6hjx

X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) 7'C pore mutant (L238C) in complex with nanobody 72

Method: X-RAY DIFFRACTION

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

Cys-loop ligand-gated ion channel

Dickeya chrysanthemi

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 10	nanobody 72 × 5 HEXAETHYLENE GLYCOL × 4 PHOSPHATIDYLETHANOLAMINE × 1 DODECYL-BETA-D-MALTOSIDE × 5 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 SODIUM ION × 1 water × 10	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ELIC_DICCH
Isoform	—
PDB entities	1, 2, 3, 4, 5
Chains and sequence ranges	Author chain A； PDBConstruct 1–306； UniProt 9–313 Author chain B； PDBConstruct 3–309； UniProt 8–313 Author chain C； PDBConstruct 3–312； UniProt 8–316 Author chain D； PDBConstruct 1–310； UniProt 9–317 Author chain E； PDBConstruct 1–307； UniProt 8–313

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	6hjx
Deposition date deposition_date	2018-09-04
Structure title title	X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) 7'C pore mutant (L238C) in complex with nanobody 72
Keywords keywords	ion channel, pentameric ligand-gated ion channel, cya-loop receptor, MEMBRANE PROTEIN; MEMBRANE 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.

6hjx__assembly_1__model_1

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

Download this curve (.dat)

6hjx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6hjx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.53 Å
Rg (electron density)	39.56 Å
Total Rg	40.10 Å
Atom count	16830
Residues	2131
Excluded volume	299840 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6hjx__assembly_1__model_1`	decameric （10）	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 (12)

Entity 1 Entity 1 polymer

Description description	Cys-loop ligand-gated ion channel
Molecular weight formula_weight	35244.1 kDa
Mutation mutation	C300S, C313S, L238C
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	17226

ARPVDVSVSIFINKIYGVNTLEQTYKVDGYIVAQWTGKPRKTPGDKPLIVENTQIERWINNGLWVPALEFINVVGSPDTGNKRLMLFPDGRVIYNARFLGSFSNDMDFRLFPFDRQQFVLELEPFSYNNQQLRFSDIQVYTENIDNEEIDEWWIRGKASTHISDIRYDHLSSVQPNQNEFSRITVRIDAVRNPSYYLWSFILPLGLIIAASWSVFWLESFSERLQTSFTCMLTVVAYAFYTSNILPRLPYTTVIDQMIIAGYGSIFAAILLIIFAHHRQANGVEDDLLIQRSRLAFPLGFLAIGSV

Source Source

Source organism organism	Dickeya chrysanthemi
Common name common_name	Pectobacterium chrysanthemi
NCBI taxonomy ID ncbi_taxonomy_id	556
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Cys-loop ligand-gated ion channel
Molecular weight formula_weight	35555.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

PVDARPVDVSVSIFINKIYGVNTLEQTYKVDGYIVAQWTGKPRKTPGDKPLIVENTQIERWINNGLWVPALEFINVVGSPDTGNKRLMLFPDGRVIYNARFLGSFSNDMDFRLFPFDRQQFVLELEPFSYNNQQLRFSDIQVYTENIDNEEIDEWWIRGKASTHISDIRYDHLSSVQPNQNEFSRITVRIDAVRNPSYYLWSFILPLGLIIAASWSVFWLESFSERLQTSFTCMLTVVAYAFYTSNILPRLPYTTVIDQMIIAGYGSIFAAILLIIFAHHRQANGVEDDLLIQRSRLAFPLGFLAIGSV

Source Source

Source organism organism	Dickeya chrysanthemi
Common name common_name	Pectobacterium chrysanthemi
NCBI taxonomy ID ncbi_taxonomy_id	556
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Cys-loop ligand-gated ion channel
Molecular weight formula_weight	35880.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

Source Source

Source organism organism	Dickeya chrysanthemi
Common name common_name	Pectobacterium chrysanthemi
NCBI taxonomy ID ncbi_taxonomy_id	556
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Cys-loop ligand-gated ion channel
Molecular weight formula_weight	35726.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

Source Source

Source organism organism	Dickeya chrysanthemi
Common name common_name	Pectobacterium chrysanthemi
NCBI taxonomy ID ncbi_taxonomy_id	556
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	Cys-loop ligand-gated ion channel
Molecular weight formula_weight	35359.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

DARPVDVSVSIFINKIYGVNTLEQTYKVDGYIVAQWTGKPRKTPGDKPLIVENTQIERWINNGLWVPALEFINVVGSPDTGNKRLMLFPDGRVIYNARFLGSFSNDMDFRLFPFDRQQFVLELEPFSYNNQQLRFSDIQVYTENIDNEEIDEWWIRGKASTHISDIRYDHLSSVQPNQNEFSRITVRIDAVRNPSYYLWSFILPLGLIIAASWSVFWLESFSERLQTSFTCMLTVVAYAFYTSNILPRLPYTTVIDQMIIAGYGSIFAAILLIIFAHHRQANGVEDDLLIQRSRLAFPLGFLAIGSV

Source Source

Source organism organism	Dickeya chrysanthemi
Common name common_name	Pectobacterium chrysanthemi
NCBI taxonomy ID ncbi_taxonomy_id	556
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	nanobody 72
Molecular weight formula_weight	13368.0 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

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

QVQLQESGGGLVQAGGSLRLSCAASGRIFSTNVMGWFRQAPGKEREFVATVGRIGGSTVYADFVKGRFTLSRDNAKNMVYLQMNSLKPEDTAVYYCGARIGGSDRLAPENYGYWGQGTQVTVSS

Source Source

Source organism organism	Lama glama
NCBI taxonomy ID ncbi_taxonomy_id	9844
Host organism host_organism	Escherichia coli

Entity 7 Entity 7 non-polymer

Description description	HEXAETHYLENE GLYCOL
Molecular weight formula_weight	282.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 non-polymer

Description description	PHOSPHATIDYLETHANOLAMINE
Molecular weight formula_weight	734.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	DODECYL-BETA-D-MALTOSIDE
Molecular weight formula_weight	510.6 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 10 Entity 10 non-polymer

Description description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Molecular weight formula_weight	195.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 11 Entity 11 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 12 Entity 12 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	308

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d6hjxf1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d6hjxf2
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	d6hjxg1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d6hjxg2
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	d6hjxh1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d6hjxh2
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	d6hjxi1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d6hjxi2
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	d6hjxj1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d6hjxj2
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

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Unit-cell length a length_a	96.251 Å
Unit-cell length b length_b	156.277 Å
Unit-cell length c length_c	102.496 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.88 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	10

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

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	47.587 Å
R factor r_factor	0.2063
R_work r_work	0.2042
R_free r_free	0.2451

X-ray structure of a pentameric ligand gated ion channel from Erwinia chrysanthemi (ELIC) 7'C pore mutant (L238C) in complex with nanobody 72

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

Cys-loop ligand-gated ion 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6hjx__assembly_1__model_1

6hjx__assembly_1__model_1 | I(q)

6hjx__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 (12)

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

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (10 domains)

7. Citations (1)