SAXSdb — 1uvk

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

RNA-directed RNA polymerase

Cystovirus phi6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Monomer	Protein 1 RNA 1	RNA (pppGpG) × 1 MANGANESE (II) ION × 1 MAGNESIUM ION × 2 PYROPHOSPHATE 2- × 1 water × 2	Consistent with all polymers
2	Protein–RNA	Monomer	Protein 1 RNA 1	RNA (pppGpG) × 1 MANGANESE (II) ION × 1 MAGNESIUM ION × 2 PYROPHOSPHATE 2- × 1 water × 2	Consistent with all polymers
3	Protein–RNA	Monomer	Protein 1 RNA 1	RNA (pppGpG) × 1 MANGANESE (II) ION × 1 MAGNESIUM ION × 2 PYROPHOSPHATE 2- × 1 water × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RDRP_BPPH6
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–664； UniProt 2–665 Author chain C； PDBConstruct 1–664； UniProt 2–665 Author chain E； PDBConstruct 1–664； UniProt 2–665

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	1uvk
Deposition date deposition_date	2004-01-21
Structure title title	The structural basis for RNA specificity and Ca2 inhibition of an RNA-dependent RNA polymerase phi6p2 dead-end complex
Keywords keywords	TRANSFERASE, POLYMERASE-COMPLEX, OLIGONUCLEOTIDE, POLYMERASE; 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.

1uvk__assembly_1__model_1

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

Download this curve (.dat)

1uvk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1uvk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.73 Å
Rg (electron density)	24.79 Å
Total Rg	25.59 Å
Atom count	5332
Residues	665
Excluded volume	94316 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1uvk__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1uvk__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1uvk__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 (6)

Entity 1 Entity 1 polymer

Description description	RNA-directed RNA polymerase
Molecular weight formula_weight	74903.2 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,C,E
Atom count atom_count	16257

PRRAPAFPLSDIKAQMLFANNIKAQQASKRSFKEGAIETYEGLLSVDPRFLSFKNELSRYLTDHFPANVDEYGRVYGNGVRTNFFGMRHMNGFPMIPATWPLASNLKKRADADLADGPVSERDNLLFRAAVRLMFSDLEPVPLKIRKGSSTCIPYFSNDMGTKIEIAERALEKAEEAGNLMLQGKFDDAYQLHQMGGAYYVVYRAQSTDAITLDPKTGKFVSKDRMVADFEYAVTGGEQGSLFAASKDASRLKEQYGIDVPDGFFCERRRTAMGGPFALNAPIMAVAQPVRNKIYSKYAYTFHHTTRLNKEEKVKEWSLCVATDVSDHDTFWPGWLRDLICDELLNMGYAPWWVKLFETSLKLPVYVGAPAPEQGHTLLGDPSNPDLEVGLSSGQGATDLMGTLLMSITYLVMQLDHTAPHLNSRIKDMPSACRFLDSYWQGHEEIRQISKSDDAMLGWTKGRALVGGHRLFEMLKEGKVNPSPYMKISYEHGGAFLGDILLYDSRREPGSAIFVGNINSMLNNQFSPEYGVQSGVRDRSKRKRPFPGLAWASMKDTYGACPIYSDVLEAIERCWWNAFGESYRAYREDMLKRDTLELSRYVASMARQAGLAELTPIDLEVLADPNKLQYKWTEADVSANIHEVLMHGVSVEKTERFLRSVMPR

Source Source

Source organism organism	Cystovirus phi6
NCBI taxonomy ID ncbi_taxonomy_id	10879
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	RNA (pppGpG)
Molecular weight formula_weight	805.4 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	B,D,F

GG

Entity 3 Entity 3 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	PYROPHOSPHATE 2-
Molecular weight formula_weight	176.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	261

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1uvka_
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.8.1.6 — dsRNA phage RNA-dependent RNA-polymerase

Domain ID domain_id	d1uvkc_
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.8.1.6 — dsRNA phage RNA-dependent RNA-polymerase

Domain ID domain_id	d1uvke_
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.8.1.6 — dsRNA phage RNA-dependent RNA-polymerase

CATH v4.4 (9 domains)

Domain ID domain_id	1uvkA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	60 — Phage p2 RNA dependent RNA polymerase domain

Domain ID domain_id	1uvkA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1600 —

Domain ID domain_id	1uvkA04
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	410 — Dihydrolipoamide Transferase
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1uvkC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	60 — Phage p2 RNA dependent RNA polymerase domain

Domain ID domain_id	1uvkC03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1600 —

Domain ID domain_id	1uvkC04
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	410 — Dihydrolipoamide Transferase
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1uvkE02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	60 — Phage p2 RNA dependent RNA polymerase domain

Domain ID domain_id	1uvkE03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1600 —

Domain ID domain_id	1uvkE04
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	410 — Dihydrolipoamide Transferase
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	106.290 Å
Unit-cell length b length_b	93.800 Å
Unit-cell length c length_c	140.770 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.35 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.450 Å
Low-resolution limit resolution_low	19.980 Å
R factor r_factor	0.2430
R_work r_work	0.2430
R_free r_free	0.2650

The structural basis for RNA specificity and Ca2 inhibition of an RNA-dependent RNA polymerase phi6p2 dead-end 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1uvk__assembly_1__model_1

1uvk__assembly_1__model_1 | I(q)

1uvk__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (3 domains)

CATH v4.4 (9 domains)

7. Citations (1)

The structural basis for RNA specificity and Ca2 inhibition of an RNA-dependent RNA polymerase phi6p2 dead-end 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1uvk__assembly_1__model_1

1uvk__assembly_1__model_1 | I(q)

1uvk__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (3 domains)

CATH v4.4 (9 domains)

7. Citations (1)