8ok9

Heterodimeric complex of Archaeoglobus fulgidus Argonaute protein Af1318 (AfAgo) with DNA and AfAgo-N protein containing N-L1-L2 domains

Method: X-RAY DIFFRACTION

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

Piwi protein AF_1318

Archaeoglobus fulgidus DSM 4304

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 2 DNA 2	Archaeoglobus fulgidus AfAgo-N protein × 1 （A0A075WKW4） ;DNA (5'-D(PAPTPCPGPAPCPCPAPGPGPCPTPAPCP*G)-3') ; × 2 MAGNESIUM ION × 1 ACETIC ACID × 8 1,2-ETHANEDIOL × 6 DI(HYDROXYETHYL)ETHER × 1 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PIWI_ARCFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 15–441； UniProt 1–427

Archaeoglobus fulgidus AfAgo-N protein

Archaeoglobus fulgidus DSM 4304

UniProt A0A075WKW4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 2 DNA 2	Piwi protein AF_1318 × 1 （O28951） ;DNA (5'-D(PAPTPCPGPAPCPCPAPGPGPCPTPAPCP*G)-3') ; × 2 MAGNESIUM ION × 1 ACETIC ACID × 8 1,2-ETHANEDIOL × 6 DI(HYDROXYETHYL)ETHER × 1 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A075WKW4_ARCFL
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 15–264； UniProt 1–250

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	8ok9
Deposition date deposition_date	2023-03-27
Structure title title	Heterodimeric complex of Archaeoglobus fulgidus Argonaute protein Af1318 (AfAgo) with DNA and AfAgo-N protein containing N-L1-L2 domains
Keywords keywords	Protein-nucleic acid interactions, Argonaute, pAgo, guide and target specificity, 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.

8ok9__assembly_1__model_1

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

Download this curve (.dat)

8ok9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8ok9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.49 Å
Rg (electron density)	27.44 Å
Total Rg	28.16 Å
Atom count	5991
Residues	689
Excluded volume	106120 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8ok9__assembly_1__model_1`	tetrameric （4）	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	Piwi protein AF_1318
Molecular weight formula_weight	50921.1 kDa
Mutation mutation	N-terminal His tag
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6207

MGSSHHHHHHSQDPMMEYKIVENGLTYRIGNGASVPISNTGELIKGLRNYGPYEVPSLKYNQIALIHNNQFSSLINQLKSQISSKIDEVWHIHNINISEFIYDSPHFDSIKSQVDNAIDTGVDGIMLVLPEYNTPLYYKLKSYLINSIPSQFMRYDILSNRNLTFYVDNLLVQFVSKLGGKPWILNVDPEKGSDIIIGTGATRIDNVNLFCFAMVFKKDGTMLWNEISPIVTSSEYLTYLKSTIKKVVYGFKKSNPDWDVEKLTLHVSGKRPKMKDGETKILKETVEELKKQEMVSRDVKYAILHLNETHPFWVMGDPNNRFHPYEGTKVKLSSKRYLLTLLQPYLKRNGLEMVTPIKPLSVEIVSDNWTSEEYYHNVHEILDEIYYLSKMNWRGFRSRNLPVTVNYPKLVAGIIANVNRYGGYPINPEGNRSLQTNPWFL

Source Source

Source organism organism	Archaeoglobus fulgidus DSM 4304
NCBI taxonomy ID ncbi_taxonomy_id	224325
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Archaeoglobus fulgidus AfAgo-N protein
Molecular weight formula_weight	30575.8 kDa
Mutation mutation	N-terminal His tag
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MGSSHHHHHHSQDPMEIPLSSGNVNTPDVRSSGILYINIYPIVNYPETIKVSAIPYYEEFLPGKWKKRIGDLIYLYGYGIENEFDEIDNSNALFGKIFRKYLLDILSENIATPWQLKELGSTLRLVKEITENYEFSNIIKLQYELIINVHHWQNTNFGIIVDLKINILDRENNQRISYTKIKDKYGESVKKKIWVSVQAFHRHLTPEGKKYATAMRDKFNLLTGLLKEAFGSSEDEKTFSTPDGEIKIVFKPLEIVEVSNNDGI

Source Source

Source organism organism	Archaeoglobus fulgidus DSM 4304
NCBI taxonomy ID ncbi_taxonomy_id	224325
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(PAPTPCPGPAPCPCPAPGPGPCPTPAPCP*G)-3') ;
Molecular weight formula_weight	4579.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	R,S

ATCGACCAGGCTACG

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	1

Entity 5 Entity 5 non-polymer

Description description	ACETIC ACID
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 6 Entity 6 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 7 Entity 7 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 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	200

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Unit-cell length a length_a	81.714 Å
Unit-cell length b length_b	105.893 Å
Unit-cell length c length_c	144.347 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	8

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

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	64.690 Å
R factor r_factor	0.2010
R_work r_work	0.1981
R_free r_free	0.2269

Heterodimeric complex of Archaeoglobus fulgidus Argonaute protein Af1318 (AfAgo) with DNA and AfAgo-N protein containing N-L1-L2 domains

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

Piwi protein AF_1318

State in the Current Structure

Other States of the Same Protein in the Database

Archaeoglobus fulgidus AfAgo-N protein

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

8ok9__assembly_1__model_1

8ok9__assembly_1__model_1 | I(q)

8ok9__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

Source Source

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)

Heterodimeric complex of Archaeoglobus fulgidus Argonaute protein Af1318 (AfAgo) with DNA and AfAgo-N protein containing N-L1-L2 domains

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

Piwi protein AF_1318

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Archaeoglobus fulgidus AfAgo-N protein

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

8ok9__assembly_1__model_1

8ok9__assembly_1__model_1 | I(q)

8ok9__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

Source Source

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)