2nuu

Regulating the Escherichia coli ammonia channel: the crystal structure of the AmtB-GlnK complex

Method: X-RAY DIFFRACTION

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

Ammonia channel

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Nitrogen regulatory protein P-II 2 × 3 （P0AC55） ADENOSINE-5'-DIPHOSPHATE × 3 water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Nitrogen regulatory protein P-II 2 × 3 （P0AC55） ADENOSINE-5'-DIPHOSPHATE × 3 water × 6	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 12	Nitrogen regulatory protein P-II 2 × 6 （P0AC55） ADENOSINE-5'-DIPHOSPHATE × 6 water × 12	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 12	Nitrogen regulatory protein P-II 2 × 6 （P0AC55） ADENOSINE-5'-DIPHOSPHATE × 6 water × 12	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 12	Nitrogen regulatory protein P-II 2 × 6 （P0AC55） ADENOSINE-5'-DIPHOSPHATE × 6 water × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AMTB_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 12–415； UniProt 25–428 Author chain B； PDBConstruct 12–415； UniProt 25–428 Author chain C； PDBConstruct 12–415； UniProt 25–428 Author chain D； PDBConstruct 12–415； UniProt 25–428 Author chain E； PDBConstruct 12–415； UniProt 25–428 Author chain F； PDBConstruct 12–415； UniProt 25–428

Nitrogen regulatory protein P-II 2

Escherichia coli

UniProt P0AC55

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 6	Ammonia channel × 3 （P69681） ADENOSINE-5'-DIPHOSPHATE × 3 water × 6	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 6	Ammonia channel × 3 （P69681） ADENOSINE-5'-DIPHOSPHATE × 3 water × 6	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 12	Ammonia channel × 6 （P69681） ADENOSINE-5'-DIPHOSPHATE × 6 water × 12	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 12	Ammonia channel × 6 （P69681） ADENOSINE-5'-DIPHOSPHATE × 6 water × 12	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 12	Ammonia channel × 6 （P69681） ADENOSINE-5'-DIPHOSPHATE × 6 water × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GLNK_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain G； PDBConstruct 1–112； UniProt 1–112 Author chain H； PDBConstruct 1–112； UniProt 1–112 Author chain I； PDBConstruct 1–112； UniProt 1–112 Author chain J； PDBConstruct 1–112； UniProt 1–112 Author chain K； PDBConstruct 1–112； UniProt 1–112 Author chain L； PDBConstruct 1–112； UniProt 1–112

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	2nuu
Deposition date deposition_date	2006-11-09
Structure title title	Regulating the Escherichia coli ammonia channel: the crystal structure of the AmtB-GlnK complex
Keywords keywords	Membrane protein complex, nitrogen regulation, ammonia transport, TRANSPORT PROTEIN-SIGNALING PROTEIN COMPLEX; TRANSPORT PROTEIN/SIGNALING PROTEIN
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.

2nuu__assembly_5__model_1

Assembly 5 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2nuu__assembly_5__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2nuu__assembly_5__model_1 | P(r) · Pending

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

Rg（Guinier）	47.62 Å
Rg (electron density)	47.12 Å
Total Rg	47.36 Å
Atom count	23476
Residues	3127
Excluded volume	425010 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2nuu__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2nuu__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2nuu__assembly_3__model_1`	dodecameric （12）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2nuu__assembly_4__model_1`	dodecameric （12）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2nuu__assembly_5__model_1`	dodecameric （12）	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 (4)

Entity 1 Entity 1 polymer

Description description	Ammonia channel
Molecular weight formula_weight	43397.7 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	24026

APAVAHHHHHHAVADKADNAFMMICTALVLFMTIPGIALFYGGLIRGKNVLSMLTQVTVTFALVCILWVVYGYSLAFGEGNNFFGNINWLMLKNIELTAVMGSIYQYIHVAFQGSFACITVGLIVGALAERIRFSAVLIFVVVWLTLSYIPIAHMVWGGGLLASHGALDFAGGTVVHINAAIAGLVGAYLIGKRVGFGKEAFKPHNLPMVFTGTAILYIGWFGFNAGSAGTANEIAALAFVNTVVATAAAILGWIFGEWALRGKPSLLGACSGAIAGLVGVTPACGYIGVGGALIIGVVAGLAGLWGVTMLKRLLRVDDPCDVFGVHGVCGIVGCIMTGIFAASSLGGVGFAEGVTMGHQLLVQLESIAITIVWSGVVAFIGYKLADLTVGLRVPEEQEREGLDVNSHGENAYNA

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Nitrogen regulatory protein P-II 2
Molecular weight formula_weight	12276.2 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

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

MKLVTVIIKPFKLEDVREALSSIGIQGLTVTEVKGFGRQKGHAELYRGAEYSVNFLPKVKIDVAIADDQLDEVIDIVSKAAYTGKIGDGKIFVAELQRVIRIRTGEADEAAL

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	550

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6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (18 domains)

Domain ID domain_id	d2nuua2
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.44 — Ammonium transporter
Superfamily Superfamily superfamily	f.44.1 — Ammonium transporter
Family Family family	f.44.1.0 — automated matches

Domain ID domain_id	d2nuua3
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	d2nuub2
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.44 — Ammonium transporter
Superfamily Superfamily superfamily	f.44.1 — Ammonium transporter
Family Family family	f.44.1.0 — automated matches

Domain ID domain_id	d2nuub3
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	d2nuuc2
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.44 — Ammonium transporter
Superfamily Superfamily superfamily	f.44.1 — Ammonium transporter
Family Family family	f.44.1.0 — automated matches

Domain ID domain_id	d2nuuc3
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	d2nuud2
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.44 — Ammonium transporter
Superfamily Superfamily superfamily	f.44.1 — Ammonium transporter
Family Family family	f.44.1.0 — automated matches

Domain ID domain_id	d2nuud3
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	d2nuue2
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.44 — Ammonium transporter
Superfamily Superfamily superfamily	f.44.1 — Ammonium transporter
Family Family family	f.44.1.0 — automated matches

Domain ID domain_id	d2nuue3
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	d2nuuf2
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.44 — Ammonium transporter
Superfamily Superfamily superfamily	f.44.1 — Ammonium transporter
Family Family family	f.44.1.0 — automated matches

Domain ID domain_id	d2nuuf3
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	d2nuug_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.5 — GlnB-like
Family Family family	d.58.5.1 — Prokaryotic signal transducing protein

Domain ID domain_id	d2nuuh_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.5 — GlnB-like
Family Family family	d.58.5.1 — Prokaryotic signal transducing protein

Domain ID domain_id	d2nuui_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.5 — GlnB-like
Family Family family	d.58.5.1 — Prokaryotic signal transducing protein

Domain ID domain_id	d2nuuj_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.5 — GlnB-like
Family Family family	d.58.5.1 — Prokaryotic signal transducing protein

Domain ID domain_id	d2nuuk_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.5 — GlnB-like
Family Family family	d.58.5.1 — Prokaryotic signal transducing protein

Domain ID domain_id	d2nuul_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.5 — GlnB-like
Family Family family	d.58.5.1 — Prokaryotic signal transducing protein

CATH v4.4 (12 domains)

Domain ID domain_id	2nuuA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3430 — Ammonium transporter fold
Homologous superfamily homologous superfamily	10 — Ammonium transporter AmtB like domains

Domain ID domain_id	2nuuB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3430 — Ammonium transporter fold
Homologous superfamily homologous superfamily	10 — Ammonium transporter AmtB like domains

Domain ID domain_id	2nuuC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3430 — Ammonium transporter fold
Homologous superfamily homologous superfamily	10 — Ammonium transporter AmtB like domains

Domain ID domain_id	2nuuD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3430 — Ammonium transporter fold
Homologous superfamily homologous superfamily	10 — Ammonium transporter AmtB like domains

Domain ID domain_id	2nuuE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3430 — Ammonium transporter fold
Homologous superfamily homologous superfamily	10 — Ammonium transporter AmtB like domains

Domain ID domain_id	2nuuF00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3430 — Ammonium transporter fold
Homologous superfamily homologous superfamily	10 — Ammonium transporter AmtB like domains

Domain ID domain_id	2nuuG00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	2nuuH00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	2nuuI00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	2nuuJ00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	2nuuK00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	120 —

Domain ID domain_id	2nuuL00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	120 —

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Unit-cell length a length_a	99.691 Å
Unit-cell length b length_b	107.865 Å
Unit-cell length c length_c	280.162 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	24

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.1751
R_work r_work	0.1712
R_free r_free	0.2494

Regulating the Escherichia coli ammonia channel: the crystal structure of the AmtB-GlnK complex

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

Ammonia channel

State in the Current Structure

Other States of the Same Protein in the Database

Nitrogen regulatory protein P-II 2

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

2nuu__assembly_5__model_1

2nuu__assembly_5__model_1 | I(q)

2nuu__assembly_5__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) 30 domains

SCOP 2.08 (18 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Regulating the Escherichia coli ammonia channel: the crystal structure of the AmtB-GlnK complex

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

Ammonia channel

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Nitrogen regulatory protein P-II 2

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

2nuu__assembly_5__model_1

2nuu__assembly_5__model_1 | I(q)

2nuu__assembly_5__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) 30 domains

SCOP 2.08 (18 domains)

CATH v4.4 (12 domains)

7. Citations (1)