SAXSdb — 3p8b

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

;DNA-directed RNA polymerase, subunit e'' ;

Pyrococcus furiosus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Transcription antitermination protein nusG × 1 （Q8TZK1） ZINC ION × 1 BETA-MERCAPTOETHANOL × 4 GLYCEROL × 3 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Transcription antitermination protein nusG × 1 （Q8TZK1） ZINC ION × 1 BETA-MERCAPTOETHANOL × 2 GLYCEROL × 2 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Transcription antitermination protein nusG × 2 （Q8TZK1） ZINC ION × 2 BETA-MERCAPTOETHANOL × 6 GLYCEROL × 5 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8U440_PYRFU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–81； UniProt 1–61 Author chain C； PDBConstruct 21–81； UniProt 1–61

Transcription antitermination protein nusG

Pyrococcus furiosus

UniProt Q8TZK1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	;DNA-directed RNA polymerase, subunit e'' ; × 1 （Q8U440） ZINC ION × 1 BETA-MERCAPTOETHANOL × 4 GLYCEROL × 3 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	;DNA-directed RNA polymerase, subunit e'' ; × 1 （Q8U440） ZINC ION × 1 BETA-MERCAPTOETHANOL × 2 GLYCEROL × 2 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	;DNA-directed RNA polymerase, subunit e'' ; × 2 （Q8U440） ZINC ION × 2 BETA-MERCAPTOETHANOL × 6 GLYCEROL × 5 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8TZK1_PYRFU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–152； UniProt 1–152 Author chain D； PDBConstruct 1–152； UniProt 1–152

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	3p8b
Deposition date deposition_date	2010-10-13
Structure title title	X-ray crystal structure of Pyrococcus furiosus transcription elongation factor Spt4/5
Keywords keywords	transcription elongation factor, RNA polymerase, TRANSFERASE-TRANSCRIPTION complex; TRANSFERASE/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.

3p8b__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3p8b__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3p8b__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	25.12 Å
Rg (electron density)	24.41 Å
Total Rg	25.27 Å
Atom count	3294
Residues	414
Excluded volume	59708 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3p8b__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3p8b__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3p8b__assembly_3__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 (6)

Entity 1 Entity 1 polymer

Description description	;DNA-directed RNA polymerase, subunit e'' ;
Molecular weight formula_weight	9136.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	3405

MGSSHHHHHHSSGLVPRGSHMSEKACRHCHYITSEDRCPVCGSRDLSEEWFDLVIIVDVENSEIAKKIGAKVPGKYAIRVR

Source Source

Source organism organism	Pyrococcus furiosus
NCBI taxonomy ID ncbi_taxonomy_id	2261
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Transcription antitermination protein nusG
Molecular weight formula_weight	16816.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

MAGKIFAVRVTHGQEETTAKLIYSKVRTYNLPIYAILAPSRVKGYIFVEAPNKGVVDEAIRGIRHARGVLPGEVPFKEIEHFLEEKPAVSGLEPGDLVEVIAGPFKGQKAKVVKIDESKDEVVVQFIDAIVPIPVTIKGDYVRLISKLQKEE

Source Source

Source organism organism	Pyrococcus furiosus
NCBI taxonomy ID ncbi_taxonomy_id	2261
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	BETA-MERCAPTOETHANOL
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	111

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3p8ba_
Class class	g — Small proteins
Fold Fold fold	g.41 — Rubredoxin-like
Superfamily Superfamily superfamily	g.41.9 — RNA polymerase subunits
Family Family family	g.41.9.3 — RpoE2-like

Domain ID domain_id	d3p8bc_
Class class	g — Small proteins
Fold Fold fold	g.41 — Rubredoxin-like
Superfamily Superfamily superfamily	g.41.9 — RNA polymerase subunits
Family Family family	g.41.9.3 — RpoE2-like

CATH v4.4 (6 domains)

Domain ID domain_id	3p8bA00
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	28 — Rubrerythrin, domain 2
Homologous superfamily homologous superfamily	90 —

Domain ID domain_id	3p8bB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	940 — NusG, N-terminal domain

Domain ID domain_id	3p8bB02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	3p8bC00
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	28 — Rubrerythrin, domain 2
Homologous superfamily homologous superfamily	90 —

Domain ID domain_id	3p8bD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	940 — NusG, N-terminal domain

Domain ID domain_id	3p8bD02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	30 —

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Unit-cell length a length_a	40.532 Å
Unit-cell length b length_b	87.213 Å
Unit-cell length c length_c	133.107 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 2 21 21
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2393
R_work r_work	0.2364
R_free r_free	0.2923

X-ray crystal structure of Pyrococcus furiosus transcription elongation factor Spt4/5

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

;DNA-directed RNA polymerase, subunit e'' ;

State in the Current Structure

Other States of the Same Protein in the Database

Transcription antitermination protein nusG

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

3p8b__assembly_3__model_1

3p8b__assembly_3__model_1 | I(q)

3p8b__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

CATH v4.4 (6 domains)

7. Citations (1)

X-ray crystal structure of Pyrococcus furiosus transcription elongation factor Spt4/5

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

;DNA-directed RNA polymerase, subunit e'' ;

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Transcription antitermination protein nusG

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

3p8b__assembly_3__model_1

3p8b__assembly_3__model_1 | I(q)

3p8b__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (2 domains)

CATH v4.4 (6 domains)

7. Citations (1)