SAXSdb — 3d3c

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

N utilization substance protein B

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	30S ribosomal protein S10 × 1 （P0A7R5） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	30S ribosomal protein S10 × 1 （P0A7R5） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	30S ribosomal protein S10 × 1 （P0A7R5） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NUSB_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–141； UniProt 1–139 Author chain B； PDBConstruct 3–141； UniProt 1–139 Author chain C； PDBConstruct 3–141； UniProt 1–139

30S ribosomal protein S10

Escherichia coli

UniProt P0A7R5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	N utilization substance protein B × 1 （P0A780） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	N utilization substance protein B × 1 （P0A780） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	N utilization substance protein B × 1 （P0A780） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RS10_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain J； PDBConstruct 6–50； UniProt 1–45 Author chain J； PDBConstruct 52–87； UniProt 68–103 Author chain K； PDBConstruct 6–50； UniProt 1–45 Author chain K； PDBConstruct 52–87； UniProt 68–103 Author chain L； PDBConstruct 6–50； UniProt 1–45 Author chain L； PDBConstruct 52–87； UniProt 68–103

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	3d3c
Deposition date deposition_date	2008-05-09
Structure title title	Structural and functional analysis of the E. coli NusB-S10 transcription antitermination complex.
Keywords keywords	;NusB, S10, NusE, Nut, phage lambda, lambda N antitermination, rrn antitermination, transcription regulation, RNA-binding, Transcription, Transcription termination, Ribonucleoprotein, Ribosomal protein ;; TRANSCRIPTION
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.

3d3c__assembly_1__model_1

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

Download this curve (.dat)

3d3c__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3d3c__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.12 Å
Rg (electron density)	18.13 Å
Total Rg	19.22 Å
Atom count	1762
Residues	223
Excluded volume	31505 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3d3c__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3d3c__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3d3c__assembly_3__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	N utilization substance protein B
Molecular weight formula_weight	15838.1 kDa
Mutation mutation	K2E
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	5505

GAMEPAARRRARECAVQALYSWQLSQNDIADVEYQFLAEQDVKDVDVLYFRELLAGVATNTAYLDGLMKPYLSRLLEELGQVEKAVLRIALYELSKRSDVPYKVAINEAIELAKSFGAEDSHKFVNGVLDKAAPVIRPNKK

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	30S ribosomal protein S10
Molecular weight formula_weight	9652.2 kDa
Mutation mutation	A86D
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

GPLGSMQNQRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRSRTHLRLVDIVEPTEKTVDDLMRLDLAAGVDVQISLG

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
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	197

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6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d3d3ca_
Class class	a — All alpha proteins
Fold Fold fold	a.79 — NusB-like
Superfamily Superfamily superfamily	a.79.1 — NusB-like
Family Family family	a.79.1.1 — Antitermination factor NusB

Domain ID domain_id	d3d3cb_
Class class	a — All alpha proteins
Fold Fold fold	a.79 — NusB-like
Superfamily Superfamily superfamily	a.79.1 — NusB-like
Family Family family	a.79.1.1 — Antitermination factor NusB

Domain ID domain_id	d3d3cc_
Class class	a — All alpha proteins
Fold Fold fold	a.79 — NusB-like
Superfamily Superfamily superfamily	a.79.1 — NusB-like
Family Family family	a.79.1.1 — Antitermination factor NusB

CATH v4.4 (6 domains)

Domain ID domain_id	3d3cA00
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	3d3cB00
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	3d3cC00
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	3d3cJ00
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	3d3cK00
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	3d3cL00
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	113.000 Å
Unit-cell length b length_b	113.000 Å
Unit-cell length c length_c	267.200 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	I 41 2 2
Space-group number int_tables_number	98
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2208
R_work r_work	0.2177
R_free r_free	0.2799

Structural and functional analysis of the E. coli NusB-S10 transcription antitermination complex.

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

3d3c__assembly_1__model_1

3d3c__assembly_1__model_1 | I(q)

3d3c__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Structural and functional analysis of the E. coli NusB-S10 transcription antitermination complex.

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

3d3c__assembly_1__model_1

3d3c__assembly_1__model_1 | I(q)

3d3c__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

CATH v4.4 (6 domains)

7. Citations (1)