9sjd

Type I-F_HNH variant Cascade bound to dsDNA, HNH domain in outwards position

Method: ELECTRON MICROSCOPY

▼

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

Cas8f

Selenomonas sp.

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 9 DNA 2 RNA 1	Cas5f × 1 （A0AAX7FM22） Cas6f × 1 （A0AAX7FM27） Non-target strand × 1 Cas7f × 6 （A0AAX7FM28） Target strand × 1 crRNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0AAX7FM29_9FIRM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–344； UniProt 1–344

Cas5f

Selenomonas sp.

UniProt A0AAX7FM22

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 9 DNA 2 RNA 1	Cas8f × 1 （A0AAX7FM29） Cas6f × 1 （A0AAX7FM27） Non-target strand × 1 Cas7f × 6 （A0AAX7FM28） Target strand × 1 crRNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0AAX7FM22_9FIRM
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–255； UniProt 1–255

Cas6f

Selenomonas sp.

UniProt A0AAX7FM27

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 9 DNA 2 RNA 1	Cas8f × 1 （A0AAX7FM29） Cas5f × 1 （A0AAX7FM22） Non-target strand × 1 Cas7f × 6 （A0AAX7FM28） Target strand × 1 crRNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0AAX7FM27_9FIRM
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain I； PDBConstruct 1–181； UniProt 1–181

Cas7f

Selenomonas sp.

UniProt A0AAX7FM28

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 9 DNA 2 RNA 1	Cas8f × 1 （A0AAX7FM29） Cas5f × 1 （A0AAX7FM22） Cas6f × 1 （A0AAX7FM27） Non-target strand × 1 Target strand × 1 crRNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0AAX7FM28_9FIRM
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain C； PDBConstruct 1–335； UniProt 1–335 Author chain D； PDBConstruct 1–335； UniProt 1–335 Author chain E； PDBConstruct 1–335； UniProt 1–335 Author chain F； PDBConstruct 1–335； UniProt 1–335 Author chain G； PDBConstruct 1–335； UniProt 1–335 Author chain H； PDBConstruct 1–335； UniProt 1–335

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9sjd
Deposition date deposition_date	2025-08-31
Structure title title	Type I-F_HNH variant Cascade bound to dsDNA, HNH domain in outwards position
Keywords keywords	CRISPR-Cas Type I-F HNH nuclease, RNA BINDING PROTEIN; RNA BINDING PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

▼

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.

9sjd__assembly_1__model_1

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

Download this curve (.dat)

9sjd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9sjd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	50.01 Å
Rg (electron density)	49.72 Å
Total Rg	49.92 Å
Atom count	23176
Residues	2713
Excluded volume	407520 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9sjd__assembly_1__model_1`	12-meric （12）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Cas8f
Molecular weight formula_weight	39339.7 kDa
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	23176

MLRNKILAAISQKIPEEQKINKYIEGLFQSIDKNHLATHVAKFTETNSPGNIGAYDILSSDMNCGYLDTANAGWKEPDIVTNDAKYKRPQGFVAMEMSDGRTVMEHLQEDSAELRHEMEELTDKYDEIRDGILNMPSMQPYRTNQFIKQVFFPVGGSYHLLSILPSTVLNYEVSDRLYRSKIPKIRLRLLSSNAASTTGSRLVSKNKWPLVFQALPPKFLEKNLAKALDKEYLLPDINIDELEGVDNGCLIDEALLPLIIDEGKRKGEGNYRPRHLRDERKEETVQAFLDKYGYCNIPVGYEVHHIVPLSQGGADSIKNMIMLSIEHHERVTEAHASYFKWRNT

Source Source

Source organism organism	Selenomonas sp.
NCBI taxonomy ID ncbi_taxonomy_id	2053611
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Cas5f
Molecular weight formula_weight	28703.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MMKGYILLEKVNIENANAFNNIIVGIPAITSFLGFARALERKLNAKEIAIRINGVGLEFHEYELKGYKNKRGQYVTSCPLPGSIPGQNEKKLDAHIMNQAYIDLNMSFLLEVEGPHVDMSTCKSIKSTMETLRIAGGIIRNYKKIRLIDTLADIPYGYFLTLRQDNLNDAAGDDMLDKMIHALQQEDTLVPIAVGFKALSEVGHVEGQRDPEKDHCFVESIFSLGGFECSKILEDINSCLWRYKTEEGLYLCTII

Source Source

Source organism organism	Selenomonas sp.
NCBI taxonomy ID ncbi_taxonomy_id	2053611
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Cas6f
Molecular weight formula_weight	20735.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

MFSQILIIKPGTGISPNIIISEDIFPVLHSLFVEHDKKFGITFPAYSFDKKGHLGNIIEVLSEDKEALASLCLEEHLAEVTDYVKVKKEITFTDDYVLFKRIREENQYETTARRMRKRGHTELGRPLEMHIKKKNQQIFCHAYIKVKSASTGQSYNIFLAPTDIKHGSFSAYGLLRGDTHA

Source Source

Source organism organism	Selenomonas sp.
NCBI taxonomy ID ncbi_taxonomy_id	2053611
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 polymer

Description description	Non-target strand
Molecular weight formula_weight	14233.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	L

AAAAAGCGGAGAAGTCATTTAATAAGGCCACTGTTAAAAACCGTAC

Entity 5 Entity 5 polymer

Description description	Cas7f
Molecular weight formula_weight	38700.2 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F,C,G,H

MAANKKATNVTLKSRPENLSFARCLNTTEAKFWQTDFLKRHTFKLPLLITDKAVLASKGHEMPPDKLEKEIMDPNPQKSQSCTLSTECDTLRIDFGIKVLPVKESMYSCSDYNYRTAIYQKIDEYIAEDGFLTLAKRYVNNIANARFLWRNRKGAEIIETIVTIEDKEYPSFNSKSFNLDTFVEDNATINEIAQQIADTFAGKREYLNIYVTCFVKIGCAMEVYPSQEMTFDDDDKGKKLFKFEGSAGMHSQKINNALRTIDTWYPDYTTYEFPIPVENYGAARSIGIPFRPDTKSFYKLIDRMILKNEDLPIEDKHYVMAILIRGGMFSKKQEK

Source Source

Source organism organism	Selenomonas sp.
NCBI taxonomy ID ncbi_taxonomy_id	2053611
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 6 Entity 6 polymer

Description description	Target strand
Molecular weight formula_weight	14094.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	K

GTACGGTTTTTAACAGTGGCCTTATTAAATGACTTCTCCGCTTTTT

Entity 7 Entity 7 polymer

Description description	crRNA
Molecular weight formula_weight	19440.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	J

UUUAGAAGGAGAAGUCAUUUAAUAAGGCCACUGUUAAAAAGUGUACCGCCGGAUAGGCGG

Source Source

Source organism organism	Selenomonas sp.
NCBI taxonomy ID ncbi_taxonomy_id	2053611
Host organism host_organism	Escherichia coli BL21(DE3)

▶

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	—

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

Resolution resolution	3.05 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	24776

Type I-F_HNH variant Cascade bound to dsDNA, HNH domain in outwards position

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

Cas8f

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cas5f

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cas6f

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cas7f

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

9sjd__assembly_1__model_1

9sjd__assembly_1__model_1 | I(q)

9sjd__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (7)

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

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 polymer

Polymer Polymer

Source Source

7. Citations (1)