7y7s

QDE-1 in complex with DNA template, RNA primer and AMPNPP

Method: X-RAY DIFFRACTION

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

RNA-dependent RNA polymerase

Neurospora crassa

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Homooligomer	Protein 2 DNA 2 RNA 2	;DNA (5'-D(GPAPAPCPTPAPTPGPGPTPCPGPGPA)-3') ; × 2 ;RNA (5'-R(UPCPCPGPAPCP*C)-3') ; × 2 CALCIUM ION × 7 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine × 2 DI(HYDROXYETHYL)ETHER × 1 MAGNESIUM ION × 1 water × 5	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9Y7G6_NEUCS
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1026； UniProt 377–1402 Author chain B； PDBConstruct 1–1026； UniProt 377–1402

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	7y7s
Deposition date deposition_date	2022-06-22
Structure title title	QDE-1 in complex with DNA template, RNA primer and AMPNPP
Keywords keywords	RNA polymerase, QDE-1, Complex, DdRP, AMPNPP, RNA BINDING PROTEIN; RNA BINDING 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.

7y7s__assembly_1__model_1

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

Download this curve (.dat)

7y7s__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7y7s__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	41.04 Å
Rg (electron density)	40.89 Å
Total Rg	41.11 Å
Atom count	15432
Residues	1894
Excluded volume	271360 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7y7s__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 (8)

Entity 1 Entity 1 polymer

Description description	RNA-dependent RNA polymerase
Molecular weight formula_weight	117139.4 kDa
EC 编号 ec_number	2.7.7.48
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	15570

ARSEESARSQVQVHAPVVAARLRNIWPKFPKWLHEAPLAVAWEVTRLFMHCKVDLEDESLGLKYDPSWSTARDVTDIWKTLYRLDAFRGKPFPEKPPNDVFVTAMTGNFESKGSAVVLSAVLDYNPDNSPTAPLYLVKLKPLMFEQGCRLTRRFGPDRFFEILIPSPTSTSPSVPPVVSKQPGAVEEVIQWLTMGQHSLVGRQWRAFFAKDAGYRKPLREFQLRAEDPKPIIKERVHFFAETGITFRPDVFKTRSVVPAEEPVEQRTEFKVSQMLDWLLQLDNNTWQPHLKLFSRIQLGLSKTYAIMTLEPHQIRHHKTDLLSPSGTGEVMNDGVGRMSRSVAKRIRDVLGLGDVPSAVQGRFGSAKGMWVIDVDDTGDEDWIETYPSQRKWECDFVDKHQRTLEVRSVASELKSAGLNLQLLPVLEDRARDKVKMRQAIGDRLINDLQRQFSEQKHALNRPVEFRQWVYESYSSRATRVSHGRVPFLAGLPDSQEETLNFLMNSGFDPKKQKYLQDIAWDLQKRKCDTLKSKLNIRVGRSAYIYMIADFWGVLEENEVHVGFSSKFRDEEESFTLLSDCDVLVARSPAHFPSDIQRVRAVFKPELHSLKDVIIFSTKGDVPLAKKLSGGDYDGDMAWVCWDPEIVDGFVNAEMPLEPDLSRYLKKDKTTFKQLMASHGTGSAAKEQTTYDMIQKSFHFALQPNFLGMCTNYKERLCYINNSVSNKPAIILSSLVGNLVDQSKQGIVFNEASWAQLRRELLGGALSLPDPMYKSDSWLGRGEPTHIIDYLKFSIARPAIDKELEAFHNAMKAAKDTEDGAHFWDPDLASYYTFFKEISDKSRSSALLFTTLKNRIGEVEKEYGRLVKNKEMRDSKDPYPVRVNQVYEKWCAITPEAMDKSGANYDSKVIRLLELSFLADREMNTWALLRASTAFKLYYHKSPKFVWQMAGRQLAYIKAQMTSRPGEGAPALMTAFMYAGLMPDKKFTKQYVARLEGDGSEYPDPEVYEVLGDDDFDGIGFTGNGDY

Source Source

Source organism organism	Neurospora crassa
NCBI taxonomy ID ncbi_taxonomy_id	5141
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(GPAPAPCPTPAPTPGPGPTPCPGPGPA)-3') ;
Molecular weight formula_weight	4344.8 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C,I

GAACTATGGTCGGA

Entity 3 Entity 3 polymer

Description description	;RNA (5'-R(UPCPCPGPAPCP*C)-3') ;
Molecular weight formula_weight	2156.3 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	D,J

UCCGACC

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 5 Entity 5 non-polymer

Description description	5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine
Molecular weight formula_weight	506.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	138

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Unit-cell length a length_a	101.954 Å
Unit-cell length b length_b	120.412 Å
Unit-cell length c length_c	114.993 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.71 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	30.100 Å
R factor r_factor	0.2100
R_work r_work	0.2081
R_free r_free	0.2452

QDE-1 in complex with DNA template, RNA primer and AMPNPP

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

RNA-dependent 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

7y7s__assembly_1__model_1

7y7s__assembly_1__model_1 | I(q)

7y7s__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)

QDE-1 in complex with DNA template, RNA primer and AMPNPP

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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7y7s__assembly_1__model_1

7y7s__assembly_1__model_1 | I(q)

7y7s__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Citations (1)