2yi8

Structure of the RNA polymerase VP1 from Infectious Pancreatic Necrosis Virus

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 monomer	Monomer	Protein 1	POTASSIUM ION × 1 CHLORIDE ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	POTASSIUM ION × 1 CHLORIDE ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	POTASSIUM ION × 1 CHLORIDE ION × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	POTASSIUM ION × 1 CHLORIDE ION × 1 water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	POTASSIUM ION × 1 CHLORIDE ION × 2 water × 1	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 1–790； UniProt 1–790 Author chain B； PDBConstruct 1–790； UniProt 1–790 Author chain C； PDBConstruct 1–790； UniProt 1–790 Author chain D； PDBConstruct 1–790； UniProt 1–790 Author chain E； PDBConstruct 1–790； UniProt 1–790

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	2yi8
Deposition date deposition_date	2011-05-11
Structure title title	Structure of the RNA polymerase VP1 from Infectious Pancreatic Necrosis Virus
Keywords keywords	TRANSFERASE, REVERSE TRANSCRIPTASE, IPNV; TRANSFERASE
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.

2yi8__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2yi8__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2yi8__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	28.75 Å
Rg (electron density)	27.82 Å
Total Rg	28.71 Å
Atom count	6032
Residues	771
Excluded volume	107640 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2yi8__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2yi8__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2yi8__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2yi8__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2yi8__assembly_5__model_1`	monomeric （1）	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 (4)

Entity 1 Entity 1 polymer

Description description	RNA-DIRECTED RNA POLYMERASE
Molecular weight formula_weight	89576.6 kDa
EC 编号 ec_number	2.7.7.48, 2.7.7.49
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	33471

MSDIFNSPQNKASILTALMKSTTGDVEDVLIPKRFRPAKDPLDSPQAAAQFLKDNKYRILRPRAIPTMVELETDAALPRLRQMVEDGKLKDTVSVPEGTTAFYPKYYPFHKPDHDEVGTFGAPDITLLKQLTFFLLENDFPTGPETLRQVREAIATLQYGSGSYSGQLNRLLAMKGVATGRNPNKTPKTVGYTNEQLAKLLEQTLPINTPKHEDPDLRWAPSWLINYTGDLSTDKSYLPHVTIKSSAGLPYIGKTKGDTTAEALVLADSFIRDLGRAATSADPEAGVKKTITDFWYLSCGLLFPKGERYTQVDWDKKTRNIWSAPYPTHLLLSMVSTPVMNESKLNITNTQTPSLYGFSPFHGGMDRIMTIIRDSLDNDEDLVMIYADNIYILQDNTWYSIDLEKGEANCTPQHMQAMMYYLLTRGWTNEDGSPRYNPTWATFAMNVAPSMVVDSSCLLMNLQLKTYGQGSGNAFTFLNNHLMSTIVVAEWVKAGKPNPMTKEFMDLEEKTGINFKIERELKNLRETIVEAVETAPQDGYLADGSDLPPIRPGKAVELDLLGWSAIYSRQMEMFVPVLENERLIASAAYPKGLENKALARKPGAEIAYQIVRYEAIRLVGGWNNPLLETAAKHMSLDKRKRLEVKGIDVTGFLDDWNNMSEFGGDLEGITLSEPLTNQTLVDINTPLDSFDPKARPQTPRSPKKTLDEVTTAITSGTYKDPKSAVWRLLDQRTKLRVSTLRDQALALKPASSSVDNWAEATEELAQQQQLLMKANNLLKSSLTETREALEKTGHHHHHH

Source Source

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

Entity 2 Entity 2 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	3143

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6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d2yi8a1
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	d2yi8a2
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	d2yi8b1
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	d2yi8b2
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	d2yi8c1
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	d2yi8c2
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	d2yi8d1
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	d2yi8d2
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	d2yi8e1
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	d2yi8e2
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 (20 domains)

Domain ID domain_id	2yi8A01
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	2yi8A02
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	2yi8A04
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	300 —

Domain ID domain_id	2yi8A05
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	2yi8B01
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	2yi8B02
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	2yi8B04
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	300 —

Domain ID domain_id	2yi8B05
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	2yi8C01
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	2yi8C02
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	2yi8C04
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	300 —

Domain ID domain_id	2yi8C05
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	2yi8D01
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	2yi8D02
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	2yi8D04
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	300 —

Domain ID domain_id	2yi8D05
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	2yi8E01
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	2yi8E02
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	2yi8E04
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	300 —

Domain ID domain_id	2yi8E05
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	134.048 Å
Unit-cell length b length_b	183.874 Å
Unit-cell length c length_c	244.521 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	20

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	90.330 Å
R factor r_factor	0.1663
R_work r_work	0.1661
R_free r_free	0.1868

Structure of the RNA polymerase VP1 from Infectious Pancreatic Necrosis Virus

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2yi8__assembly_3__model_1

2yi8__assembly_3__model_1 | I(q)

2yi8__assembly_3__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (10 domains)

CATH v4.4 (20 domains)

7. Citations (1)

Structure of the RNA polymerase VP1 from Infectious Pancreatic Necrosis Virus

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2yi8__assembly_3__model_1

2yi8__assembly_3__model_1 | I(q)

2yi8__assembly_3__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (10 domains)

CATH v4.4 (20 domains)

7. Citations (1)