1t3e

Structural basis of dynamic glycine receptor clustering

Method: X-RAY DIFFRACTION

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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 heterocomplex	Heteromer	Protein 3	49-mer fragment of Glycine receptor beta chain × 1 （P20781） SULFATE ION × 8	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 1–421； UniProt 348–768 Author chain B； PDBConstruct 1–421； UniProt 348–768

49-mer fragment of Glycine receptor beta chain

Rattus norvegicus

UniProt P20781

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Gephyrin × 2 （Q03555） SULFATE ION × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GLRB_RAT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain P； PDBConstruct 1–49； UniProt 378–426

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	1t3e
Deposition date deposition_date	2004-04-26
Structure title title	Structural basis of dynamic glycine receptor clustering
Keywords keywords	alfa-beta, STRUCTURAL PROTEIN-SIGNALING PROTEIN COMPLEX; STRUCTURAL 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.

1t3e__assembly_1__model_1

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

Download this curve (.dat)

1t3e__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1t3e__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.45 Å
Rg (electron density)	32.12 Å
Total Rg	32.44 Å
Atom count	6243
Residues	822
Excluded volume	111270 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1t3e__assembly_1__model_1`	trimeric （3）	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 (3)

Entity 1 Entity 1 polymer

Description description	Gephyrin
Molecular weight formula_weight	45947.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6243

HRMSPFPLTSMDKAFITVLEMTPVLGTEIINYRDGMGRVLAQDVYAKDNLPPFPASVKDGYAVRAADGPGDRFIIGESQAGEQPTQTVMPGQVMRVTTGAPIPCGADAVVQVEDTELIRESDDGTEELEVRILVQARPGQDIRPIGHDIKRGECVLAKGTHMGPSEIGLLATVGVTEVEVNKFPVVAVMSTGNELLNPEDDLLPGKIRDSNRSTLLATIQEHGYPTINLGIVGDNPDDLLNALNEGISRADVIITSGGVSMGEKDYLKQVLDIDLHAQIHFGRVFMKPGLPTTFATLDIDGVRKIIFALPGNPVSAVVTCNLFVVPALRKMQGILDPRPTIIKARLSCDVKLDPRPEYHRCILTWHHQEPLPWAQSTGNQMSSRLMSMRSANGLLMLPPKTEQYVELHKGEVVDVMVIGRL

Source Source

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

Entity 2 Entity 2 polymer

Description description	49-mer fragment of Glycine receptor beta chain
Molecular weight formula_weight	5128.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

GNAAKKNTVNGTGTPVHISTLQVGETRCKKVCTSKSDLRSNDFSIVGSL

Source Source

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

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	8

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1t3ea1
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	d1t3ea2
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	d1t3ea3
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	d1t3eb1
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	d1t3eb2
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	d1t3eb3
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	1t3eA01
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	1t3eA02
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	1t3eA03
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	1t3eA04
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	1t3eB01
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	1t3eB02
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	1t3eB03
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	1t3eB04
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

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Unit-cell length a length_a	161.547 Å
Unit-cell length b length_b	161.547 Å
Unit-cell length c length_c	126.252 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	3.250 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2458
R_work r_work	0.2429
R_free r_free	0.3031

Structural basis of dynamic glycine receptor clustering

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

49-mer fragment of Glycine receptor beta chain

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

1t3e__assembly_1__model_1

1t3e__assembly_1__model_1 | I(q)

1t3e__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Structural basis of dynamic glycine receptor clustering

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

49-mer fragment of Glycine receptor beta chain

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

1t3e__assembly_1__model_1

1t3e__assembly_1__model_1 | I(q)

1t3e__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

CATH v4.4 (8 domains)

7. Citations (1)