4h4k

Structure of the Cmr2-Cmr3 subcomplex of the Cmr RNA-silencing complex

Method: X-RAY DIFFRACTION

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

CRISPR system Cmr subunit Cmr3

Pyrococcus furiosus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	CRISPR system Cmr subunit Cmr2 × 1 （Q8U1S6） ADENOSINE-5'-TRIPHOSPHATE × 1 ZINC ION × 1 SODIUM ION × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CMR3_PYRFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–322； UniProt 1–322

CRISPR system Cmr subunit Cmr2

Pyrococcus furiosus

UniProt Q8U1S6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	CRISPR system Cmr subunit Cmr3 × 1 （Q8U1S7） ADENOSINE-5'-TRIPHOSPHATE × 1 ZINC ION × 1 SODIUM ION × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CMR2_PYRFU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 40–696； UniProt 215–871

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	4h4k
Deposition date deposition_date	2012-09-17
Structure title title	Structure of the Cmr2-Cmr3 subcomplex of the Cmr RNA-silencing complex
Keywords keywords	;Ferredoxin, Palm, RAMP, Repeat Associated Mysterious Protein, Polymerase, Nuclease, RNA-interference, Cmr proteins CRISPR RNA, 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.

4h4k__assembly_1__model_1

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

Download this curve (.dat)

4h4k__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4h4k__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.73 Å
Rg (electron density)	29.64 Å
Total Rg	30.38 Å
Atom count	7017
Residues	863
Excluded volume	127140 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4h4k__assembly_1__model_1`	dimeric （2）	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 (6)

Entity 1 Entity 1 polymer

Description description	CRISPR system Cmr subunit Cmr3
Molecular weight formula_weight	36366.4 kDa
Mutation mutation	none
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	7018

MIEVTFTPYDVLLFRESRPFDAGSESVARSIIPLPQTVAGAIRTLLFYKGLKNCVGVGEEEPEFTLVGIAIGTEKGRIYPLPFNIIKSEKFYKVVNPGRFLGKLILPPKGKYKSGYVTESILEKYLKGELKEVEENKVIRIEKEKRIGIKLSREKKVVEEGMLYTVEFLRIEKIYAWIEDPGCGIKDILSSYEFLTLGGESRVAFVEVDDKTPDIFNRELGSTKKALFYFSTPTIGKVGEIVQELEKRLNAKIDDYLLVSSRPTAISGWDMHEKKPKGTKFAIPPGSVLFVEFKEEVEVPPYIKLGKLKKLGYGLALGGIWE

Source Source

Source organism organism	Pyrococcus furiosus
NCBI taxonomy ID ncbi_taxonomy_id	186497
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	CRISPR system Cmr subunit Cmr2
Molecular weight formula_weight	80461.8 kDa
Mutation mutation	dHD
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MRGSHHHHHHGMASMTGGQQMGRDLYDDDDKDHPFTMALSVKDPTLLRIKIVPVQPFIANSRKQLDLWASSHLLSMLMYKALEVIVDKFGPEHVIYPSLRDQPFFLKFYLGENIGDEILVANLPNKALAIVSGKEAEKIEEEIKKRIRDFLLQLYREAVDWAVENGVVKVDRSEKDSMLKEAYLKIVREYFTVSITWVSLSEKEDIYQVTENAGLSDEDVKKWLKFAEKKENSRVLERIAIYPLLVKILDSLGERKVTEERFEKSEQLKGWKCHVCGENLAIFGDMYDHDNLKSLWLDEEPLCPMCLIKRYYPVWIRSKTGQKIRFESVVDVALLYKNWRKIFDEKYGKDLVSKAREVSEDFVKDNMLVDSDLYYSSTWESGLSKKLKNKKEIDEEKVKEVVDFLNAAYKEIGNPPKYYAILVMDGDDMGKVISGEVLGEISTRIHPNIRDYVEIPEAKYYSTPQVHVAISQALANFSIREVRSVVKDEGLLIYAGGDDVLAILPVDKALEVAYKIRKEFGKSFENGSLLPGWKLSAGILIVHYKHPLYDALEKARDLLNNKAKNVPGKDTLAIGLLKRSGSYYISLVGWELIRVFYNSELRKKLLEEKGGVGKRFIYHVLREVDTWPKVGIDEMLKFEVIRHIRGRNKEETKELREKIYGEIKDLLEHVRGNNEVEKVRGLFTFLKIITDAEVFP

Source Source

Source organism organism	Pyrococcus furiosus
NCBI taxonomy ID ncbi_taxonomy_id	186497
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d4h4kc1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.53 — Ferredoxin-like domains from CRISPR-associated proteins
Family Family family	d.58.53.7 — Nucleotide cyclase domains from Cmr2-like

Domain ID domain_id	d4h4kc2
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.30 — Helical bundle domains from Csm1/Cmr1-like
Family Family family	a.24.30.1 — Helical bundle domains from Csm1/Cmr1

Domain ID domain_id	d4h4kc3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.53 — Ferredoxin-like domains from CRISPR-associated proteins
Family Family family	d.58.53.7 — Nucleotide cyclase domains from Cmr2-like

Domain ID domain_id	d4h4kc4
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.30 — Helical bundle domains from Csm1/Cmr1-like
Family Family family	a.24.30.1 — Helical bundle domains from Csm1/Cmr1

Domain ID domain_id	d4h4kc5
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (7 domains)

Domain ID domain_id	4h4kA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	2940 —

Domain ID domain_id	4h4kA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1040 — Carboxypeptidase Inhibitor; Chain A
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	4h4kA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	4350 —

Domain ID domain_id	4h4kC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	2220 — CRISPR-Cas system, Cmr2 subunit, D1 domain, cysteine cluster

Domain ID domain_id	4h4kC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1720 — CRISPR-Cas system, Cmr2 subunit, D2 domain, helical bundle

Domain ID domain_id	4h4kC03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	270 — Reverse transcriptase/Diguanylate cyclase domain

Domain ID domain_id	4h4kC04
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	1260 — CRISPR-Cas system, Cmr2 subunit, D4 domain, six-helix bundle

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Unit-cell length a length_a	102.523 Å
Unit-cell length b length_b	135.958 Å
Unit-cell length c length_c	189.655 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	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.804 Å
Low-resolution limit resolution_low	36.833 Å
R factor r_factor	0.2185
R_work r_work	0.2143
R_free r_free	0.2838

Structure of the Cmr2-Cmr3 subcomplex of the Cmr RNA-silencing complex

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

CRISPR system Cmr subunit Cmr3

State in the Current Structure

Other States of the Same Protein in the Database

CRISPR system Cmr subunit Cmr2

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

4h4k__assembly_1__model_1

4h4k__assembly_1__model_1 | I(q)

4h4k__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (5 domains)

CATH v4.4 (7 domains)

7. Citations (1)

Structure of the Cmr2-Cmr3 subcomplex of the Cmr RNA-silencing complex

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

CRISPR system Cmr subunit 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 system Cmr subunit Cmr2

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

4h4k__assembly_1__model_1

4h4k__assembly_1__model_1 | I(q)

4h4k__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (5 domains)

CATH v4.4 (7 domains)

7. Citations (1)