2fu3

Crystal structure of gephyrin E-domain

Method: X-RAY DIFFRACTION

▼

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

gephyrin

Rattus norvegicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GEPH_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–419； UniProt 350–768 Author chain B； PDBConstruct 1–419； UniProt 350–768

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	2fu3
Deposition date deposition_date	2006-01-25
Structure title title	Crystal structure of gephyrin E-domain
Keywords keywords	Glycine receptor, gephyrin, neuroreceptor anchoring, BIOSYNTHETIC PROTEIN-STRUCTURAL PROTEIN COMPLEX; BIOSYNTHETIC PROTEIN/STRUCTURAL PROTEIN
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.

2fu3__assembly_1__model_1

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

Download this curve (.dat)

2fu3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2fu3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.94 Å
Rg (electron density)	31.38 Å
Total Rg	31.72 Å
Atom count	6191
Residues	824
Excluded volume	110660 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2fu3__assembly_1__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 (2)

▼

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2fu3a1
Class class	b — All beta proteins
Fold Fold fold	b.85 — beta-clip
Superfamily Superfamily superfamily	b.85.6 — MoeA C-terminal domain-like
Family Family family	b.85.6.1 — MoeA C-terminal domain-like

Domain ID domain_id	d2fu3a2
Class class	b — All beta proteins
Fold Fold fold	b.103 — MoeA N-terminal region -like
Superfamily Superfamily superfamily	b.103.1 — MoeA N-terminal region -like
Family Family family	b.103.1.1 — MoeA N-terminal region -like

Domain ID domain_id	d2fu3a3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.57 — Molybdenum cofactor biosynthesis proteins
Superfamily Superfamily superfamily	c.57.1 — Molybdenum cofactor biosynthesis proteins
Family Family family	c.57.1.2 — MoeA central domain-like

Domain ID domain_id	d2fu3b1
Class class	b — All beta proteins
Fold Fold fold	b.85 — beta-clip
Superfamily Superfamily superfamily	b.85.6 — MoeA C-terminal domain-like
Family Family family	b.85.6.1 — MoeA C-terminal domain-like

Domain ID domain_id	d2fu3b2
Class class	b — All beta proteins
Fold Fold fold	b.103 — MoeA N-terminal region -like
Superfamily Superfamily superfamily	b.103.1 — MoeA N-terminal region -like
Family Family family	b.103.1.1 — MoeA N-terminal region -like

Domain ID domain_id	d2fu3b3
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.57 — Molybdenum cofactor biosynthesis proteins
Superfamily Superfamily superfamily	c.57.1 — Molybdenum cofactor biosynthesis proteins
Family Family family	c.57.1.2 — MoeA central domain-like

CATH v4.4 (8 domains)

Domain ID domain_id	2fu3A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	980 — Molybdenum Cofactor Biosythetic Enzyme; Chain A
Homologous superfamily homologous superfamily	10 — MoaB/Mog-like domain

Domain ID domain_id	2fu3A02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	105 — Molybdopterin biosynthesis moea protein, domain 2
Homologous superfamily homologous superfamily	10 — Molybdopterin biosynthesis moea protein, domain 2

Domain ID domain_id	2fu3A03
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	190 — Molybdopterin biosynthesis moeA protein; domain 3
Homologous superfamily homologous superfamily	11 — Molybdopterin biosynthesis moea protein, domain 3.

Domain ID domain_id	2fu3A04
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	340 — Beta-clip
Homologous superfamily homologous superfamily	10 — MoeA, C-terminal, domain IV

Domain ID domain_id	2fu3B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	980 — Molybdenum Cofactor Biosythetic Enzyme; Chain A
Homologous superfamily homologous superfamily	10 — MoaB/Mog-like domain

Domain ID domain_id	2fu3B02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	105 — Molybdopterin biosynthesis moea protein, domain 2
Homologous superfamily homologous superfamily	10 — Molybdopterin biosynthesis moea protein, domain 2

Domain ID domain_id	2fu3B03
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	190 — Molybdopterin biosynthesis moeA protein; domain 3
Homologous superfamily homologous superfamily	11 — Molybdopterin biosynthesis moea protein, domain 3.

Domain ID domain_id	2fu3B04
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	340 — Beta-clip
Homologous superfamily homologous superfamily	10 — MoeA, C-terminal, domain IV

▶

Unit-cell length a length_a	108.820 Å
Unit-cell length b length_b	156.195 Å
Unit-cell length c length_c	51.362 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 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2020
R_free r_free	0.2730

Description description	gephyrin
Molecular weight formula_weight	45652.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6257

Crystal structure of gephyrin E-domain

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

gephyrin

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

2fu3__assembly_1__model_1

2fu3__assembly_1__model_1 | I(q)

2fu3__assembly_1__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Source organism organism	Rattus norvegicus
Common name common_name	Norway rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	66

Crystal structure of gephyrin E-domain

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

gephyrin

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

2fu3__assembly_1__model_1

2fu3__assembly_1__model_1 | I(q)

2fu3__assembly_1__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. Citations (1)