3zed

X-ray structure of the birnavirus VP1-VP3 complex

Method: X-RAY DIFFRACTION

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

RNA-DIRECTED RNA POLYMERASE

INFECTIOUS PANCREATIC NECROSIS VIRUS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	CAPSID PROTEIN VP3 × 1 （P05844） POTASSIUM ION × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	CAPSID PROTEIN VP3 × 1 （P05844） GLYCEROL × 1 POTASSIUM ION × 2 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	CAPSID PROTEIN VP3 × 1 （P05844） GLYCEROL × 2 POTASSIUM ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RDRP_IPNVJ
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–845； UniProt 1–845 Author chain B； PDBConstruct 1–845； UniProt 1–845 Author chain C； PDBConstruct 1–845； UniProt 1–845

CAPSID PROTEIN VP3

INFECTIOUS PANCREATIC NECROSIS VIRUS

UniProt P05844

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	RNA-DIRECTED RNA POLYMERASE × 1 （P22173） POTASSIUM ION × 2 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	RNA-DIRECTED RNA POLYMERASE × 1 （P22173） GLYCEROL × 1 POTASSIUM ION × 2 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	RNA-DIRECTED RNA POLYMERASE × 1 （P22173） GLYCEROL × 2 POTASSIUM ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POLS_IPNVJ
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 5–242； UniProt 735–972 Author chain E； PDBConstruct 5–242； UniProt 735–972 Author chain F； PDBConstruct 5–242； UniProt 735–972

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	3zed
Deposition date deposition_date	2012-12-04
Structure title title	X-ray structure of the birnavirus VP1-VP3 complex
Keywords keywords	VIRAL PROTEIN, VIRUS MORPHOGENESIS; 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.

3zed__assembly_1__model_1

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

Download this curve (.dat)

3zed__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3zed__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.53 Å
Rg (electron density)	27.41 Å
Total Rg	28.24 Å
Atom count	6031
Residues	774
Excluded volume	107460 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3zed__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3zed__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3zed__assembly_3__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	RNA-DIRECTED RNA POLYMERASE
Molecular weight formula_weight	95632.5 kDa
EC 编号 ec_number	2.7.7.48
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	19298

MSDIFNSPQNKASILTALMKSTTGDVEDVLIPKRFRPAKDPLDSPQAAAQFLKDNKYRILRPRAIPTMVELETDAALPRLRQMVEDGKLKDTVSVPEGTTAFYPKYYPFHKPDHDEVGTFGAPDITLLKQLTFFLLENDFPTGPETLRQVREAIATLQYGSGSYSGQLNRLLAMKGVATGRNPNKTPKTVGYTNEQLAKLLEQTLPINTPKHEDPDLRWAPSWLINYTGDLSTDKSYLPHVTIKSSAGLPYIGKTKGDTTAEALVLADSFIRDLGRAATSADPEAGVKKTITDFWYLSCGLLFPKGERYTQVDWDKKTRNIWSAPYPTHLLLSMVSTPVMNESKLNITNTQTPSLYGFSPFHGGMDRIMTIIRDSLDNDEDLVMIYADNIYILQDNTWYSIDLEKGEANCTPQHMQAMMYYLLTRGWTNEDGSPRYNPTWATFAMNVAPSMVVDSSCLLMNLQLKTYGQGSGNAFTFLNNHLMSTIVVAEWVKAGKPNPMTKEFMDLEEKTGINFKIERELKNLRETIVEAVETAPQDGYLADGSDLPPIRPGKAVELDLLGWSAIYSRQMEMFVPVLENERLIASAAYPKGLENKALARKPGAEIAYQIVRYEAIRLVGGWNNPLLETAAKHMSLDKRKRLEVKGIDVTGFLDDWNNMSEFGGDLEGITLSEPLTNQTLVDINTPLDSFDPKARPQTPRSPKKTLDEVTTAITSGTYKDPKSAVWRLLDQRTKLRVSTLRDQALALKPASSSVDNWAEATEELAQQQQLLMKANNLLKSSLTETREALETIQSDKIIAGKSNPEKNPGTAANPVVGYGEFSEKIPLTPTQKKNAKRREKQRRNQVEHHHHHH

Source Source

Source organism organism	INFECTIOUS PANCREATIC NECROSIS VIRUS
NCBI taxonomy ID ncbi_taxonomy_id	11002
Host organism host_organism	ESCHERICHIA COLI B

Entity 2 Entity 2 polymer

Description description	CAPSID PROTEIN VP3
Molecular weight formula_weight	27244.5 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

GPTASGMDAELQGLLQATMARAKEVKDAEVFKLLKLMSWTRKNDLTDHMYEWSKEDPDAIKFGRLVSTPPKHQEKPKGPDQHTAQEAKATRISLDAVKAGADFASPEWIAENNYRGPSPGQFKYYMITGRVPNPGEEYEDYVRKPITRPTDMDKIRRLANSVYGLPHQEPAPDDFYQAVVEVFAENGGRGPDQDQMQDLRDLARQMKRRPRPAETRRQTKTPPRAATSSGSRFTPSGDDGEV

Source Source

Source organism organism	INFECTIOUS PANCREATIC NECROSIS VIRUS
NCBI taxonomy ID ncbi_taxonomy_id	11002
Host organism host_organism	ESCHERICHIA COLI B

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1109

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6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3zeda_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.8 — DNA/RNA polymerases
Superfamily Superfamily superfamily	e.8.1 — DNA/RNA polymerases
Family Family family	e.8.1.0 — automated matches

Domain ID domain_id	d3zedb_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.8 — DNA/RNA polymerases
Superfamily Superfamily superfamily	e.8.1 — DNA/RNA polymerases
Family Family family	e.8.1.0 — automated matches

Domain ID domain_id	d3zedc_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.8 — DNA/RNA polymerases
Superfamily Superfamily superfamily	e.8.1 — DNA/RNA polymerases
Family Family family	e.8.1.0 — automated matches

CATH v4.4 (12 domains)

Domain ID domain_id	3zedA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1730 — Infectious bursal virus vp1 polymerase fold
Homologous superfamily homologous superfamily	10 — Infectious bursal virus vp1 polymerase domain

Domain ID domain_id	3zedA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	540 — Helix hairpin bin

Domain ID domain_id	3zedA04
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	300 —

Domain ID domain_id	3zedA05
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	270 — VP1, C-terminal extension domain

Domain ID domain_id	3zedB01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1730 — Infectious bursal virus vp1 polymerase fold
Homologous superfamily homologous superfamily	10 — Infectious bursal virus vp1 polymerase domain

Domain ID domain_id	3zedB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	540 — Helix hairpin bin

Domain ID domain_id	3zedB04
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	300 —

Domain ID domain_id	3zedB05
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	270 — VP1, C-terminal extension domain

Domain ID domain_id	3zedC01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1730 — Infectious bursal virus vp1 polymerase fold
Homologous superfamily homologous superfamily	10 — Infectious bursal virus vp1 polymerase domain

Domain ID domain_id	3zedC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	540 — Helix hairpin bin

Domain ID domain_id	3zedC04
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	300 —

Domain ID domain_id	3zedC05
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	270 — VP1, C-terminal extension domain

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Unit-cell length a length_a	118.270 Å
Unit-cell length b length_b	341.870 Å
Unit-cell length c length_c	59.700 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	12

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

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	59.130 Å
R factor r_factor	0.1810
R_work r_work	0.1793
R_free r_free	0.2145

X-ray structure of the birnavirus VP1-VP3 complex

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

RNA-DIRECTED RNA POLYMERASE

State in the Current Structure

Other States of the Same Protein in the Database

CAPSID PROTEIN VP3

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

3zed__assembly_1__model_1

3zed__assembly_1__model_1 | I(q)

3zed__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (3 domains)

CATH v4.4 (12 domains)

7. Citations (1)

X-ray structure of the birnavirus VP1-VP3 complex

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

RNA-DIRECTED RNA POLYMERASE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

CAPSID PROTEIN VP3

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

3zed__assembly_1__model_1

3zed__assembly_1__model_1 | I(q)

3zed__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (3 domains)

CATH v4.4 (12 domains)

7. Citations (1)