SAXSdb — 4z92

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

capsid subunit VP1

Human parechovirus 1 (strain Harris)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Homooligomer	Protein 180 RNA 60	;RNA (5'-R(APUPUPUPUPU)-3') ; × 60	Consistent with all polymers
2	Protein–RNA	Homooligomer	Protein 3 RNA 1	;RNA (5'-R(APUPUPUPUPU)-3') ; × 1	Consistent with all polymers
3	Protein–RNA	Homooligomer	Protein 15 RNA 5	;RNA (5'-R(APUPUPUPUPU)-3') ; × 5	Consistent with all polymers
4	Protein–RNA	Homooligomer	Protein 18 RNA 6	;RNA (5'-R(APUPUPUPUPU)-3') ; × 6	Consistent with all polymers
5	Protein–RNA	Homooligomer	Protein 3 RNA 1	;RNA (5'-R(APUPUPUPUPU)-3') ; × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POLG_HPE1H
Isoform	—
PDB entities	1, 2, 3
Chains and sequence ranges	Author chain A； PDBConstruct 1–234； UniProt 543–776 Author chain B； PDBConstruct 1–253； UniProt 290–542 Author chain C； PDBConstruct 1–289； UniProt 1–289

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	4z92
Deposition date deposition_date	2015-04-09
Structure title title	crystal structure of parechovirus-1 virion
Keywords keywords	parechovirus, picornavirus, virion, pathogen, virus; VIRUS
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.

4z92__assembly_1__model_1

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

Download this curve (.dat)

4z92__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4z92__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)	128.60 Å
Total Rg	128.60 Å
Atom count	324240
Residues	41640
Excluded volume	5716100 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4z92__assembly_1__model_1`	240-meric （240）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4z92__assembly_2__model_1`	tetrameric （4）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`4z92__assembly_3__model_1`	eicosameric （20）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`4z92__assembly_4__model_1`	24-meric （24）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5	1	`4z92__assembly_5__model_1`	tetrameric （4）	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 (4)

Entity 1 Entity 1 polymer

Description description	capsid subunit VP1
Molecular weight formula_weight	26417.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	5404

NSWGSQMDLTDPLCIEDDTENCKQTMSPNELGLTSAQDDGPLGQEKPNYFLNFRSMNVDIFTVSHTKVDNLFGRAWFFMEHTFTNEGQWRVPLEFPKQGHGSLSLLFAYFTGELNIHVLFLSERGFLRVAHTYDTSNDRVNFLSSNGVITVPAGEQMTLSAPYYSNKPLRTVRDNNSLGYLMCKPFLTGTSTGKIEVYLSLRCPNFFFPLPAPKVTSSRALRGDMANLTNQSPY

Source Source

Source organism organism	Human parechovirus 1 (strain Harris)
Common name common_name	HPeV-1
NCBI taxonomy ID ncbi_taxonomy_id	103911
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Capsid subunit VP3
Molecular weight formula_weight	28293.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

APNGKKKNWKKIMTMSTKYKWTRTKIDIAEGPGSMNMANVLCTTGAQSVALVGERAFYDPRTAGSKSRFDDLVKIAQLFSVMADSTTPSENHGVDAKGYFKWSATTAPQSIVHRNIVYLRLFPNLNVFVNSYSYFRGSLVLRLSVYASTFNRGRLRMGFFPNATTDSTSTLDNAIYTICDIGSDNSFEITIPYSFSTWMRKTNGHPIGLFQIEVLNRLTYNSSSPSEVYCIVQGKMGQDARFFCPTGSVVTFQ

Source Source

Source organism organism	Human parechovirus 1 (strain Harris)
Common name common_name	HPeV-1
NCBI taxonomy ID ncbi_taxonomy_id	103911
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	capsid subunit VP0
Molecular weight formula_weight	31693.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

METIKSIADMATGVVSSVDSTINAVNEKVESVGNEIGGNLLTKVADDASNILGPNCFATTAEPENKNVVQATTTVNTTNLTQHPSAPTMPFSPDFSNVDNFHSMAYDITTGDKNPSKLVRLETHEWTPSWARGYQITHVELPKVFWDHQDKPAYGQSRYFAAVRCGFHFQVQVNVNQGTAGSALVVYEPKPVVTYDSKLEFGAFTNLPHVLMNLAETTQADLCIPYVADTNYVKTDSSDLGQLKVYVWTPLSIPTGSANQVDVTILGSLLQLDFQNPRVFAQDVNIYDN

Source Source

Source organism organism	Human parechovirus 1 (strain Harris)
Common name common_name	HPeV-1
NCBI taxonomy ID ncbi_taxonomy_id	103911
Host organism host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	;RNA (5'-R(APUPUPUPUPU)-3') ;
Molecular weight formula_weight	1815.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	D

AUUUUU

Source Source

Source organism organism	Human parechovirus 1 (strain Harris)
Common name common_name	HPeV-1
NCBI taxonomy ID ncbi_taxonomy_id	103911
Host organism host_organism	Homo sapiens

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6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	4z92B00
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	399.500 Å
Unit-cell length b length_b	399.500 Å
Unit-cell length c length_c	332.860 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	120

Space group space_group	P 63 2 2
Space-group number int_tables_number	182
Crystal system crystal_system	—

Resolution resolution	3.100 Å
Low-resolution limit resolution_low	65.000 Å
R factor r_factor	—
R_work r_work	0.2900
R_free r_free	—

crystal structure of parechovirus-1 virion

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

capsid subunit 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

4z92__assembly_1__model_1

4z92__assembly_1__model_1 | I(q)

4z92__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)

crystal structure of parechovirus-1 virion

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

capsid subunit 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

4z92__assembly_1__model_1

4z92__assembly_1__model_1 | I(q)

4z92__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

7. Citations (1)