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4oo8

Crystal structure of Streptococcus pyogenes Cas9 in complex with guide RNA and target DNA

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

CRISPR-associated endonuclease Cas9/Csn1

Streptococcus pyogenes serotype M1

UniProt Q99ZW2

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Monomer Protein 1 DNA 1 RNA 1 RNA (97-MER) × 1 ;DNA (5'-D(*CP*CP*AP*GP*CP*CP*AP*AP*GP*CP*GP*CP*AP*CP*CP*TP*AP*AP*TP*TP*TP*CP*C)-3') ; × 1 water × 3 Consistent with all polymers
2 Other combination Monomer Protein 1 DNA 1 RNA 1 RNA (97-MER) × 1 ;DNA (5'-D(*CP*CP*AP*GP*CP*CP*AP*AP*GP*CP*GP*CP*AP*CP*CP*TP*AP*AP*TP*TP*TP*CP*C)-3') ; × 1 water × 3 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
4cmp 4cmp 4cmq 4cmq 6o56 6o56 7vk9 8sca 9jl4

9 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
4oo8 4oo8 4un3 4un4 4un5 5b2r 5b2s 5b2t 5f9r 5fq5 5fw1 5fw2

138 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name CAS9_STRP1
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 5–1372； UniProt 1–1368 Author chain D； PDBConstruct 5–1372； UniProt 1–1368

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_id4oo8
Deposition date deposition_date2014-01-31
Structure title titleCrystal structure of Streptococcus pyogenes Cas9 in complex with guide RNA and target DNA
Keywords keywordsHydrolase-DNA-RNA complex; Hydrolase/DNA/RNA
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.

4oo8__assembly_1__model_1

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

Download this curve (.dat)

4oo8__assembly_1__model_1 | I(q)

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

4oo8__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）38.59 Å
Rg (electron density)38.09 Å
Total Rg38.43 Å
Atom count12485
Residues1419
Excluded volume213200 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4oo8__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 4oo8__assembly_2__model_1 trimeric （3） 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 (4)

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6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (7 domains)

Domain ID domain_idd4oo8a1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.3 — Ribonuclease H-like
Family Family familyc.55.3.16 — RuvC-like domain from CRISPR-associated protein Cas9
Domain ID domain_idd4oo8a2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.4 — His-Me finger endonucleases
Superfamily Superfamily superfamilyd.4.1 — His-Me finger endonucleases
Family Family familyd.4.1.8 — HNH domain from CRISPR-associated protein Cas9
Domain ID domain_idd4oo8a3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.393 — CRISPR-associated endonuclease Cas9/Csn1, Target recognition (REC) lobe
Superfamily Superfamily superfamilyd.393.1 — CRISPR-associated endonuclease Cas9/Csn1, Target recognition (REC) lobe
Family Family familyd.393.1.1 — CRISPR-associated endonuclease Cas9/Csn1, Target recognition (REC) lobe
Domain ID domain_idd4oo8a4
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.80 — CRISPR-associated endonuclease Cas9/Csn1, Protospace-adjacent motif (PAM)-interacting domain
Superfamily Superfamily superfamilye.80.1 — CRISPR-associated endonuclease Cas9/Csn1, PAM-interacting (PI) domain
Family Family familye.80.1.1 — CRISPR-associated endonuclease Cas9/Csn1, PAM-interacting (PI) domain
Domain ID domain_idd4oo8d1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.3 — Ribonuclease H-like
Family Family familyc.55.3.16 — RuvC-like domain from CRISPR-associated protein Cas9
Domain ID domain_idd4oo8d2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.393 — CRISPR-associated endonuclease Cas9/Csn1, Target recognition (REC) lobe
Superfamily Superfamily superfamilyd.393.1 — CRISPR-associated endonuclease Cas9/Csn1, Target recognition (REC) lobe
Family Family familyd.393.1.1 — CRISPR-associated endonuclease Cas9/Csn1, Target recognition (REC) lobe
Domain ID domain_idd4oo8d3
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.80 — CRISPR-associated endonuclease Cas9/Csn1, Protospace-adjacent motif (PAM)-interacting domain
Superfamily Superfamily superfamilye.80.1 — CRISPR-associated endonuclease Cas9/Csn1, PAM-interacting (PI) domain
Family Family familye.80.1.1 — CRISPR-associated endonuclease Cas9/Csn1, PAM-interacting (PI) domain
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7. Citations (1)