6ssi

Structure of the pentameric ligand-gated ion channel ELIC in complex with a PAM nanobody

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 22 × 5 GAMMA-AMINO-BUTANOIC ACID × 5 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 5 GLYCEROL × 6 CALCIUM ION × 5 TETRAETHYLENE GLYCOL × 4 UNDECYL-MALTOSIDE × 5 ACETATE ION × 2 water × 9	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
Chains and sequence ranges	Author chain A； PDBConstruct 4–317； UniProt 8–320 Author chain B； PDBConstruct 4–317； UniProt 8–320 Author chain C； PDBConstruct 4–317； UniProt 8–320 Author chain D； PDBConstruct 4–317； UniProt 8–320 Author chain E； PDBConstruct 4–317； UniProt 8–320

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	6ssi
Deposition date deposition_date	2019-09-07
Structure title title	Structure of the pentameric ligand-gated ion channel ELIC in complex with a PAM nanobody
Keywords keywords	ION CHANNEL, CYS-LOOP RECEPTOR, PENTAMERIC LIGAND GATED ION CHANNEL, LGIC, ELIC, NANOBODY, TRANSPORT PROTEIN; TRANSPORT 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.

6ssi__assembly_1__model_1

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

Download this curve (.dat)

6ssi__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6ssi__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.27 Å
Rg (electron density)	42.32 Å
Total Rg	42.72 Å
Atom count	16779
Residues	2081
Excluded volume	299630 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6ssi__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 (10)

Entity 1 Entity 1 polymer

Description description	Cys-loop ligand-gated ion channel
Molecular weight formula_weight	36465.6 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E
Atom count atom_count	16941

GPVDARPVDVSVSIFINKIYGVNTLEQTYKVDGYIVAQWTGKPRKTPGDKPLIVENTQIERWINNGLWVPALEFINVVGSPDTGNKRLMLFPDGRVIYNARFLGSFSNDMDFRLFPFDRQQFVLELEPFSYNNQQLRFSDIQVYTENIDNEEIDEWWIRGKASTHISDIRYDHLSSVQPNQNEFSRITVRIDAVRNPSYYLWSFILPLGLIIAASWSVFWLESFSERLQTSFTLMLTVVAYAFYTSNILPRLPYTTVIDQMIIAGYGSIFAAILLIIFAHHRQANGVEDDLLIQRCRLAFPLGFLAIGCVLVIRGITG

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	NANOBODY 22
Molecular weight formula_weight	13316.7 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

QVQLQESGGGLAQAGGSMRLSCIASGRNFFINIMNWYRQAPGKQRELVAQITRAGTTTYADSVKGRFTISRDNAKNTVYLQMSTLQSEDTAVYYCNVGASWGQGTQVTVSSHHHHHHEPEA

Source Source

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

Entity 3 Entity 3 non-polymer

Description description	GAMMA-AMINO-BUTANOIC ACID
Molecular weight formula_weight	103.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 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	5

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	6

Entity 6 Entity 6 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 7 Entity 7 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 non-polymer

Description description	UNDECYL-MALTOSIDE
Molecular weight formula_weight	496.6 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 9 Entity 9 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	nat
Copy count entity_count	2

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	145

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6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (13 domains)

Domain ID domain_id	d6ssif1
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	d6ssif2
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	d6ssig1
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	d6ssig2
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	d6ssig3
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	d6ssih1
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	d6ssih2
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	d6ssih3
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	d6ssii1
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	d6ssii2
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	d6ssii3
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	d6ssij1
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	d6ssij2
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	105.604 Å
Unit-cell length b length_b	146.563 Å
Unit-cell length c length_c	140.242 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.39 °
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	2.590 Å
Low-resolution limit resolution_low	47.060 Å
R factor r_factor	0.2310
R_work r_work	0.2300
R_free r_free	0.2460

Structure of the pentameric ligand-gated ion channel ELIC in complex with a PAM nanobody

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6ssi__assembly_1__model_1

6ssi__assembly_1__model_1 | I(q)

6ssi__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 (10)

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 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (13 domains)

7. Citations (1)

Structure of the pentameric ligand-gated ion channel ELIC in complex with a PAM nanobody

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

6ssi__assembly_1__model_1

6ssi__assembly_1__model_1 | I(q)

6ssi__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 (10)

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 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (13 domains)

7. Citations (1)