SAXSdb — 4qxf

▼

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

Leucine-rich repeat-containing G-protein coupled receptor 4, Variable lymphocyte receptor B

Eptatretus burgeri

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	R-spondin-1 × 1 （Q2MKA7） water × 2	Consistent with protein count
2	Insufficient information	Heteromer	Protein 2	R-spondin-1 × 1 （Q2MKA7） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q4G1L2_EPTBU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 229–301； UniProt 128–200 Author chain B； PDBConstruct 229–301； UniProt 128–200

Leucine-rich repeat-containing G-protein coupled receptor 4, Variable lymphocyte receptor B

Eptatretus burgeri

UniProt Q9BXB1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	R-spondin-1 × 1 （Q2MKA7） water × 2	Consistent with protein count
2	Insufficient information	Heteromer	Protein 2	R-spondin-1 × 1 （Q2MKA7） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LGR4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–228； UniProt 27–252 Author chain B； PDBConstruct 3–228； UniProt 27–252

R-spondin-1

Homo sapiens

UniProt Q2MKA7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	Leucine-rich repeat-containing G-protein coupled receptor 4, Variable lymphocyte receptor B × 1 （Q4G1L2,Q9BXB1） water × 2	Consistent with protein count
2	Insufficient information	Heteromer	Protein 2	Leucine-rich repeat-containing G-protein coupled receptor 4, Variable lymphocyte receptor B × 1 （Q4G1L2,Q9BXB1） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RSPO1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–102； UniProt 34–135 Author chain E； PDBConstruct 1–102； UniProt 34–135

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	4qxf
Deposition date deposition_date	2014-07-20
Structure title title	crystal structure of human LGR4 and Rspo1
Keywords keywords	ligand-receptor complex, LRR repeats, Beta-Hairpins, Glucosylation, Cell Membrane, MEMBRANE PROTEIN; MEMBRANE 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.

4qxf__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4qxf__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4qxf__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	23.57 Å
Rg (electron density)	22.68 Å
Total Rg	23.64 Å
Atom count	2933
Residues	379
Excluded volume	52396 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4qxf__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4qxf__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	Leucine-rich repeat-containing G-protein coupled receptor 4, Variable lymphocyte receptor B
Molecular weight formula_weight	33151.8 kDa
Mutation mutation	D75G
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	6122

MDPLCAAPCSCDGDRRVDCSGKGLTAVPEGLSAFTQALDISMNNITQLPEGAFKNFPFLEELQLAGNDLSFIHPKALSGLKELKVLTLQNNQLKTVPSEAIRGLSALQSLRLDANHITSVPEDSFEGLVQLRHLWLDDNSLTEVPVHPLSNLPTLQALTLALNKISSIPDFAFTNLSSLVVLHLHNNKIRSLSQHCFDGLDNLETLDLNYNNLGEFPQAIKALPSLKELALDTNQLKSVPDGIFDRLTSLQKIWLHTNPWDCSCPRIDYLSRWLNKNSQKEQGSAKCSGSGKPVRSIICPT

Source Source

Source organism organism	Eptatretus burgeri
Common name common_name	human, Inshore hagfish
NCBI taxonomy ID ncbi_taxonomy_id	7764
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	R-spondin-1
Molecular weight formula_weight	11185.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,C

AEGSQACAKGCELCSEVNGCLKCSPKLFILLERNDIRQVGVCLPSCPPGYFDARNPDMNKCIKCKIEHCEACFSHNFCTKCKEGLYLHKGRCYPACPEGSSA

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

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	263

▼

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4qxfc_
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.9 — Growth factor receptor domain
Family Family family	g.3.9.1 — Growth factor receptor domain

Domain ID domain_id	d4qxfe_
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.9 — Growth factor receptor domain
Family Family family	g.3.9.1 — Growth factor receptor domain

CATH v4.4 (2 domains)

Domain ID domain_id	4qxfC00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	220 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2
Homologous superfamily homologous superfamily	10 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2

Domain ID domain_id	4qxfE00
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	220 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2
Homologous superfamily homologous superfamily	10 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2

▶

Unit-cell length a length_a	44.867 Å
Unit-cell length b length_b	137.913 Å
Unit-cell length c length_c	82.560 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.13 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.250 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2147
R_work r_work	0.2132
R_free r_free	0.2427

crystal structure of human LGR4 and Rspo1

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

Leucine-rich repeat-containing G-protein coupled receptor 4, Variable lymphocyte receptor B

State in the Current Structure

Other States of the Same Protein in the Database

Leucine-rich repeat-containing G-protein coupled receptor 4, Variable lymphocyte receptor B

State in the Current Structure

Other States of the Same Protein in the Database

R-spondin-1

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

4qxf__assembly_2__model_1

4qxf__assembly_2__model_1 | I(q)

4qxf__assembly_2__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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

crystal structure of human LGR4 and Rspo1

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

Leucine-rich repeat-containing G-protein coupled receptor 4, Variable lymphocyte receptor B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Leucine-rich repeat-containing G-protein coupled receptor 4, Variable lymphocyte receptor B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

R-spondin-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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4qxf__assembly_2__model_1

4qxf__assembly_2__model_1 | I(q)

4qxf__assembly_2__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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)