SAXSdb — 2v5e

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

GDNF FAMILY RECEPTOR ALPHA-1

RATTUS NORVEGICUS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 4 其他Polymer 2	GLIAL CELL LINE-DERIVED NEUROTROPHIC FACTOR × 2 （P39905） 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose-(2-1)-2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose × 2 1,2-ETHANEDIOL × 8 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GFRA1_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–200； UniProt 150–349

GLIAL CELL LINE-DERIVED NEUROTROPHIC FACTOR

HOMO SAPIENS

UniProt P39905

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 4 其他Polymer 2	GDNF FAMILY RECEPTOR ALPHA-1 × 2 （Q62997） 1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose-(2-1)-2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose × 2 1,2-ETHANEDIOL × 8 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GDNF_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–101； UniProt 111–211

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	2v5e
Deposition date deposition_date	2008-10-03
Structure title title	The structure of the GDNF:Coreceptor complex: Insights into RET signalling and heparin binding.
Keywords keywords	;RECEPTOR-GLYCOPROTEIN COMPLEX, ALTERNATIVE SPLICING, CELL MEMBRANE, GROWTH FACTOR, LIGAND-CORECEPTOR, GPI-ANCHOR, LIPOPROTEIN, POLYMORPHISM, GLYCOPROTEIN, MEMBRANE, RECEPTOR, SECRETED, GFRALPHA1, CLEAVAGE ON PAIR OF BASIC RESIDUES, RECEPTOR-GLYCOPROTEIN COMPLEX complex ;; RECEPTOR/GLYCOPROTEIN COMPLEX
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.

2v5e__assembly_1__model_1

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

Download this curve (.dat)

2v5e__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2v5e__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.09 Å
Rg (electron density)	39.27 Å
Total Rg	39.34 Å
Atom count	4866
Residues	602
Excluded volume	85392 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2v5e__assembly_1__model_1`	tetrameric （4）	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 (6)

Entity 1 Entity 1 polymer

Description description	GDNF FAMILY RECEPTOR ALPHA-1
Molecular weight formula_weight	22538.6 kDa
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	2664

KGNNCLDAAKACNLDDTCKKYRSAYITPCTTSMSNEVCNRRKCHKALRQFFDKVPAKHSYGMLFCSCRDIACTERRRQTIVPVCSYEERERPNCLSLQDSCKTNYICRSRLADFFTNCQPESRSVSNCLKENYADCLLAYSGLIGTVMTPNYVDSSSLSVAPWCDCSNSGNDLEDCLKFLNFFKDNTCLKNAIQAFGNGS

Source Source

Source organism organism	RATTUS NORVEGICUS
Common name common_name	NORWAY RAT
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	SPODOPTERA FRUGIPERDA; EXPRESSION_SYSTEM_COMMON_FALL ARMYWORM

Entity 2 Entity 2 polymer

Description description	GLIAL CELL LINE-DERIVED NEUROTROPHIC FACTOR
Molecular weight formula_weight	11430.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

QRGKNRGCVLTAIHLNVTDLGLGYETKEELIFRYCSGSCDAAETTYDKILKNLSRNRRLVSDKVGQACCRPIAFDDDLSFLDDNLVYHILRKHSAKRCGCI

Source Source

Source organism organism	HOMO SAPIENS
Common name common_name	HUMAN
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	SPODOPTERA FRUGIPERDA; EXPRESSION_SYSTEM_COMMON_FALL ARMYWORM

Entity 3 Entity 3 branched

Description description	1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose-(2-1)-2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose
Molecular weight formula_weight	982.8 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	223

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2v5eb_
Class class	g — Small proteins
Fold Fold fold	g.17 — Cystine-knot cytokines
Superfamily Superfamily superfamily	g.17.1 — Cystine-knot cytokines
Family Family family	g.17.1.2 — Transforming growth factor (TGF)-beta

CATH v4.4 (1 domains)

Domain ID domain_id	2v5eB00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	90 — Cystine Knot Cytokines, subunit B
Homologous superfamily homologous superfamily	10 — Cystine-knot cytokines

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Unit-cell length a length_a	58.900 Å
Unit-cell length b length_b	75.700 Å
Unit-cell length c length_c	105.500 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.90 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1870
R_work r_work	0.1840
R_free r_free	0.2370

The structure of the GDNF:Coreceptor complex: Insights into RET signalling and heparin binding.

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

GDNF FAMILY RECEPTOR ALPHA-1

State in the Current Structure

Other States of the Same Protein in the Database

GLIAL CELL LINE-DERIVED NEUROTROPHIC FACTOR

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

2v5e__assembly_1__model_1

2v5e__assembly_1__model_1 | I(q)

2v5e__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

The structure of the GDNF:Coreceptor complex: Insights into RET signalling and heparin binding.

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

GDNF FAMILY RECEPTOR ALPHA-1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

GLIAL CELL LINE-DERIVED NEUROTROPHIC FACTOR

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

2v5e__assembly_1__model_1

2v5e__assembly_1__model_1 | I(q)

2v5e__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)