9l7d

Type III-B CRISPR-Cas effector from Archaeoglobus fulgidus (Form 2)

Method: ELECTRON MICROSCOPY

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

Type III-B CRISPR module RAMP protein Cmr4

Archaeoglobus fulgidus DSM 4304

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 7 RNA 1	Cmr1 C-terminal domain-containing protein × 1 （O28411） GGDEF domain-containing protein × 1 （O28412） Type III-B CRISPR module-associated protein Cmr3 × 1 （O28413） Type III-B CRISPR module RAMP protein Cmr6 × 1 （O28418） CRISPR system Cmr subunit Cmr5 × 1 （O28417） ;RNA (5'-R(UPGPUPAPGPUPAPUPGPCPGPGPUPCPCPUPUPGPCPGPGPC)-3') ; × 1 MAGNESIUM ION × 1 ADENOSINE-5'-TRIPHOSPHATE × 2 ZINC ION × 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	1
Chains and sequence ranges	Author chain E； PDBConstruct 15–369； UniProt 1–355 Author chain F； PDBConstruct 15–369； UniProt 1–355

Cmr1 C-terminal domain-containing protein

Archaeoglobus fulgidus

UniProt O28411

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 7 RNA 1	Type III-B CRISPR module RAMP protein Cmr4 × 2 （O28416） GGDEF domain-containing protein × 1 （O28412） Type III-B CRISPR module-associated protein Cmr3 × 1 （O28413） Type III-B CRISPR module RAMP protein Cmr6 × 1 （O28418） CRISPR system Cmr subunit Cmr5 × 1 （O28417） ;RNA (5'-R(UPGPUPAPGPUPAPUPGPCPGPGPUPCPCPUPUPGPCPGPGPC)-3') ; × 1 MAGNESIUM ION × 1 ADENOSINE-5'-TRIPHOSPHATE × 2 ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O28411_ARCFU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–329； UniProt 1–329

GGDEF domain-containing protein

Archaeoglobus fulgidus DSM 4304

UniProt O28412

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 7 RNA 1	Type III-B CRISPR module RAMP protein Cmr4 × 2 （O28416） Cmr1 C-terminal domain-containing protein × 1 （O28411） Type III-B CRISPR module-associated protein Cmr3 × 1 （O28413） Type III-B CRISPR module RAMP protein Cmr6 × 1 （O28418） CRISPR system Cmr subunit Cmr5 × 1 （O28417） ;RNA (5'-R(UPGPUPAPGPUPAPUPGPCPGPGPUPCPCPUPUPGPCPGPGPC)-3') ; × 1 MAGNESIUM ION × 1 ADENOSINE-5'-TRIPHOSPHATE × 2 ZINC ION × 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	3
Chains and sequence ranges	Author chain B； PDBConstruct 1–1004； 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	Protein–RNA	Heteromer	Protein 7 RNA 1	Type III-B CRISPR module RAMP protein Cmr4 × 2 （O28416） Cmr1 C-terminal domain-containing protein × 1 （O28411） GGDEF domain-containing protein × 1 （O28412） Type III-B CRISPR module RAMP protein Cmr6 × 1 （O28418） CRISPR system Cmr subunit Cmr5 × 1 （O28417） ;RNA (5'-R(UPGPUPAPGPUPAPUPGPCPGPGPUPCPCPUPUPGPCPGPGPC)-3') ; × 1 MAGNESIUM ION × 1 ADENOSINE-5'-TRIPHOSPHATE × 2 ZINC ION × 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	4
Chains and sequence ranges	Author chain C； PDBConstruct 1–341； UniProt 1–341

Type III-B CRISPR module RAMP protein Cmr6

Archaeoglobus fulgidus DSM 4304

UniProt O28418

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 7 RNA 1	Type III-B CRISPR module RAMP protein Cmr4 × 2 （O28416） Cmr1 C-terminal domain-containing protein × 1 （O28411） GGDEF domain-containing protein × 1 （O28412） Type III-B CRISPR module-associated protein Cmr3 × 1 （O28413） CRISPR system Cmr subunit Cmr5 × 1 （O28417） ;RNA (5'-R(UPGPUPAPGPUPAPUPGPCPGPGPUPCPCPUPUPGPCPGPGPC)-3') ; × 1 MAGNESIUM ION × 1 ADENOSINE-5'-TRIPHOSPHATE × 2 ZINC ION × 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	5
Chains and sequence ranges	Author chain I； PDBConstruct 1–343； UniProt 1–343

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	Protein–RNA	Heteromer	Protein 7 RNA 1	Type III-B CRISPR module RAMP protein Cmr4 × 2 （O28416） Cmr1 C-terminal domain-containing protein × 1 （O28411） GGDEF domain-containing protein × 1 （O28412） Type III-B CRISPR module-associated protein Cmr3 × 1 （O28413） Type III-B CRISPR module RAMP protein Cmr6 × 1 （O28418） ;RNA (5'-R(UPGPUPAPGPUPAPUPGPCPGPGPUPCPCPUPUPGPCPGPGPC)-3') ; × 1 MAGNESIUM ION × 1 ADENOSINE-5'-TRIPHOSPHATE × 2 ZINC ION × 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	6
Chains and sequence ranges	Author chain G； PDBConstruct 1–155； UniProt 1–155

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	9l7d
Deposition date deposition_date	2024-12-26
Structure title title	Type III-B CRISPR-Cas effector from Archaeoglobus fulgidus (Form 2)
Keywords keywords	CRISPR-Cas effector, ANTIVIRAL PROTEIN; ANTIVIRAL PROTEIN
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.

9l7d__assembly_1__model_1

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

Download this curve (.dat)

9l7d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9l7d__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	48.06 Å
Rg (electron density)	48.06 Å
Total Rg	48.13 Å
Atom count	21366
Residues	2801
Excluded volume	381670 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9l7d__assembly_1__model_1`	octameric （8）	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 (10)

Entity 1 Entity 1 polymer

Description description	Type III-B CRISPR module RAMP protein Cmr4
Molecular weight formula_weight	41252.3 kDa
Mutation mutation	D31A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,E
Atom count atom_count	21366

MGSSHHHHHHSQDPMFDMFEKAVVFGLYSITPVHAGSGAELSVIALPIQRERHTGFPVIWGQSLKGVLRSRFRQLELDEKIEVESQKWKWKEKTKEVLKEKADEFIKKVEERKRDPLLTEIVFGPATDGASEHAGAVSVGDAKILLFPVRSAKGVFAFVTSPIVIQRLKEDFELVSEIENDIELKQILSRFKVELSNNETIAGNALILNGENKVILEDIVLKVKSDSNVIENLVEVLKTLFGDNFFGKPIESIKERIAIVSDDVFKSFTRFSTEIVARVRIDAEKGTVARGGLWYEEFLPSDTLMYSLIAVGSPKKENLPKEVDNTQKIVNVLKVTFNNAFLQIGGDETVGKGFVKVRAGVLTGGHKGN

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	Cmr1 C-terminal domain-containing protein
Molecular weight formula_weight	38017.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MCMYSATFTLEAITPVFMRGANQSKAEIRAASIKGLMRWWFRALSGSYFGNDVEGLRRVEEYVFGSTKRESRVVVEVVKEHVEERFCPLPMVWKKKKGVTTRVSQRAIAPGSKFTLLLTSDDEEVLKLACYSLIGLVYFGGIGFRCSRGAGSLKISSLKSDVQLIDLPKNKNQLGQMVNDLTVEIAKILKKTFLCDHENKNCTSYSSFWCFYLFLWGEKAELEEVYYRSNNLENERLTLLDLFEKEFKNKNNHLSNYGYRDFVFGLPRGTKKDRRASPIKVGITELSEKYHVRVSVFKTKIFKPGMNVKWDNIFVFLENIGAERIYPER

Source Source

Source organism organism	Archaeoglobus fulgidus
NCBI taxonomy ID ncbi_taxonomy_id	2234
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	GGDEF domain-containing protein
Molecular weight formula_weight	115211.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MGQYFRVSGKYRGRENLPREVNKMADNEFWLNKIRAFFHDPPDKSFELKTHERRASFILGELKPSKSLKRIIKNADIQASSLQRVDLEKSIHKKELKSTFDRIHNTEKYEYIGQPIIRHPVTGEIKEYGTILANLPQTQREVYDVDDEGKEDYEEQFQEILSRILKIEKKVFDDFKNRYSDPKDLYISLWAFYAEKLKEALEEEFSASFAEEFVNLPAYTLSPDHTLFDHADATSAIFGAEIDGKKPVLVLFKISPVQKFIADARKEKDLWAASHMLSTLTFKAISFIADKFGPDVVIYPHLRGNPFFHAWLHSKKIWEFSDSHSLKIASVPNKFLALVGVSDEKELNNLREGIRNEIESFLADLFDKLWNEVIVGALEHSDALKHLGDKKEIHKEILLKRFTLTLSSLKIHDVDVSGSKEEAYEKVKDFVRSLGLPNAIESKYLQWLDMLGSVEASNNRPTKYDLYSLYYEILTVLNAIESTHFDKPAEPAGYKCTLCGEHLAIGGESREMMENVWGKIHKRWPSHLRSNERLCAVCAVKRFYPKFIETLDIFEGVGKVVPDIESVSEVAMCRRTKHGITWKEVYDYLRGLKNVDDEKLLGKLENLKHSVQTLINNVKSELKSRKVYPEEFLEGLNRNFSNEILYSERLRDFNTLLDTLGFDAAKLGLDDVKNYETMISELRERLSEVYKMLGEPPKYYAILMMDGDEMGKLLSGEKLKTAEHYLHSAILERVSDALRVKAKTVRRLITPAAHSSISRALKNFSVNHVPDVVRKGNGTLIYSGGDDVLVLLPVDTAFDVATELAMTFSTSWNGWEMLPGNKLSAGLLIVHYKHPLYDALEKTRELLQKAKKLGRNAIAVGLLKRSGSYYESVVNFETLEDAKAVANLLVKEQVSPRIIYELLNFADVISKEFLHQLVKYEAVRHSIDKNLAEEFQSVFARGHQGVRVELEGNDEEINKYISDGANLETFLDKYEKAVDVIRKQVRGFLNLVKILYESIRGGAK

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	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 5 Entity 5 polymer

Description description	Type III-B CRISPR module RAMP protein Cmr6
Molecular weight formula_weight	39469.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

MKSNVVVKYPVNSELANYAEKFWKKELAIYNLSLILNKMTPFVKRRSESYKSSLSAVKEIFKNVDDFQNFLNSVLRRSLDEYRVFFENYERLFNSFSSKIFSMRTKSRLVVGLGDESVYETSIRLHRNYGVPYIPGSALKGVAKHYAFSILARENGDEILRIYESVKEDLKARIAKRDKIKKNDVPEDYYLTAAVIQELFEKKFDELGAIRNTRVEIGDTVISVGDIVKIFGTQKEEGSVIFFDAFPTPEQLKDKPNLELDIMNPHYQPYYQHGEPPGDWHSPNPIFFLTVPAGVEFTFAVASRDLDDLAEKAEKLLKEALKKFGVGAKTSLGYGRFDARDDR

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 system Cmr subunit Cmr5
Molecular weight formula_weight	17407.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

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 7 Entity 7 polymer

Description description	;RNA (5'-R(UPGPUPAPGPUPAPUPGPCPGPGPUPCPCPUPUPGPCPGPGPC)-3') ;
Molecular weight formula_weight	14501.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	V

AUUGAAAGUUGUAGUAUGCGGUCCUUGCGGCUGAGAGCACUUCAG

Entity 8 Entity 8 non-polymer

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

Entity 9 Entity 9 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

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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	triclinic

Resolution resolution	3.10 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	66164

Type III-B CRISPR-Cas effector from Archaeoglobus fulgidus (Form 2)

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

Type III-B CRISPR module RAMP protein Cmr4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cmr1 C-terminal 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

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

Type III-B CRISPR module RAMP protein Cmr6

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9l7d__assembly_1__model_1

9l7d__assembly_1__model_1 | I(q)

9l7d__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 (10)

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

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