3kz4

Crystal Structure of the Rotavirus Double Layered Particle

Method: X-RAY DIFFRACTION

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

Intermediate capsid protein VP6

Bovine rotavirus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 900	Inner capsid protein VP2 × 120 ZINC ION × 300	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 15	Inner capsid protein VP2 × 2 ZINC ION × 5	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 75	Inner capsid protein VP2 × 10 ZINC ION × 25	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 90	Inner capsid protein VP2 × 12 ZINC ION × 30	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 15	Inner capsid protein VP2 × 2 ZINC ION × 5	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 900	Inner capsid protein VP2 × 120 ZINC ION × 300	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VP6_ROTBN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–397； UniProt 1–397 Author chain D； PDBConstruct 1–397； UniProt 1–397 Author chain E； PDBConstruct 1–397； UniProt 1–397 Author chain F； PDBConstruct 1–397； UniProt 1–397 Author chain G； PDBConstruct 1–397； UniProt 1–397 Author chain H； PDBConstruct 1–397； UniProt 1–397 Author chain I； PDBConstruct 1–397； UniProt 1–397 Author chain J； PDBConstruct 1–397； UniProt 1–397 Author chain K； PDBConstruct 1–397； UniProt 1–397 Author chain L； PDBConstruct 1–397； UniProt 1–397 Author chain M； PDBConstruct 1–397； UniProt 1–397 Author chain N； PDBConstruct 1–397； UniProt 1–397 Author chain O； PDBConstruct 1–397； UniProt 1–397

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	3kz4
Deposition date deposition_date	2009-12-07
Structure title title	Crystal Structure of the Rotavirus Double Layered Particle
Keywords keywords	icosahedral virus, capsid, Core protein, RNA-binding, dsRNA virus, Metal-binding, Virion, Zinc, Rotavirus, 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.

3kz4__assembly_1__model_1

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

Download this curve (.dat)

3kz4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3kz4__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)	294.10 Å
Total Rg	293.80 Å
Atom count	3246540
Residues	405120
Excluded volume	57659000 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3kz4__assembly_1__model_1`	900-meric （900）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3kz4__assembly_2__model_1`	pentadecameric （15）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`3kz4__assembly_3__model_1`	75-meric （75）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`3kz4__assembly_4__model_1`	90-meric （90）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5	1	`3kz4__assembly_5__model_1`	pentadecameric （15）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
6	1	`3kz4__assembly_6__model_1`	900-meric （900）	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 (3)

Entity 1 Entity 1 polymer

Description description	Inner capsid protein VP2
Molecular weight formula_weight	102595.0 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	54109

MAYRKRGARREANINNNDRMQEKDDEKQDQNNRMQLSDKVLSKKEEVVTDSQEEIKIADEVKKSTKEESKQLLEVLKTKEEHQKEIQYEILQKTIPTFEPKESILKKLEDIKPEQAKKQTKLFRIFEPRQLPIYRANGEKELRNRWYWKLKKDTLPDGDYDVREYFLNLYDQVLTEMPDYLLLKDMAVENKNSRDAGKVVDSETASICDAIFQDEETEGAVRRFIAEMRQRVQADRNVVNYPSILHPIDYAFNEYFLQHQLVEPLNNDIIFNYIPERIRNDVNYILNMDRNLPSTARYIRPNLLQDRLNLHDNFESLWDTITTSNYILARSVVPDLKELVSTEAQIQKMSQDLQLEALTIQSETQFLTGINSQAANDCFKTLIAAMLSQRTMSLDFVTTNYMSLISGMWLLTVVPNDMFIRESLVACQLAIVNTIIYPAFGMQRMHYRNGDPQTPFQIAEQQIQNFQVANWLHFVNNNQFRQVVIDGVLNQVLNDNIRNGHVINQLMEALMQLSRQQFPTMPVDYKRSIQRGILLLSNRLGQLVDLTRLLAYNYETLMACVTMNMQHVQTLTTEKLQLTSVTSLCMLIGNATVIPSPQTLFHYYNVNVNFHSNYNERINDAVAIITAANRLNLYQKKMKAIVEDFLKRLHIFDVARVPDDQMYRLRDRLRLLPVEVRRLDIFNLILMNMDQIERASDKIAQGVIIAYRDMQLERDEMYGYVNIARNLDGFQQINLEELMRTGDYAQITNMLLNNQPVALVGALPFVTDSSVISLIAKLDATVFAQIVKLRKVDTLKPILYKINSDSNDFYLVANYDWVPTSTTKVYKQVPQQFDFRNSMHMLTSNLTFTVYSDLLAFVSADTVEPINAVAFDNMRIMNEL

Source Source

Source organism organism	Bovine Rotavirus
Common name common_name	RV-A
NCBI taxonomy ID ncbi_taxonomy_id	10934
Host organism host_organism	Chlorocebus sabaeus

Entity 2 Entity 2 polymer

Description description	Intermediate capsid protein VP6
Molecular weight formula_weight	44922.6 kDa
Source method src_method	man
Copy count entity_count	13

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D,E,F,G,H,I,J,K,L,M,N,O

MDVLYSLSKTLKDARDKIVEGTLYSNVSDLIQQFNQMIITMNGNEFQTGGIGNLPIRNWNFDFGLLGTTLLNLDANYVETARNTIDYFVDFVDNVCMDEMVRESQRNGIAPQSDSLRKLSGLKFKRINFDNSSEYIENWNLQNRRQRTGFTFHKPNIFPYSASFTLNRSQPAHDNLMGTMWLNAGSEIQVAGFDYSCAINAPANTQQFEHIVQLRRVLTTATITLLPDAERFSFPRVINSADGATTWYFNPVILRPNNVEVEFLLNGQIINTYQARFGTIIARNFDTIRLSFQLMRPPNMTPAVAALFPNAQPFEHHATVGLTLRIESAVCESVLADASETMLANVTSVRQEYAIPVGPVFPPGMNWTDLITNYSPSREDNLQRVFTVASIRSMLVK

Source Source

Source organism organism	Bovine rotavirus
Common name common_name	RV-A
NCBI taxonomy ID ncbi_taxonomy_id	10934
Host organism host_organism	Chlorocebus sabaeus

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	5

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6. Fold Classification (SCOP + CATH) 26 domains

CATH v4.4 (26 domains)

Domain ID domain_id	3kz4C01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1350 — Viral capsid alpha domain
Homologous superfamily homologous superfamily	10 — Viral capsid alpha domain

Domain ID domain_id	3kz4C02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	3kz4D01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1350 — Viral capsid alpha domain
Homologous superfamily homologous superfamily	10 — Viral capsid alpha domain

Domain ID domain_id	3kz4D02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	3kz4E01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1350 — Viral capsid alpha domain
Homologous superfamily homologous superfamily	10 — Viral capsid alpha domain

Domain ID domain_id	3kz4E02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	3kz4F01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1350 — Viral capsid alpha domain
Homologous superfamily homologous superfamily	10 — Viral capsid alpha domain

Domain ID domain_id	3kz4F02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	3kz4G01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1350 — Viral capsid alpha domain
Homologous superfamily homologous superfamily	10 — Viral capsid alpha domain

Domain ID domain_id	3kz4G02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	3kz4H01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1350 — Viral capsid alpha domain
Homologous superfamily homologous superfamily	10 — Viral capsid alpha domain

Domain ID domain_id	3kz4H02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	3kz4I01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1350 — Viral capsid alpha domain
Homologous superfamily homologous superfamily	10 — Viral capsid alpha domain

Domain ID domain_id	3kz4I02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	3kz4J01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1350 — Viral capsid alpha domain
Homologous superfamily homologous superfamily	10 — Viral capsid alpha domain

Domain ID domain_id	3kz4J02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	3kz4K01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1350 — Viral capsid alpha domain
Homologous superfamily homologous superfamily	10 — Viral capsid alpha domain

Domain ID domain_id	3kz4K02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	3kz4L01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1350 — Viral capsid alpha domain
Homologous superfamily homologous superfamily	10 — Viral capsid alpha domain

Domain ID domain_id	3kz4L02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	3kz4M01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1350 — Viral capsid alpha domain
Homologous superfamily homologous superfamily	10 — Viral capsid alpha domain

Domain ID domain_id	3kz4M02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	3kz4N01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1350 — Viral capsid alpha domain
Homologous superfamily homologous superfamily	10 — Viral capsid alpha domain

Domain ID domain_id	3kz4N02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	170 —

Domain ID domain_id	3kz4O01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1350 — Viral capsid alpha domain
Homologous superfamily homologous superfamily	10 — Viral capsid alpha domain

Domain ID domain_id	3kz4O02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	170 —

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Unit-cell length a length_a	740.750 Å
Unit-cell length b length_b	1198.070 Å
Unit-cell length c length_c	1345.410 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	3120

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.800 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.3280
R_free r_free	0.3390

Crystal Structure of the Rotavirus Double Layered Particle

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

Intermediate capsid protein VP6

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

3kz4__assembly_1__model_1

3kz4__assembly_1__model_1 | I(q)

3kz4__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 26 domains

CATH v4.4 (26 domains)

7. Citations (1)

Crystal Structure of the Rotavirus Double Layered Particle

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

Intermediate capsid protein VP6

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

3kz4__assembly_1__model_1

3kz4__assembly_1__model_1 | I(q)

3kz4__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 26 domains

CATH v4.4 (26 domains)

7. Citations (1)