9x25

Target analog-bound type III-B Cmr complex of Archaeoglobus fulgidus

Method: ELECTRON MICROSCOPY

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

GGDEF domain-containing protein

Archaeoglobus fulgidus DSM 4304

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 8 DNA 1 RNA 1	crRNA × 1 Type III-B CRISPR module-associated protein Cmr3 × 1 （O28413） CRISPR type III-associated protein domain-containing protein × 3 （O28416） CRISPR system Cmr subunit Cmr5 × 2 （O28417） CRISPR type III-associated protein domain-containing protein × 1 （O28418） Target analog DNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O28412_ARCFU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 21–1024； UniProt 1–1004

Type III-B CRISPR module-associated protein Cmr3

Archaeoglobus fulgidus DSM 4304

UniProt O28413

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 8 DNA 1 RNA 1	crRNA × 1 GGDEF domain-containing protein × 1 （O28412） CRISPR type III-associated protein domain-containing protein × 3 （O28416） CRISPR system Cmr subunit Cmr5 × 2 （O28417） CRISPR type III-associated protein domain-containing protein × 1 （O28418） Target analog DNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O28413_ARCFU
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–341； UniProt 1–341

CRISPR type III-associated protein domain-containing protein

Archaeoglobus fulgidus DSM 4304

UniProt O28416

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 8 DNA 1 RNA 1	crRNA × 1 GGDEF domain-containing protein × 1 （O28412） Type III-B CRISPR module-associated protein Cmr3 × 1 （O28413） CRISPR system Cmr subunit Cmr5 × 2 （O28417） CRISPR type III-associated protein domain-containing protein × 1 （O28418） Target analog DNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O28416_ARCFU
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–355； UniProt 1–355 Author chain E； PDBConstruct 1–355； UniProt 1–355 Author chain F； PDBConstruct 1–355； UniProt 1–355

CRISPR system Cmr subunit Cmr5

Archaeoglobus fulgidus DSM 4304

UniProt O28417

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 8 DNA 1 RNA 1	crRNA × 1 GGDEF domain-containing protein × 1 （O28412） Type III-B CRISPR module-associated protein Cmr3 × 1 （O28413） CRISPR type III-associated protein domain-containing protein × 3 （O28416） CRISPR type III-associated protein domain-containing protein × 1 （O28418） Target analog DNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CMR5_ARCFU
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain G； PDBConstruct 1–155； UniProt 1–155 Author chain H； PDBConstruct 1–155； UniProt 1–155

CRISPR type III-associated protein domain-containing protein

Archaeoglobus fulgidus DSM 4304

UniProt O28418

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 8 DNA 1 RNA 1	crRNA × 1 GGDEF domain-containing protein × 1 （O28412） Type III-B CRISPR module-associated protein Cmr3 × 1 （O28413） CRISPR type III-associated protein domain-containing protein × 3 （O28416） CRISPR system Cmr subunit Cmr5 × 2 （O28417） Target analog DNA × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O28418_ARCFU
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain I； PDBConstruct 1–343； UniProt 1–343

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	9x25
Deposition date deposition_date	2025-10-03
Last revision last_revision	2025-12-10
Structure title title	Target analog-bound type III-B Cmr complex of Archaeoglobus fulgidus
Keywords keywords	Type III-B CRISPR-Cas effector, RNA BINDING PROTEIN, RNA BINDING PROTEIN-RNA-DNA complex; RNA BINDING PROTEIN/RNA/DNA
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.

9x25__assembly_1__model_1

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

Download this curve (.dat)

9x25__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9x25__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	48.49 Å
Rg (electron density)	48.69 Å
Total Rg	48.70 Å
Atom count	21810
Residues	2992
Excluded volume	383060 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9x25__assembly_1__model_1`	decameric （10）	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	crRNA
Molecular weight formula_weight	12604.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	A
Atom count atom_count	21810

AUUGAAAGUUGUAGUAUGCGGUCCUUGCGGCUGAGAGCA

Entity 2 Entity 2 polymer

Description description	GGDEF domain-containing protein
Molecular weight formula_weight	117383.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MGSSHHHHHHSSGLVPRGSHMGQYFRVSGKYRGRENLPREVNKMADNEFWLNKIRAFFHDPPDKSFELKTHERRASFILGELKPSKSLKRIIKNADIQASSLQRVDLEKSIHKKELKSTFDRIHNTEKYEYIGQPIIRHPVTGEIKEYGTILANLPQTQREVYDVDDEGKEDYEEQFQEILSRILKIEKKVFDDFKNRYSDPKDLYISLWAFYAEKLKEALEEEFSASFAEEFVNLPAYTLSPDHTLFDHADATSAIFGAEIDGKKPVLVLFKISPVQKFIADARKEKDLWAASHMLSTLTFKAISFIADKFGPDVVIYPHLRGNPFFHAWLHSKKIWEFSDSHSLKIASVPNKFLALVGVSDEKELNNLREGIRNEIESFLADLFDKLWNEVIVGALEHSDALKHLGDKKEIHKEILLKRFTLTLSSLKIHDVDVSGSKEEAYEKVKDFVRSLGLPNAIESKYLQWLDMLGSVEASNNRPTKYDLYSLYYEILTVLNAIESTHFDKPAEPAGYKCTLCGEHLAIGGESREMMENVWGKIHKRWPSHLRSNERLCAVCAVKRFYPKFIETLDIFEGVGKVVPDIESVSEVAMCRRTKHGITWKEVYDYLRGLKNVDDEKLLGKLENLKHSVQTLINNVKSELKSRKVYPEEFLEGLNRNFSNEILYSERLRDFNTLLDTLGFDAAKLGLDDVKNYETMISELRERLSEVYKMLGEPPKYYAILMMDGDEMGKLLSGEKLKTAEHYLHSAILERVSDALRVKAKTVRRLITPAAHSSISRALKNFSVNHVPDVVRKGNGTLIYSGGDDVLVLLPVDTAFDVATELAMTFSTSWNGWEMLPGNKLSAGLLIVHYKHPLYDALEKTRELLQKAKKLGRNAIAVGLLKRSGSYYESVVNFETLEDAKAVANLLVKEQVSPRIIYELLNFADVISKEFLHQLVKYEAVRHSIDKNLAEEFQSVFARGHQGVRVELEGNDEEINKYISDGANLETFLDKYEKAVDVIRKQVRGFLNLVKILYESIRGGAK

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	Type III-B CRISPR module-associated protein Cmr3
Molecular weight formula_weight	39043.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MILVMKPYDSLLFREPRPFDVNNHVARTILPLPQTLAGAVRSAIYVKYGSKVKDLIGFGKEEPEFEILGHFFYRYDGKFELLVESPHDVTQNLGLVKPHRIDKLGITILMDSEGIKFRPFNGFLKFSGLIDYLQGRIAEDSVVERQKIFKKERRVGIALTKAKVTKEEHFYQVEMLRFSDDCGIAVWVEDGVDFDDEGILGVGGERRFVKFEKREEPECITNLRSKWKKIRDKINETGRLKIYLATPAILGAKGYSSKLDYDLLGDIGIERVRSVNFIGGKPVIFSGWDFVTRKPKPTRYAVPAGSVYFVEFEGEVKLDMPYLKLGKLTKLGYGLCFMGVW

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 4 Entity 4 polymer

Description description	CRISPR type III-associated protein domain-containing protein
Molecular weight formula_weight	39677.6 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

MFDMFEKAVVFGLYSITPVHAGSGAELSVIDLPIQRERHTGFPVIWGQSLKGVLRSRFRQLELDEKIEVESQKWKWKEKTKEVLKEKADEFIKKVEERKRDPLLTEIVFGPATDGASEHAGAVSVGDAKILLFPVRSAKGVFAFVTSPIVIQRLKEDFELVSEIENDIELKQILSRFKVELSNNETIAGNALILNGENKVILEDIVLKVKSDSNVIENLVEVLKTLFGDNFFGKPIESIKERIAIVSDDVFKSFTRFSTEIVARVRIDAEKGTVARGGLWYEEFLPSDTLMYSLIAVGSPKKENLPKEVDNTQKIVNVLKVTFNNAFLQIGGDETVGKGFVKVRAGVLTGGHKGN

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 5 Entity 5 polymer

Description description	CRISPR system Cmr subunit Cmr5
Molecular weight formula_weight	17407.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H

MDIREIEQERASFAFKVVSDIKDKYSQNKKVQGKYSSYAEKAPTIILNNGLGATLAFFLSKLEKPIDDVDYKSINPESFGNAENIAYAFLYKHLSTWLAEGNGKDSAFSGLTNGEDPLKYIMEKTAIDVAISTEEALSILNWIKKFAKAMLEEEL

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 6 Entity 6 polymer

Description description	CRISPR type III-associated protein domain-containing protein
Molecular weight formula_weight	40298.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

MKSNVVVKYPVNSELANYAEKFWKKELAIYNLSLILNKMTPFVKRRSESYKSSLSAVKEIFKNVDDFQNFLNSVLRRSLDEYRVFFENYERLFNSFSSKIFSMRTKSRLVVGLGDESVYETSIRLHRNYGVPYIPGSALKGVAKHYAFSILARENGDEILRIYESVKEDLKARIAKRDKIKKNDVPEDYYLTAAVIQELFEKKFDELGAIRNTRVEIGDTVISVGDIVKIFGTQKEEGSVIFFDAFPTPEQLKDKPNLELDIMNPHYQPYYQHGEPPGDWHSPNPIFFLTVPAGVEFTFAVASRDLDDLAEKAEKLLKEALKKFGVGAKTSLGYGRFDARDDRHHHHHH

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 7 Entity 7 polymer

Description description	Target analog DNA
Molecular weight formula_weight	9451.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	K

TGCTCTCAGCCGCAAGGACCGCATACTACAA

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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	—

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

Resolution resolution	3.400 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.40 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	81835

Target analog-bound type III-B Cmr complex of Archaeoglobus fulgidus

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

GGDEF domain-containing 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

Type III-B CRISPR module-associated protein Cmr3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

CRISPR type III-associated protein domain-containing 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

CRISPR system Cmr subunit Cmr5

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

CRISPR type III-associated protein domain-containing 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

9x25__assembly_1__model_1

9x25__assembly_1__model_1 | I(q)

9x25__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

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 polymer

Polymer Polymer

7. Citations (1)