3jb7

In situ structures of the segmented genome and RNA polymerase complex inside a dsRNA virus

Method: ELECTRON MICROSCOPY

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

CPV RNA-dependent RNA polymerase

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 4 RNA 2	Viral structural protein 4 × 1 （Q9IR43） VP1 CSP × 2 （D3JWE6） ;RNA (5'-R(PGPGPGPGPGPG)-3') ; × 1 ;RNA (5'-R(PCPCPCPCP*C)-3') ; × 1 GUANOSINE-5'-TRIPHOSPHATE × 2 CYTIDINE-5'-TRIPHOSPHATE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D0EZK6_CPVBM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1225； UniProt 1–1225

Viral structural protein 4

OrganismNot specified

UniProt Q9IR43

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 4 RNA 2	CPV RNA-dependent RNA polymerase × 1 （D0EZK6） VP1 CSP × 2 （D3JWE6） ;RNA (5'-R(PGPGPGPGPGPG)-3') ; × 1 ;RNA (5'-R(PCPCPCPCP*C)-3') ; × 1 GUANOSINE-5'-TRIPHOSPHATE × 2 CYTIDINE-5'-TRIPHOSPHATE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9IR43_CPVBM
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–561； UniProt 1–561

VP1 CSP

OrganismNot specified

UniProt D3JWE6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 4 RNA 2	CPV RNA-dependent RNA polymerase × 1 （D0EZK6） Viral structural protein 4 × 1 （Q9IR43） ;RNA (5'-R(PGPGPGPGPGPG)-3') ; × 1 ;RNA (5'-R(PCPCPCPCP*C)-3') ; × 1 GUANOSINE-5'-TRIPHOSPHATE × 2 CYTIDINE-5'-TRIPHOSPHATE × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D3JWE6_CPVBM
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–24； UniProt 111–134 Author chain D； PDBConstruct 1–24； UniProt 111–134

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	3jb7
Deposition date deposition_date	2015-08-03
Structure title title	In situ structures of the segmented genome and RNA polymerase complex inside a dsRNA virus
Keywords keywords	dsRNA genome organization, viral polymerase, TRANSFERASE-VIRAL PROTEIN-RNA complex; TRANSFERASE/VIRAL PROTEIN/RNA
Experimental Method method	ELECTRON MICROSCOPY

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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.

3jb7__assembly_1__model_1

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

Download this curve (.dat)

3jb7__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3jb7__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.92 Å
Rg (electron density)	38.72 Å
Total Rg	39.11 Å
Atom count	14176
Residues	1744
Excluded volume	251080 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3jb7__assembly_1__model_1`	hexameric （6）	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 (7)

Entity 1 Entity 1 polymer

Description description	CPV RNA-dependent RNA polymerase
Molecular weight formula_weight	138810.9 kDa
EC 编号 ec_number	2.7.7.48
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	14176

MLPNTKLHNTIFSETRKFTRESFKEIEHLTARLANDRVARHDFLFNTSIVLISDYSGEDSNGNQLQATITIPNEIINPKEYDPSDYPLAEDESFFKQGHKYDYLVTFRAGSLTNTYEPKTKMYKLHAALDKLMHVKQRKSRFADLWRELCAVIASLDVWYQTTNYPLRTYVKLLFHKGDEFPFYESPSQDRIIFNDKSVASILPTFVYTCCQVGTAIMSGILTHVESIVAMNHFLHCAKDSYIDEKLKIKGIGRSWYQEALHNVCQATVPVWSQFNEVIGHRTKSTSEPHFVSSTFISLRAKRAELLYPEFNAYINRAIQLSKTQNDVANYYAACRAMTNDGTFLATLTELSLDAAVFPRIEQHLVTRPAVLMSNTRHESLKQKYTNGVGSIAQSYLSSFTDEIAKRVNGRHHDEAWLNFLTTSSPGRKLTEIEKLEVGGDVAAWSNSRIVMQAVFAREYRTPERIFKSLKAPIKLVERQQSDRRQRAISGLDNDRLFLSFMPYTIGKQIYELNDNAAQGKQAGNAFDIGEMLYWTSQRNVLLSSIDVAGMDASVTTNTKDIYNTFVLDVASKCTVPRFGPYYAKNMEVFEAGNRQSQVRYVNAAWQACALEAANSQTSTSYESEIFGQVKNAEGTYPSGRADTSTHHTVLLQGLVRGNELKRASDGKNSCLATIKILGDDIMEIFQGSESDTYDHAVSNASILNESGFATTAELSQNSIVLLQQLVVNGTFWGFADRISLWTREDTKDIGRLNLAMMELNALIDDLVFRVRRPEGLKMLGFFCGAICLRRFTLSVDNKLYDSTYNNLSKYMTLTKYDKNPDSDSTLMSLILPLAWLFMPRGGEYPAYPFERRDGTFTEDESMFTARGAYKRRLLYDVSNIGEMIQQNSMALDDDLLHEYGFTGALLLIDLNILDLIDEVKKEDISPVKVSELATSLEQLGKLGEREKSRRAASDLKIRGHALSNDIVYGYGLQEKIQKSAMATKETTVQSKRVSSRLHDVIVAKTRDYKISTIPADALHLHEFEVEDVTVDLLPHAKHTSYSSLAYNMSFGSDGWFAFALLGGLDRSANLLRLDVASIRGNYHKFSYDDPVFKQGYKIYKSDATLLNDFFTAISAGPKEQGILLRAFAYYSLYGNVEYHYVLSPRQLFFLSDNPVSAERLVRIPPKYYVSTQCRALYNIFSYLHILRSIANNRGKRLKMVLHPGLIAYVRGTSQGAILPEADNV

Entity 2 Entity 2 polymer

Description description	Viral structural protein 4
Molecular weight formula_weight	63683.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MFAIDPLKHSKLYEEYGLYLRPHQINQEIKPTTIKKKELAPTIRSIKYASLIHSMLAKHAARHNGTLINPRMYADMITLGNTKVTVTKGTPKAQIDTLKMNGLTVVSKSRRNNKKKPVSDTTATIDENTDDIVTYKALTEMSTLIESFRLPSGLALIIFDDEKYQSLIPNYINQLIAYTQPHIIPTWQGIADFSDTYLRSYFKRPFELTASNLAAPQKYNLSPMTRSIFNNTGREDAVIRKLYGYGEYVFIRYEGCLITWTGIYGEVTMMVNLSKRDLGLDVGDDYLKEYKKLLFYGVITDAIPSGISARSTIMKISPHKMMNPSGGALAVLSKFLEAVVSTNVINATLVVYAEKGAGKTSFLSTYAEQLSLASGQVVGHLSSDAYGRWLAKNKDVEEPSFAYDYVLSLDTDDNESYYEQKASELLISHGISEVAQYELLSVRKKIKMMDEMNEVLIAQLENADTHSERNFYYMVSTGKTTPRTLIVEGHFNAQDATIARTDTTVLLRTINDTTQAMRDRQRGGVVQLFLRDTYYRLLPALHTTVYPFEMLESIRRWKWVH

Entity 3 Entity 3 polymer

Description description	VP1 CSP
Molecular weight formula_weight	2734.0 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

PTVVQSRTDVFNEQFANEALHPMT

Entity 4 Entity 4 polymer

Description description	;RNA (5'-R(PGPGPGPGPGPG)-3') ;
Molecular weight formula_weight	2026.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	t

GGGGGG

Entity 5 Entity 5 polymer

Description description	;RNA (5'-R(PCPCPCPCP*C)-3') ;
Molecular weight formula_weight	1481.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	m

CCCCC

Entity 6 Entity 6 non-polymer

Description description	GUANOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	CYTIDINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	483.2 kDa
Source method src_method	syn
Copy count entity_count	1

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	4.000 Å
Low-resolution limit resolution_low	4.000 Å
R factor r_factor	0.2164
R_work r_work	0.2164
R_free r_free	0.1965

Resolution resolution	4.00 Å
Resolution测定Method resolution_method	Frealign
颗粒数 num_particles	81887

In situ structures of the segmented genome and RNA polymerase complex inside a dsRNA virus

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

CPV RNA-dependent RNA polymerase

State in the Current Structure

Other States of the Same Protein in the Database

Viral structural protein 4

State in the Current Structure

Other States of the Same Protein in the Database

VP1 CSP

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

3jb7__assembly_1__model_1

3jb7__assembly_1__model_1 | I(q)

3jb7__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

7. Citations (1)

In situ structures of the segmented genome and RNA polymerase complex inside a dsRNA virus

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

CPV RNA-dependent 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

Viral structural protein 4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

VP1 CSP

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

3jb7__assembly_1__model_1

3jb7__assembly_1__model_1 | I(q)

3jb7__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

7. Citations (1)