SAXSdb — 3lpe

▼

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

Putative transcription antitermination protein nusG

Methanocaldococcus jannaschii

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 （Q57839） ZINC ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	;DNA-directed RNA polymerase subunit E'' ; × 1 （Q57839） ZINC ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	;DNA-directed RNA polymerase subunit E'' ; × 1 （Q57839） ZINC ION × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	;DNA-directed RNA polymerase subunit E'' ; × 1 （Q57839） ZINC ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NUSG_METJA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 11–92； UniProt 1–82 Author chain C； PDBConstruct 11–92； UniProt 1–82 Author chain E； PDBConstruct 11–92； UniProt 1–82 Author chain G； PDBConstruct 11–92； UniProt 1–82

;DNA-directed RNA polymerase subunit E'' ;

Methanocaldococcus jannaschii

UniProt Q57839

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Putative transcription antitermination protein nusG × 1 （Q57818） ZINC ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Putative transcription antitermination protein nusG × 1 （Q57818） ZINC ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Putative transcription antitermination protein nusG × 1 （Q57818） ZINC ION × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Putative transcription antitermination protein nusG × 1 （Q57818） ZINC ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOE2_METJA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–59； UniProt 1–59 Author chain D； PDBConstruct 1–59； UniProt 1–59 Author chain F； PDBConstruct 1–59； UniProt 1–59 Author chain H； PDBConstruct 1–59； UniProt 1–59

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3lpe
Deposition date deposition_date	2010-02-05
Structure title title	Crystal structure of Spt4/5NGN heterodimer complex from Methanococcus jannaschii
Keywords keywords	;Transcription Regulation, Spt4, Spt5, NusG, Archaea, evolution, DNA-directed RNA polymerase, Metal-binding, Nucleotidyltransferase, Transcription, Transferase, Zinc-finger ;; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

3lpe__assembly_1__model_1

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

Download this curve (.dat)

3lpe__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3lpe__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.25 Å
Rg (electron density)	14.81 Å
Total Rg	16.02 Å
Atom count	1099
Residues	143
Excluded volume	20001 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3lpe__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3lpe__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3lpe__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3lpe__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Putative transcription antitermination protein nusG
Molecular weight formula_weight	9935.5 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	4745

GSRRASVGAHMIFAVRTMVGQEKNIAGLMASRAEKEQLDVYSILASESLKGYVLVEAETKGDVEELIKGMPRVRGIVPGTIAIEEIEPLLTP

Source Source

Source organism organism	Methanocaldococcus jannaschii
Common name common_name	Methanococcus jannaschii
NCBI taxonomy ID ncbi_taxonomy_id	2190
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;DNA-directed RNA polymerase subunit E'' ;
Molecular weight formula_weight	6587.8 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

MRACLKCKYLTNDEICPICHSPTSENWIGLLIVINPEKSEIAKKAGIDIKGKYALSVKE

Source Source

Source organism organism	Methanocaldococcus jannaschii
Common name common_name	Methanococcus jannaschii
NCBI taxonomy ID ncbi_taxonomy_id	2190
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	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	349

▼

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3lpeb_
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.41.9.0 — automated matches

Domain ID domain_id	d3lped_
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.41.9.0 — automated matches

Domain ID domain_id	d3lpef_
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.41.9.0 — automated matches

Domain ID domain_id	d3lpeh_
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.41.9.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id	3lpeA00
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	3lpeB00
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	3lpeC00
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	3lpeD00
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	3lpeE00
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	3lpeF00
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	3lpeG00
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	3lpeH00
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	28 — Rubrerythrin, domain 2
Homologous superfamily homologous superfamily	90 —

▶

Unit-cell length a length_a	64.360 Å
Unit-cell length b length_b	63.970 Å
Unit-cell length c length_c	83.040 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	106.98 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	44.355 Å
R factor r_factor	0.2100
R_work r_work	0.2076
R_free r_free	0.2549

Crystal structure of Spt4/5NGN heterodimer complex from Methanococcus jannaschii

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

Putative transcription antitermination protein nusG

State in the Current Structure

Other States of the Same Protein in the Database

;DNA-directed RNA polymerase subunit E'' ;

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

3lpe__assembly_1__model_1

3lpe__assembly_1__model_1 | I(q)

3lpe__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of Spt4/5NGN heterodimer complex from Methanococcus jannaschii

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

Putative 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

;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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3lpe__assembly_1__model_1

3lpe__assembly_1__model_1 | I(q)

3lpe__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)