2yib

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	No other associated polymer	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	No other associated polymer	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	No other associated polymer	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	No other associated polymer	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, 2
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 Author chain D； PDBConstruct 1–687； UniProt 1–687

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	2yib
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.

2yib__assembly_1__model_1

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

Download this curve (.dat)

2yib__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2yib__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.33 Å
Rg (electron density)	28.43 Å
Total Rg	29.23 Å
Atom count	6159
Residues	789
Excluded volume	109800 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2yib__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2yib__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2yib__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2yib__assembly_4__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 (2)

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, 2.7.7.49
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	24183

MSDIFNSPQNKASILTALMKSTTGDVEDVLIPKRFRPAKDPLDSPQAAAQFLKDNKYRILRPRAIPTMVELETDAALPRLRQMVEDGKLKDTVSVPEGTTAFYPKYYPFHKPDHDEVGTFGAPDITLLKQLTFFLLENDFPTGPETLRQVREAIATLQYGSGSYSGQLNRLLAMKGVATGRNPNKTPKTVGYTNEQLAKLLEQTLPINTPKHEDPDLRWAPSWLINYTGDLSTDKSYLPHVTIKSSAGLPYIGKTKGDTTAEALVLADSFIRDLGRAATSADPEAGVKKTITDFWYLSCGLLFPKGERYTQVDWDKKTRNIWSAPYPTHLLLSMVSTPVMNESKLNITNTQTPSLYGFSPFHGGMDRIMTIIRDSLDNDEDLVMIYADNIYILQDNTWYSIDLEKGEANCTPQHMQAMMYYLLTRGWTNEDGSPRYNPTWATFAMNVAPSMVVDSSCLLMNLQLKTYGQGSGNAFTFLNNHLMSTIVVAEWVKAGKPNPMTKEFMDLEEKTGINFKIERELKNLRETIVEAVETAPQDGYLADGSDLPPIRPGKAVELDLLGWSAIYSRQMEMFVPVLENERLIASAAYPKGLENKALARKPGAEIAYQIVRYEAIRLVGGWNNPLLETAAKHMSLDKRKRLEVKGIDVTGFLDDWNNMSEFGGDLEGITLSEPLTNQTLVDINTPLDSFDPKARPQTPRSPKKTLDEVTTAITSGTYKDPKSAVWRLLDQRTKLRVSTLRDQALALKPASSSVDNWAEATEELAQQQQLLMKANNLLKSSLTETREALETIQSDKIIAGKSNPEKNPGTAANPVVGYGEFSEKIPLTPTQKKNAKRREKQRRNQVEHHHHHH

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 polymer

Description description	RNA-DIRECTED RNA POLYMERASE
Molecular weight formula_weight	83999.9 kDa
EC 编号 ec_number	2.7.7.48, 2.7.7.49
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MSDIFNSPQNKASILTALMKSTTGDVEDVLIPKRFRPAKDPLDSPQAAAQFLKDNKYRILRPRAIPTMVELETDAALPRLRQMVEDGKLKDTVSVPEGTTAFYPKYYPFHKPDHDEVGTFGAPDITLLKQLTFFLLENDFPTGPETLRQVREAIATLQYGSGSYSGQLNRLLAMKGVATGRNPNKTPKTVGYTNEQLAKLLEQTLPINTPKHEDPDLRWAPSWLINYTGDLSTDKSYLPHVTIKSSAGLPYIGKTKGDTTAEALVLADSFIRDLGRAATSADPEAGVKKTITDFWYLSCGLLFPKGERYTQVDWDKKTRNIWSAPYPTHLLLSMVSTPVMNESKLNITNTQTPSLYGFSPFHGGMDRIMTIIRDSLDNDEDLVMIYADNIYILQDNTWYSIDLEKGEANCTPQHMQAMMYYLLTRGWTNEDGSPRYNPTWATFAMNVAPSMVVDSSCLLMNLQLKTYGQGSGNAFTFLNNHLMSTIVVAEWVKAGKPNPMTKEFMDLEEKTGINFKIERELKNLRETIVEAVETAPQDGYLADGSDLPPIRPGKAVELDLLGWSAIYSRQMEMFVPVLENERLIASAAYPKGLENKALARKPGAEIAYQIVRYEAIRLVGGWNNPLLETAAKHMSLDKRKRLEVKGIDVTGFLDDWNNMSEFGGDLEGITLSEPLTNQTLVDINTPLXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Source Source

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

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6. Fold Classification (SCOP + CATH) 15 domains

CATH v4.4 (15 domains)

Domain ID domain_id	2yibA01
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	2yibA02
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	2yibA04
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	300 —

Domain ID domain_id	2yibA05
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	2yibB01
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	2yibB02
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	2yibB04
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	300 —

Domain ID domain_id	2yibB05
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	2yibC01
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	2yibC02
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	2yibC04
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	300 —

Domain ID domain_id	2yibC05
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	2yibD01
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	2yibD02
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	2yibD04
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	300 —

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Unit-cell length a length_a	119.740 Å
Unit-cell length b length_b	195.450 Å
Unit-cell length c length_c	197.380 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.800 Å
Low-resolution limit resolution_low	44.430 Å
R factor r_factor	0.1858
R_work r_work	0.1843
R_free r_free	0.2129

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

2yib__assembly_1__model_1

2yib__assembly_1__model_1 | I(q)

2yib__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 15 domains

CATH v4.4 (15 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

2yib__assembly_1__model_1

2yib__assembly_1__model_1 | I(q)

2yib__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 15 domains

CATH v4.4 (15 domains)

7. Citations (1)