2y9h

Structure A of CRISPR endoribonuclease Cse3 bound to 19 nt RNA

Method: X-RAY DIFFRACTION

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

CSE3

THERMUS THERMOPHILUS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Monomer	Protein 1 RNA 1	;5'-R(UPCPCPCPCPAPCPGPCPGPUPGPUPGP GPGPDGPAP*UP)-3' ; × 1 water × 2	Consistent with all polymers
2	Protein–RNA	Monomer	Protein 1 RNA 1	;5'-R(UPCPCPCPCPAPCPGPCPGPUPGPUPGP GPGPDGPAP*UP)-3' ; × 1 water × 2	Consistent with all polymers
3	Protein–RNA	Monomer	Protein 1 RNA 1	;5'-R(UPCPCPCPCPAPCPGPCPGPUPGPUPGP GPGPDGPAP*UP)-3' ; × 1 water × 2	Consistent with all polymers
4	Protein–RNA	Monomer	Protein 1 RNA 1	;5'-R(UPCPCPCPCPAPCPGPCPGPUPGPUPGP GPGPDGPAP*UP)-3' ; × 1 water × 2	Consistent with all polymers
5	Protein–RNA	Monomer	Protein 1 RNA 1	;5'-R(UPCPCPCPCPAPCPGPCPGPUPGPUPGP GPGPDGPAP*UP)-3' ; × 1 water × 2	Consistent with all polymers
6	Protein–RNA	Monomer	Protein 1 RNA 1	;5'-R(UPCPCPCPCPAPCPGPCPGPUPGPUPGP GPGPDGPAP*UP)-3' ; × 1 water × 2	Consistent with all polymers
7	Protein–RNA	Monomer	Protein 1 RNA 1	;5'-R(UPCPCPCPCPAPCPGPCPGPUPGPUPGP GPGPDGPAP*UP)-3' ; × 1 water × 2	Consistent with all polymers
8	Protein–RNA	Monomer	Protein 1 RNA 1	;5'-R(UPCPCPCPCPAPCPGPCPGPUPGPUPGP GPGPDGPAP*UP)-3' ; × 1 water × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q53WG9_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–215； UniProt 1–211 Author chain C； PDBConstruct 5–215； UniProt 1–211 Author chain E； PDBConstruct 5–215； UniProt 1–211 Author chain G； PDBConstruct 5–215； UniProt 1–211 Author chain I； PDBConstruct 5–215； UniProt 1–211 Author chain K； PDBConstruct 5–215； UniProt 1–211 Author chain M； PDBConstruct 5–215； UniProt 1–211 Author chain O； PDBConstruct 5–215； UniProt 1–211

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	2y9h
Deposition date deposition_date	2011-02-14
Structure title title	Structure A of CRISPR endoribonuclease Cse3 bound to 19 nt RNA
Keywords keywords	HYDROLASE-RNA COMPLEX, FERREDOXIN-LIKE; HYDROLASE/RNA
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.

2y9h__assembly_5__model_1

Assembly 5 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2y9h__assembly_5__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2y9h__assembly_5__model_1 | P(r) · Pending

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

Rg（Guinier）	19.41 Å
Rg (electron density)	18.22 Å
Total Rg	19.18 Å
Atom count	1930
Residues	214
Excluded volume	33251 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2y9h__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2y9h__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2y9h__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2y9h__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2y9h__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`2y9h__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`2y9h__assembly_7__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`2y9h__assembly_8__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 (3)

Entity 1 Entity 1 polymer

Description description	CSE3
Molecular weight formula_weight	24050.0 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K,M,O
Atom count atom_count	15663

GTGAMWLTKLVLNPASRAARRDLANPYEMHRTLSKAVSRALEEGRERLLWRLEPARGLEPPVVLVQTLTEPDWSVLDEGYAQVFPPKPFHPALKPGQRLRFRLRANPAKRLAATGKRVALKTPAEKVAWLERRLEEGGFRLLEGERGPWVQILQDTFLEVRRKKDGEEAGKLLQVQAVLFEGRLEVVDPERALATLRRGVGPGKALGLGLLSVAP

Source Source

Source organism organism	THERMUS THERMOPHILUS
NCBI taxonomy ID ncbi_taxonomy_id	300852
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	;5'-R(UPCPCPCPCPAPCPGPCPGPUPGPUPGP GPGPDGPAP*UP)-3' ;
Molecular weight formula_weight	6069.6 kDa
Source method src_method	syn
Copy count entity_count	8

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	B,D,F,H,J,L,N,P

UCCCCACGCGUGUGGGGAU

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	475

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6. Fold Classification (SCOP + CATH) 39 domains

SCOP 2.08 (23 domains)

Domain ID domain_id	d2y9ha1
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.58.53.0 — automated matches

Domain ID domain_id	d2y9ha2
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.58.53.1 — CRISPR-associated endoribonuclease Cse3-like

Domain ID domain_id	d2y9ha3
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

Domain ID domain_id	d2y9hc1
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.58.53.0 — automated matches

Domain ID domain_id	d2y9hc2
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.58.53.1 — CRISPR-associated endoribonuclease Cse3-like

Domain ID domain_id	d2y9he1
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.58.53.0 — automated matches

Domain ID domain_id	d2y9he2
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.58.53.1 — CRISPR-associated endoribonuclease Cse3-like

Domain ID domain_id	d2y9he3
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

Domain ID domain_id	d2y9hg1
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.58.53.0 — automated matches

Domain ID domain_id	d2y9hg2
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.58.53.1 — CRISPR-associated endoribonuclease Cse3-like

Domain ID domain_id	d2y9hg3
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

Domain ID domain_id	d2y9hi1
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.58.53.0 — automated matches

Domain ID domain_id	d2y9hi2
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.58.53.1 — CRISPR-associated endoribonuclease Cse3-like

Domain ID domain_id	d2y9hi3
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

Domain ID domain_id	d2y9hk1
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.58.53.0 — automated matches

Domain ID domain_id	d2y9hk2
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.58.53.1 — CRISPR-associated endoribonuclease Cse3-like

Domain ID domain_id	d2y9hk3
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

Domain ID domain_id	d2y9hm1
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.58.53.0 — automated matches

Domain ID domain_id	d2y9hm2
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.58.53.1 — CRISPR-associated endoribonuclease Cse3-like

Domain ID domain_id	d2y9hm3
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

Domain ID domain_id	d2y9ho1
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.58.53.0 — automated matches

Domain ID domain_id	d2y9ho2
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.58.53.1 — CRISPR-associated endoribonuclease Cse3-like

Domain ID domain_id	d2y9ho3
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 (16 domains)

Domain ID domain_id	2y9hA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1200 — Crispr-associated protein; domain 1

Domain ID domain_id	2y9hA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1210 — Crispr-associated protein; domain 2

Domain ID domain_id	2y9hC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1200 — Crispr-associated protein; domain 1

Domain ID domain_id	2y9hC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1210 — Crispr-associated protein; domain 2

Domain ID domain_id	2y9hE01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1200 — Crispr-associated protein; domain 1

Domain ID domain_id	2y9hE02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1210 — Crispr-associated protein; domain 2

Domain ID domain_id	2y9hG01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1200 — Crispr-associated protein; domain 1

Domain ID domain_id	2y9hG02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1210 — Crispr-associated protein; domain 2

Domain ID domain_id	2y9hI01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1200 — Crispr-associated protein; domain 1

Domain ID domain_id	2y9hI02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1210 — Crispr-associated protein; domain 2

Domain ID domain_id	2y9hK01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1200 — Crispr-associated protein; domain 1

Domain ID domain_id	2y9hK02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1210 — Crispr-associated protein; domain 2

Domain ID domain_id	2y9hM01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1200 — Crispr-associated protein; domain 1

Domain ID domain_id	2y9hM02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1210 — Crispr-associated protein; domain 2

Domain ID domain_id	2y9hO01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1200 — Crispr-associated protein; domain 1

Domain ID domain_id	2y9hO02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1210 — Crispr-associated protein; domain 2

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Unit-cell length a length_a	85.860 Å
Unit-cell length b length_b	149.810 Å
Unit-cell length c length_c	87.260 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.60 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	58.697 Å
R factor r_factor	0.2320
R_work r_work	0.2305
R_free r_free	0.2895

Structure A of CRISPR endoribonuclease Cse3 bound to 19 nt RNA

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

CSE3

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

2y9h__assembly_5__model_1

2y9h__assembly_5__model_1 | I(q)

2y9h__assembly_5__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 39 domains

SCOP 2.08 (23 domains)

CATH v4.4 (16 domains)

7. Citations (1)

Structure A of CRISPR endoribonuclease Cse3 bound to 19 nt RNA

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

CSE3

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

2y9h__assembly_5__model_1

2y9h__assembly_5__model_1 | I(q)

2y9h__assembly_5__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 39 domains

SCOP 2.08 (23 domains)

CATH v4.4 (16 domains)

7. Citations (1)