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3x1l

Crystal Structure of the CRISPR-Cas RNA Silencing Cmr Complex Bound to a Target Analog

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

CRISPR system Cmr subunit Cmr2

Pyrococcus furiosus DSM 3638

UniProt Q8U1S6

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 CRISPR system Cmr subunit Cmr3 × 1 （Q8U1S7） Cmr4 × 3 （O28416） CRISPR system Cmr subunit Cmr5 × 2 （O28417） Cmr6 × 1 （O28418） RNA (32-MER) × 1 ;DNA (5'-D(*TP*GP*CP*TP*CP*TP*CP*AP*GP*CP*CP*GP*CP*AP*AP*GP*GP*AP*CP*CP*GP*CP*AP*TP*AP*CP*TP*AP*CP*AP*A)-3') ; × 1 ZINC ION × 1 MAGNESIUM ION × 1 water × 8 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
3ung 3ur3 4doz 4w8y 4w8y

5 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3w2v 3w2w 3w2w 3x1l 4h4k

5 assemblies

View Construct and Data Evidence
UniProt name CMR2_PYRFU
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 22–677； UniProt 216–871

CRISPR system Cmr subunit Cmr3

Pyrococcus furiosus DSM 3638

UniProt Q8U1S7

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 CRISPR system Cmr subunit Cmr2 × 1 （Q8U1S6） Cmr4 × 3 （O28416） CRISPR system Cmr subunit Cmr5 × 2 （O28417） Cmr6 × 1 （O28418） RNA (32-MER) × 1 ;DNA (5'-D(*TP*GP*CP*TP*CP*TP*CP*AP*GP*CP*CP*GP*CP*AP*AP*GP*GP*AP*CP*CP*GP*CP*AP*TP*AP*CP*TP*AP*CP*AP*A)-3') ; × 1 ZINC ION × 1 MAGNESIUM ION × 1 water × 8 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3w2v 3w2w 3w2w 3x1l 4h4k

5 assemblies

View Construct and Data Evidence
UniProt name CMR3_PYRFU
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–322； UniProt 1–322

Cmr4

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 CRISPR system Cmr subunit Cmr2 × 1 （Q8U1S6） CRISPR system Cmr subunit Cmr3 × 1 （Q8U1S7） CRISPR system Cmr subunit Cmr5 × 2 （O28417） Cmr6 × 1 （O28418） RNA (32-MER) × 1 ;DNA (5'-D(*TP*GP*CP*TP*CP*TP*CP*AP*GP*CP*CP*GP*CP*AP*AP*GP*GP*AP*CP*CP*GP*CP*AP*TP*AP*CP*TP*AP*CP*AP*A)-3') ; × 1 ZINC ION × 1 MAGNESIUM ION × 1 water × 8 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3x1l 9l7c 9l7d 9x25

4 assemblies

View Construct and Data Evidence
UniProt name O28416_ARCFU
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 3–357； UniProt 1–355 Author chain D； PDBConstruct 3–357； UniProt 1–355 Author chain E； PDBConstruct 3–357； 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 CRISPR system Cmr subunit Cmr2 × 1 （Q8U1S6） CRISPR system Cmr subunit Cmr3 × 1 （Q8U1S7） Cmr4 × 3 （O28416） Cmr6 × 1 （O28418） RNA (32-MER) × 1 ;DNA (5'-D(*TP*GP*CP*TP*CP*TP*CP*AP*GP*CP*CP*GP*CP*AP*AP*GP*GP*AP*CP*CP*GP*CP*AP*TP*AP*CP*TP*AP*CP*AP*A)-3') ; × 1 ZINC ION × 1 MAGNESIUM ION × 1 water × 8 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
2oeb

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3x1l 9l7c 9l7d 9x25

4 assemblies

View Construct and Data Evidence
UniProt name CMR5_ARCFU
Isoform —
PDB entities 4
Chains and sequence ranges Author chain F； PDBConstruct 1–155； UniProt 1–155 Author chain G； PDBConstruct 1–155； UniProt 1–155

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 Other combination Heteromer Protein 8 DNA 1 RNA 1 CRISPR system Cmr subunit Cmr2 × 1 （Q8U1S6） CRISPR system Cmr subunit Cmr3 × 1 （Q8U1S7） Cmr4 × 3 （O28416） CRISPR system Cmr subunit Cmr5 × 2 （O28417） RNA (32-MER) × 1 ;DNA (5'-D(*TP*GP*CP*TP*CP*TP*CP*AP*GP*CP*CP*GP*CP*AP*AP*GP*GP*AP*CP*CP*GP*CP*AP*TP*AP*CP*TP*AP*CP*AP*A)-3') ; × 1 ZINC ION × 1 MAGNESIUM ION × 1 water × 8 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3x1l 9l7c 9l7d 9x25

4 assemblies

View Construct and Data Evidence
UniProt name O28418_ARCFU
Isoform —
PDB entities 5
Chains and sequence ranges Author chain H； 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_id3x1l
Deposition date deposition_date2014-11-20
Structure title titleCrystal Structure of the CRISPR-Cas RNA Silencing Cmr Complex Bound to a Target Analog
Keywords keywordsRNA-recognition motif, RNA silencing, RNA binding, RNA BINDING PROTEIN-RNA-DNA complex; RNA BINDING PROTEIN/RNA/DNA
Experimental Method methodX-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.

3x1l__assembly_1__model_1

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

Download this curve (.dat)

3x1l__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 109 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3x1l__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）44.60 Å
Rg (electron density)44.90 Å
Total Rg45.10 Å
Atom count19822
Residues2524
Excluded volume352660 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3x1l__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 (10)

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id3x1lB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1040 — Carboxypeptidase Inhibitor; Chain A
Homologous superfamily homologous superfamily70 —
Domain ID domain_id3x1lB03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily4350 —
Domain ID domain_id3x1lF00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology520 — Peroxidase; domain 1
Homologous superfamily homologous superfamily30 — AF1862-like domain
Domain ID domain_id3x1lG00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology520 — Peroxidase; domain 1
Homologous superfamily homologous superfamily30 — AF1862-like domain
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7. Citations (1)