2 × 5 （P04936） Coat protein VP3 × 5 （P04936） Coat protein VP4 × 5 （P04936） LAURIC ACID × 5 CALCIUM ION × 5	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 30	Coat protein VP1 × 6 （P04936） Coat protein VP2 × 6 （P04936） Coat protein VP3 × 6 （P04936） Coat protein VP4 × 6 （P04936） LAURIC ACID × 6 CALCIUM ION × 6	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 5	Coat protein VP1 × 1 （P04936） Coat protein VP2 × 1 （P04936） Coat protein VP3 × 1 （P04936） Coat protein VP4 × 1 （P04936） LAURIC ACID × 1 CALCIUM ION × 1	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 150	Coat protein VP1 × 30 （P04936） Coat protein VP2 × 30 （P04936） Coat protein VP3 × 30 （P04936） Coat protein VP4 × 30 （P04936） LAURIC ACID × 30 CALCIUM ION × 30	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VLDLR_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain 5； PDBConstruct 1–41； UniProt 111–151

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	1v9u
Deposition date deposition_date	2004-02-03
Structure title title	Human Rhinovirus 2 bound to a fragment of its cellular receptor protein
Keywords keywords	human rhinovirus, VLDL-receptor, virus-protein complex, Icosahedral virus, Virus-Receptor COMPLEX; Virus/Receptor
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.

1v9u__assembly_1__model_1

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

Download this curve (.dat)

1v9u__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1v9u__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	0.00 Å
Rg (electron density)	134.70 Å
Total Rg	134.90 Å
Atom count	387060
Residues	49200
Excluded volume	6844700 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1v9u__assembly_1__model_1`	complete icosahedral assembly （300）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1v9u__assembly_2__model_1`	pentameric （5）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`1v9u__assembly_3__model_1`	25-meric （25）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`1v9u__assembly_4__model_1`	30-meric （30）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5	1	`1v9u__assembly_5__model_1`	pentameric （5）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
6	1	`1v9u__assembly_6__model_1`	150-meric （150）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Coat protein VP1
Molecular weight formula_weight	32924.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	1
Atom count atom_count	6451

NPVENYIDEVLNEVLVVPNINSSNPTTSNSAPALDAAETGHTSSVQPEDVIETRYVQTSQTRDEMSLESFLGRSGCIHESKLEVTLANYNKENFTVWAINLQEMAQIRRKFELFTYTRFDSEITLVPCISALSQDIGHITMQYMYVPPGAPVPNSRDDYAWQSGTNASVFWQHGQAYPRFSLPFLSVASAYYMFYDGYDEQDQNYGTANTNNMGSLCSRIVTEKHIHKVHIMTRIYHKAKHVKAWCPRPPRALEYTRAHRTNFKIEDRSIQTAIVTRPIITTAGPSDMY

Entity 2 Entity 2 polymer

Description description	Coat protein VP2
Molecular weight formula_weight	29009.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	2

SPTVEACGYSDRIIQITRGDSTITSQDVANAIVAYGVWPHYLSSKDASAIDKPSQPDTSSNRFYTLRSVTWSSSSKGWWWKLPDALKDMGIFGENMFYHYLGRSGYTIHVQCNASKFHQGTLIVALIPEHQIASALHGNVNVGYNYTHPGETGREVKAETRLNPDLQPTEEYWLNFDGTLLGNITIFPHQFINLRSNNSATIIAPYVNAVPMDSMRSHNNWSLVIIPICPLETSSAINTIPITISISPMCAEFSGARAKRQ

Entity 3 Entity 3 polymer

Description description	Coat protein VP3
Molecular weight formula_weight	26107.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	3

GLPVFITPGSGQFLTTDDFQSPCALPWYHPTKEISIPGEVKNLVEICQVDSLVPINNTDTYINSENMYSVVLQSSINAPDKIFSIRTDVASQPLATTLIGEISSYFTHWTGSLRFSFMFCGTANTTVKLLLAYTPPGIAEPTTRKDAMLGTHVIWDVGLQSTISMVVPWISASHYRNTSPGRSTSGYITCWYQTRLVIPPQTPPTARLLCFVSGCKDFCLRMARDTNLHLQSGAIAQ

Entity 4 Entity 4 polymer

Description description	Coat protein VP4
Molecular weight formula_weight	7357.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	4

GAQVSRQNVGTHSTQNSVSNGSSLNYFNINYFKDAASNGASKLEFTQDPSKFTDPVKDVLEKGIPTLQ

Entity 5 Entity 5 polymer

Description description	LDL-receptor class A 3
Molecular weight formula_weight	4532.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	5

RTCRIHEISCGAHSTQCIPVSWRCDGENDCDSGEDEENCGN

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 6 Entity 6 non-polymer

Description description	LAURIC ACID
Molecular weight formula_weight	200.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1v9u.1
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
Family Family family	b.121.4.1 — Picornaviridae-like VP (VP1, VP2, VP3 and VP4)

Domain ID domain_id	d1v9u1_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
Family Family family	b.121.4.1 — Picornaviridae-like VP (VP1, VP2, VP3 and VP4)

Domain ID domain_id	d1v9u3_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.4 — Positive stranded ssRNA viruses
Family Family family	b.121.4.1 — Picornaviridae-like VP (VP1, VP2, VP3 and VP4)

Domain ID domain_id	d1v9u5_
Class class	g — Small proteins
Fold Fold fold	g.12 — LDL receptor-like module
Superfamily Superfamily superfamily	g.12.1 — LDL receptor-like module
Family Family family	g.12.1.1 — LDL receptor-like module

CATH v4.4 (3 domains)

Domain ID domain_id	1v9u100
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1v9u200
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1v9u300
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

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Unit-cell length a length_a	313.100 Å
Unit-cell length b length_b	348.790 Å
Unit-cell length c length_c	380.890 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	120

Space group space_group	P 21 2 21
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	3.600 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2850
R_free r_free	0.2950

Human Rhinovirus 2 bound to a fragment of its cellular receptor protein

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

Coat protein VP1

State in the Current Structure

Other States of the Same Protein in the Database

LDL-receptor class A 3

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

1v9u__assembly_1__model_1

1v9u__assembly_1__model_1 | I(q)

1v9u__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Human Rhinovirus 2 bound to a fragment of its cellular receptor protein

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

Coat 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

LDL-receptor class A 3

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

1v9u__assembly_1__model_1

1v9u__assembly_1__model_1 | I(q)

1v9u__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

CATH v4.4 (3 domains)

7. Citations (1)