4s1t

Crystal structure of the mutant I26A/N52A of the endoribonuclease from human coronavirus 229E

Method: X-RAY DIFFRACTION

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

Uridylate-specific endoribonuclease

Human coronavirus 229E

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	PHOSPHATE ION × 6 water × 6	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	PHOSPHATE ION × 6 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	R1AB_CVH22
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–349； UniProt 6111–6458 Author chain B； PDBConstruct 2–349； UniProt 6111–6458 Author chain C； PDBConstruct 2–349； UniProt 6111–6458 Author chain D； PDBConstruct 2–349； UniProt 6111–6458 Author chain E； PDBConstruct 2–349； UniProt 6111–6458 Author chain F； PDBConstruct 2–349； UniProt 6111–6458

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	4s1t
Deposition date deposition_date	2015-01-15
Structure title title	Crystal structure of the mutant I26A/N52A of the endoribonuclease from human coronavirus 229E
Keywords keywords	HCoV-229e, endoribonuclease, trimeric nsp15, double mutation, HYDROLASE; 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.

4s1t__assembly_1__model_1

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

Download this curve (.dat)

4s1t__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4s1t__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.22 Å
Rg (electron density)	39.61 Å
Total Rg	40.10 Å
Atom count	16104
Residues	2052
Excluded volume	289100 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4s1t__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4s1t__assembly_2__model_1`	hexameric （6）	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	Uridylate-specific endoribonuclease
Molecular weight formula_weight	38822.2 kDa
EC 编号 ec_number	3.1.-.-
Mutation mutation	I26A, N52A
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	16623

SGLENIAFNVVNKGSFVGADGELPVAASGDKVFVRDGNTDNLVFVNKTSLPTAIAFELFAKRKVGLTPPLSILKNLGVVATYKFVLWDYEAERPLTSFTKSVCGYTDFAEDVCTCYDNSIQGSYERFTLSTNAVLFSATAVKTGGKSLPAIKLNFGMLNGNAIATVKSEDGNIKNINWFVYVRKDGKPVDHYDGFYTQGRNLQDFLPRSTMEEDFLNMDIGVFIQKYGLEDFNFEHVVYGDVSKTTLGGLHLLISQVRLSKMGILKAEEFVAASDITLKCCTVTYLNDPSSKTVCTYMDLLLDDFVSVLKSLDLTVVSKVHEVIIDNKPWRWMLWCKDNAVATFYPQLQ

Source Source

Source organism organism	Human coronavirus 229E
Common name common_name	HCoV-229E
NCBI taxonomy ID ncbi_taxonomy_id	11137
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	519

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6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (18 domains)

Domain ID domain_id	d4s1ta1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.0 — automated matches

Domain ID domain_id	d4s1ta2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.294 — EndoU-like
Superfamily Superfamily superfamily	d.294.1 — EndoU-like
Family Family family	d.294.1.0 — automated matches

Domain ID domain_id	d4s1ta3
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	d4s1tb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.0 — automated matches

Domain ID domain_id	d4s1tb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.294 — EndoU-like
Superfamily Superfamily superfamily	d.294.1 — EndoU-like
Family Family family	d.294.1.0 — automated matches

Domain ID domain_id	d4s1tb3
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	d4s1tc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.0 — automated matches

Domain ID domain_id	d4s1tc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.294 — EndoU-like
Superfamily Superfamily superfamily	d.294.1 — EndoU-like
Family Family family	d.294.1.0 — automated matches

Domain ID domain_id	d4s1tc3
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	d4s1td1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.0 — automated matches

Domain ID domain_id	d4s1td2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.294 — EndoU-like
Superfamily Superfamily superfamily	d.294.1 — EndoU-like
Family Family family	d.294.1.0 — automated matches

Domain ID domain_id	d4s1td3
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	d4s1te1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.0 — automated matches

Domain ID domain_id	d4s1te2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.294 — EndoU-like
Superfamily Superfamily superfamily	d.294.1 — EndoU-like
Family Family family	d.294.1.0 — automated matches

Domain ID domain_id	d4s1te3
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	d4s1tf1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.0 — automated matches

Domain ID domain_id	d4s1tf2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.294 — EndoU-like
Superfamily Superfamily superfamily	d.294.1 — EndoU-like
Family Family family	d.294.1.0 — automated matches

Domain ID domain_id	d4s1tf3
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 (12 domains)

Domain ID domain_id	4s1tA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	820 — Nsp15 N-terminal domain-like

Domain ID domain_id	4s1tA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11580 — nsp15 middle domain

Domain ID domain_id	4s1tB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	820 — Nsp15 N-terminal domain-like

Domain ID domain_id	4s1tB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11580 — nsp15 middle domain

Domain ID domain_id	4s1tC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	820 — Nsp15 N-terminal domain-like

Domain ID domain_id	4s1tC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11580 — nsp15 middle domain

Domain ID domain_id	4s1tD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	820 — Nsp15 N-terminal domain-like

Domain ID domain_id	4s1tD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11580 — nsp15 middle domain

Domain ID domain_id	4s1tE01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	820 — Nsp15 N-terminal domain-like

Domain ID domain_id	4s1tE02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11580 — nsp15 middle domain

Domain ID domain_id	4s1tF01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	160 — Double Stranded RNA Binding Domain
Homologous superfamily homologous superfamily	820 — Nsp15 N-terminal domain-like

Domain ID domain_id	4s1tF02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11580 — nsp15 middle domain

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Unit-cell length a length_a	86.445 Å
Unit-cell length b length_b	140.285 Å
Unit-cell length c length_c	426.933 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	48

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.504 Å
Low-resolution limit resolution_low	43.222 Å
R factor r_factor	0.2431
R_work r_work	0.2410
R_free r_free	0.2848

Crystal structure of the mutant I26A/N52A of the endoribonuclease from human coronavirus 229E

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

Uridylate-specific endoribonuclease

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

4s1t__assembly_1__model_1

4s1t__assembly_1__model_1 | I(q)

4s1t__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (18 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal structure of the mutant I26A/N52A of the endoribonuclease from human coronavirus 229E

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

Uridylate-specific endoribonuclease

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

4s1t__assembly_1__model_1

4s1t__assembly_1__model_1 | I(q)

4s1t__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (18 domains)

CATH v4.4 (12 domains)

7. Citations (1)