1knz

Recognition of the rotavirus mRNA 3' consensus by an asymmetric NSP3 homodimer

Method: X-RAY DIFFRACTION

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

Nonstructural RNA-binding Protein 34

Simian rotavirus A/SA11

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Homooligomer	Protein 2 RNA 1	5'-R(UPGPAPCP*C)-3' × 1 water × 3	Consistent with all polymers
2	Protein–RNA	Homooligomer	Protein 2 RNA 1	5'-R(UPGPAPCP*C)-3' × 1 water × 3	Consistent with all polymers
3	Protein–RNA	Homooligomer	Protein 2 RNA 1	5'-R(UPGPAPCP*C)-3' × 1 water × 3	Consistent with all polymers
4	Protein–RNA	Homooligomer	Protein 2 RNA 1	5'-R(UPGPAPCP*C)-3' × 1 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VN34_ROTS1
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 4–164； UniProt 4–164 Author chain B； PDBConstruct 4–164； UniProt 4–164 Author chain C； PDBConstruct 4–164； UniProt 4–164 Author chain D； PDBConstruct 4–164； UniProt 4–164 Author chain I； PDBConstruct 4–164； UniProt 4–164 Author chain J； PDBConstruct 4–164； UniProt 4–164 Author chain M； PDBConstruct 4–164； UniProt 4–164 Author chain N； PDBConstruct 4–164； UniProt 4–164

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	1knz
Deposition date deposition_date	2001-12-19
Structure title title	Recognition of the rotavirus mRNA 3' consensus by an asymmetric NSP3 homodimer
Keywords keywords	Protein-ssRNA complex, Viral protein-RNA COMPLEX; Viral protein/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.

1knz__assembly_1__model_1

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

Download this curve (.dat)

1knz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1knz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.28 Å
Rg (electron density)	20.63 Å
Total Rg	21.35 Å
Atom count	2240
Residues	297
Excluded volume	39265 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1knz__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1knz__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1knz__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1knz__assembly_4__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 (3)

Entity 1 Entity 1 polymer

Description description	5'-R(UPGPAPCP*C)-3'
Molecular weight formula_weight	1546.0 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	W,X,Y,Z
Atom count atom_count	9555

UGACC

Entity 2 Entity 2 polymer

Description description	Nonstructural RNA-binding Protein 34
Molecular weight formula_weight	18380.0 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,I,J,M,N

LGSMESTQQMAVSIINSSFEAAVVAATSALENMGIEYDYQDIYSRVKNKFDFVMDDSGVKNNPIGKAITIDQALNNKFGSAIRNRNWLADTSRPAKLDEDVNKLRMMLSSKGIDQKMRVLNACFSVKRIPGKSSSIIKCTKLMRDKLERGEVEVDDSFVDEKME

Source Source

Source organism organism	Simian rotavirus A/SA11
NCBI taxonomy ID ncbi_taxonomy_id	10923
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	605

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6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1knza_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.34 — NSP3 homodimer
Superfamily Superfamily superfamily	e.34.1 — NSP3 homodimer
Family Family family	e.34.1.1 — NSP3 homodimer

Domain ID domain_id	d1knzb1
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.34 — NSP3 homodimer
Superfamily Superfamily superfamily	e.34.1 — NSP3 homodimer
Family Family family	e.34.1.1 — NSP3 homodimer

Domain ID domain_id	d1knzb2
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	d1knzc_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.34 — NSP3 homodimer
Superfamily Superfamily superfamily	e.34.1 — NSP3 homodimer
Family Family family	e.34.1.1 — NSP3 homodimer

Domain ID domain_id	d1knzd1
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.34 — NSP3 homodimer
Superfamily Superfamily superfamily	e.34.1 — NSP3 homodimer
Family Family family	e.34.1.1 — NSP3 homodimer

Domain ID domain_id	d1knzd2
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	d1knzi_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.34 — NSP3 homodimer
Superfamily Superfamily superfamily	e.34.1 — NSP3 homodimer
Family Family family	e.34.1.1 — NSP3 homodimer

Domain ID domain_id	d1knzj1
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.34 — NSP3 homodimer
Superfamily Superfamily superfamily	e.34.1 — NSP3 homodimer
Family Family family	e.34.1.1 — NSP3 homodimer

Domain ID domain_id	d1knzj2
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	d1knzm_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.34 — NSP3 homodimer
Superfamily Superfamily superfamily	e.34.1 — NSP3 homodimer
Family Family family	e.34.1.1 — NSP3 homodimer

Domain ID domain_id	d1knzn1
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.34 — NSP3 homodimer
Superfamily Superfamily superfamily	e.34.1 — NSP3 homodimer
Family Family family	e.34.1.1 — NSP3 homodimer

Domain ID domain_id	d1knzn2
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	1knzA01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	280 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	20 — Rotavirus non-structural protein NSP3, N-terminal domain

Domain ID domain_id	1knzA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1610 —

Domain ID domain_id	1knzB01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	280 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	20 — Rotavirus non-structural protein NSP3, N-terminal domain

Domain ID domain_id	1knzB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1610 —

Domain ID domain_id	1knzC01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	280 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	20 — Rotavirus non-structural protein NSP3, N-terminal domain

Domain ID domain_id	1knzC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1610 —

Domain ID domain_id	1knzD01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	280 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	20 — Rotavirus non-structural protein NSP3, N-terminal domain

Domain ID domain_id	1knzD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1610 —

Domain ID domain_id	1knzI01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	280 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	20 — Rotavirus non-structural protein NSP3, N-terminal domain

Domain ID domain_id	1knzI02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1610 —

Domain ID domain_id	1knzJ01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	280 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	20 — Rotavirus non-structural protein NSP3, N-terminal domain

Domain ID domain_id	1knzJ02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1610 —

Domain ID domain_id	1knzM01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	280 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	20 — Rotavirus non-structural protein NSP3, N-terminal domain

Domain ID domain_id	1knzM02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1610 —

Domain ID domain_id	1knzN01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	280 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	20 — Rotavirus non-structural protein NSP3, N-terminal domain

Domain ID domain_id	1knzN02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	1610 —

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Unit-cell length a length_a	40.275 Å
Unit-cell length b length_b	85.359 Å
Unit-cell length c length_c	96.051 Å
Unit-cell angle α angle_alpha	89.99 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.05 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.450 Å
Low-resolution limit resolution_low	22.000 Å
R factor r_factor	—
R_work r_work	0.2280
R_free r_free	0.2800

Recognition of the rotavirus mRNA 3' consensus by an asymmetric NSP3 homodimer

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

Nonstructural RNA-binding Protein 34

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

1knz__assembly_1__model_1

1knz__assembly_1__model_1 | I(q)

1knz__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

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (12 domains)

CATH v4.4 (16 domains)

7. Citations (1)

Recognition of the rotavirus mRNA 3' consensus by an asymmetric NSP3 homodimer

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

Nonstructural RNA-binding Protein 34

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

1knz__assembly_1__model_1

1knz__assembly_1__model_1 | I(q)

1knz__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

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 28 domains

SCOP 2.08 (12 domains)

CATH v4.4 (16 domains)

7. Citations (1)