SAXSdb — 3r2d

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

N utilization substance protein B

Aquifex aeolicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 2 RNA 2	30S ribosomal protein S10 × 1 （O66430） 5'-R(GPGPCPUPCPCPUPUPGPGPCPA)-3' × 2 DI(HYDROXYETHYL)ETHER × 1 water × 4	Consistent with all polymers
2	Protein–RNA	Heteromer	Protein 2 RNA 2	30S ribosomal protein S10 × 1 （O66430） 5'-R(GPGPCPUPCPCPUPUPGPGPCPA)-3' × 2 DI(HYDROXYETHYL)ETHER × 4 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NUSB_AQUAE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–149； UniProt 1–148 Author chain B； PDBConstruct 2–149； UniProt 1–148

30S ribosomal protein S10

Aquifex aeolicus

UniProt O66430

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 2 RNA 2	N utilization substance protein B × 1 （O66530） 5'-R(GPGPCPUPCPCPUPUPGPGPCPA)-3' × 2 DI(HYDROXYETHYL)ETHER × 1 water × 4	Consistent with all polymers
2	Protein–RNA	Heteromer	Protein 2 RNA 2	N utilization substance protein B × 1 （O66530） 5'-R(GPGPCPUPCPCPUPUPGPGPCPA)-3' × 2 DI(HYDROXYETHYL)ETHER × 4 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS10_AQUAE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain J； PDBConstruct 2–47； UniProt 1–46 Author chain J； PDBConstruct 49–84； UniProt 69–104 Author chain K； PDBConstruct 2–47； UniProt 1–46 Author chain K； PDBConstruct 49–84； UniProt 69–104

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	3r2d
Deposition date deposition_date	2011-03-14
Structure title title	Crystal Structure of Antitermination Factors NusB and NusE in complex with dsRNA
Keywords keywords	;cross species NusB-NusE-RNA interaction, transcription elongation, gene regulation, protein-RNA interaction, TRANSCRIPTION-RNA complex ;; TRANSCRIPTION/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.

3r2d__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3r2d__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3r2d__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	20.70 Å
Rg (electron density)	19.50 Å
Total Rg	20.52 Å
Atom count	2211
Residues	237
Excluded volume	38520 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3r2d__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3r2d__assembly_2__model_1`	tetrameric （4）	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 (5)

Entity 1 Entity 1 polymer

Description description	N utilization substance protein B
Molecular weight formula_weight	17274.0 kDa
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	4032

MMRYRKGARDTAFLVLYRWDLRGENPGELFKEVVEEKNIKNKDAYEYAKKLVDTAVRHIEEIDSIIEKHLKGWSIDRLGYVERNALRLGVAELIFLKSKEPGRVFIDIVDLVKKYADEKAGKFVNGVLSAIYKAYITSSKEEKPSLKSE

Source Source

Source organism organism	Aquifex aeolicus
NCBI taxonomy ID ncbi_taxonomy_id	63363
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	30S ribosomal protein S10
Molecular weight formula_weight	9558.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J,K

GMEQEKIRIKLRAYDHRLLDQSVKQIIETVKRTGGVVKGPIPLPTRKSEFSRILDIIRFTPQTIEALMEISLPAGVDVEVKMRG

Source Source

Source organism organism	Aquifex aeolicus
NCBI taxonomy ID ncbi_taxonomy_id	63363
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	5'-R(GPGPCPUPCPCPUPUPGPGPCPA)-3'
Molecular weight formula_weight	3804.3 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	R,S

GGCUCCUUGGCA

Entity 4 Entity 4 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	98

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3r2dA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	940 — N-utilizing Substance Protein B Homolog; Chain A
Homologous superfamily homologous superfamily	10 — NusB-like

Domain ID domain_id	3r2dB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	940 — N-utilizing Substance Protein B Homolog; Chain A
Homologous superfamily homologous superfamily	10 — NusB-like

Domain ID domain_id	3r2dJ00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	600 — Ribosomal protein S10

Domain ID domain_id	3r2dK00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	600 — Ribosomal protein S10

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Unit-cell length a length_a	76.786 Å
Unit-cell length b length_b	79.940 Å
Unit-cell length c length_c	106.599 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.199 Å
Low-resolution limit resolution_low	33.642 Å
R factor r_factor	0.2033
R_work r_work	0.2013
R_free r_free	0.2390

Crystal Structure of Antitermination Factors NusB and NusE in complex with dsRNA

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

N utilization substance protein B

State in the Current Structure

Other States of the Same Protein in the Database

30S ribosomal protein S10

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

3r2d__assembly_2__model_1

3r2d__assembly_2__model_1 | I(q)

3r2d__assembly_2__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of Antitermination Factors NusB and NusE in complex with dsRNA

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

N utilization substance protein B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

30S ribosomal protein S10

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

3r2d__assembly_2__model_1

3r2d__assembly_2__model_1 | I(q)

3r2d__assembly_2__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)