SAXSdb — 4cmp

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

CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1

STREPTOCOCCUS PYOGENES

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	SULFATE ION × 2 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	SULFATE ION × 3 MAGNESIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

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 B； 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_id	4cmp
Deposition date deposition_date	2014-01-16
Structure title title	Crystal structure of S. pyogenes Cas9
Keywords keywords	HYDROLASE, DNASE, RNA-GUIDED, IMMUNITY, CRRNA, GENOME EDITING; HYDROLASE
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.

4cmp__assembly_1__model_1

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

Download this curve (.dat)

4cmp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4cmp__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.64 Å
Rg (electron density)	37.26 Å
Total Rg	37.68 Å
Atom count	18782
Residues	1144
Excluded volume	167080 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4cmp__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4cmp__assembly_2__model_1`	monomeric （1）	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)

Entity 1 Entity 1 polymer

Description description	CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1
Molecular weight formula_weight	158986.1 kDa
EC 编号 ec_number	3.1.-.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	38285

GAASMDKKYSIGLDIGTNSVGWAVITDEYKVPSKKFKVLGNTDRHSIKKNLIGALLFDSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLVDSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQTYNQLFEENPINASGVDAKAILSARLSKSRRLENLIAQLPGEKKNGLFGNLIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNTEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGTYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDREMIEERLKTYAHLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQGDSLHEHIANLAGSPAIKKGILQTVKVVDELVKVMGRHKPENIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVPQSFLKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPAAFKYFDTTIDRKRYTSTKEVLDATLIHQSITGLYETRIDLSQLGGD

Source Source

Source organism organism	STREPTOCOCCUS PYOGENES
NCBI taxonomy ID ncbi_taxonomy_id	301447
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	203

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d4cmpa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.3 — Ribonuclease H-like
Family Family family	c.55.3.16 — RuvC-like domain from CRISPR-associated protein Cas9

Domain ID domain_id	d4cmpa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.4 — His-Me finger endonucleases
Superfamily Superfamily superfamily	d.4.1 — His-Me finger endonucleases
Family Family family	d.4.1.8 — HNH domain from CRISPR-associated protein Cas9

Domain ID domain_id	d4cmpa3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.393 — CRISPR-associated endonuclease Cas9/Csn1, Target recognition (REC) lobe
Superfamily Superfamily superfamily	d.393.1 — CRISPR-associated endonuclease Cas9/Csn1, Target recognition (REC) lobe
Family Family family	d.393.1.1 — CRISPR-associated endonuclease Cas9/Csn1, Target recognition (REC) lobe

Domain ID domain_id	d4cmpa4
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.80 — CRISPR-associated endonuclease Cas9/Csn1, Protospace-adjacent motif (PAM)-interacting domain
Superfamily Superfamily superfamily	e.80.1 — CRISPR-associated endonuclease Cas9/Csn1, PAM-interacting (PI) domain
Family Family family	e.80.1.1 — CRISPR-associated endonuclease Cas9/Csn1, PAM-interacting (PI) domain

Domain ID domain_id	d4cmpb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.3 — Ribonuclease H-like
Family Family family	c.55.3.16 — RuvC-like domain from CRISPR-associated protein Cas9

Domain ID domain_id	d4cmpb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.393 — CRISPR-associated endonuclease Cas9/Csn1, Target recognition (REC) lobe
Superfamily Superfamily superfamily	d.393.1 — CRISPR-associated endonuclease Cas9/Csn1, Target recognition (REC) lobe
Family Family family	d.393.1.1 — CRISPR-associated endonuclease Cas9/Csn1, Target recognition (REC) lobe

Domain ID domain_id	d4cmpb3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.4 — His-Me finger endonucleases
Superfamily Superfamily superfamily	d.4.1 — His-Me finger endonucleases
Family Family family	d.4.1.8 — HNH domain from CRISPR-associated protein Cas9

Domain ID domain_id	d4cmpb4
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.80 — CRISPR-associated endonuclease Cas9/Csn1, Protospace-adjacent motif (PAM)-interacting domain
Superfamily Superfamily superfamily	e.80.1 — CRISPR-associated endonuclease Cas9/Csn1, PAM-interacting (PI) domain
Family Family family	e.80.1.1 — CRISPR-associated endonuclease Cas9/Csn1, PAM-interacting (PI) domain

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Unit-cell length a length_a	159.780 Å
Unit-cell length b length_b	209.620 Å
Unit-cell length c length_c	91.260 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	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.620 Å
Low-resolution limit resolution_low	47.481 Å
R factor r_factor	0.2532
R_work r_work	0.2523
R_free r_free	0.2858

Crystal structure of S. pyogenes Cas9

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

CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1

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

4cmp__assembly_1__model_1

4cmp__assembly_1__model_1 | I(q)

4cmp__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (8 domains)

7. Citations (1)

Crystal structure of S. pyogenes Cas9

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

CRISPR-ASSOCIATED ENDONUCLEASE CAS9/CSN1

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

4cmp__assembly_1__model_1

4cmp__assembly_1__model_1 | I(q)

4cmp__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (8 domains)

7. Citations (1)