4c9e

Mouse ZNRF3 ectodomain in complex with Xenopus RSPO2 Fu1-Fu2 (Seleno Met) crystal form II

Method: X-RAY DIFFRACTION

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

E3 UBIQUITIN-PROTEIN LIGASE ZNRF3

MUS MUSCULUS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	R-SPONDIN-2 × 2 （Q5M7L6）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	R-SPONDIN-2 × 2 （Q5M7L6）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ZNRF3_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–156； UniProt 53–205 Author chain C； PDBConstruct 4–156； UniProt 53–205 Author chain E； PDBConstruct 4–156； UniProt 53–205 Author chain G； PDBConstruct 4–156； UniProt 53–205

R-SPONDIN-2

XENOPUS (SILURANA) TROPICALIS

UniProt Q5M7L6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	E3 UBIQUITIN-PROTEIN LIGASE ZNRF3 × 2 （Q5SSZ7）	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	E3 UBIQUITIN-PROTEIN LIGASE ZNRF3 × 2 （Q5SSZ7）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RSPO2_XENTR
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–113； UniProt 35–144 Author chain D； PDBConstruct 4–113； UniProt 35–144 Author chain F； PDBConstruct 4–113； UniProt 35–144 Author chain H； PDBConstruct 4–113； UniProt 35–144

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	4c9e
Deposition date deposition_date	2013-10-02
Structure title title	Mouse ZNRF3 ectodomain in complex with Xenopus RSPO2 Fu1-Fu2 (Seleno Met) crystal form II
Keywords keywords	LIGASE-SIGNALING PROTEIN COMPLEX, WNT, RNF43, LGR4, LGR5, LGR6, RSPO, R-SPO, RSPO1, RSPO3, RSPO4, RECEPTOR, MEMBRANE, SIGNALLING; LIGASE/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.

4c9e__assembly_1__model_1

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

Download this curve (.dat)

4c9e__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4c9e__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.97 Å
Rg (electron density)	27.15 Å
Total Rg	27.95 Å
Atom count	3823
Residues	511
Excluded volume	67644 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4c9e__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4c9e__assembly_2__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 (2)

Entity 1 Entity 1 polymer

Description description	E3 UBIQUITIN-PROTEIN LIGASE ZNRF3
Molecular weight formula_weight	18203.6 kDa
EC 编号 ec_number	6.3.2.-
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	7644

ETGKETAFVEVVLFESSPSGDYTTHTTGLTGRFSRAGAMLSAEGEIVQMHPLGLCNNNDEEDLYEYGWVGVVKLEQPELDPKPCLTVLGKAKRAVQRGATAVIFDVSENPEAIDQLNQGSEDPLKRPVVYVKGADAIKLMNIVNKQKVARARIQHLGTKHHHHHH

Source Source

Source organism organism	MUS MUSCULUS
Common name common_name	HOUSE MOUSE
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	HOMO SAPIENS

Entity 2 Entity 2 polymer

Description description	R-SPONDIN-2
Molecular weight formula_weight	13828.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H

ETGGTNPICKGCLSCSKDNGCLRCQPKLFFYLRREGMRQYGECLQSCPPGYYGVRGPDMNRCSRCRIENCDSCFSRDFCIKCKSGFYSHKGQCFEECPEGFAPLDDTMVCVDGTKHHHHHH

Source Source

Source organism organism	XENOPUS (SILURANA) TROPICALIS
Common name common_name	WESTERN CLAWED FROG
NCBI taxonomy ID ncbi_taxonomy_id	8364
Host organism host_organism	HOMO SAPIENS

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d4c9eb_
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.3.9.0 — automated matches

Domain ID domain_id	d4c9ed_
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.3.9.0 — automated matches

Domain ID domain_id	d4c9ef_
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.3.9.0 — automated matches

Domain ID domain_id	d4c9eh_
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.3.9.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id	4c9eA00
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	30 — Glucose Oxidase; domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	4c9eB00
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	4c9eC00
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	30 — Glucose Oxidase; domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	4c9eD00
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	4c9eE00
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	30 — Glucose Oxidase; domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	4c9eF00
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	4c9eG00
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	30 — Glucose Oxidase; domain 1
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	4c9eH00
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

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Unit-cell length a length_a	70.991 Å
Unit-cell length b length_b	71.279 Å
Unit-cell length c length_c	72.109 Å
Unit-cell angle α angle_alpha	69.29 °
Unit-cell angle β angle_beta	61.48 °
Unit-cell angle γ angle_gamma	84.31 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	35.370 Å
R factor r_factor	0.2498
R_work r_work	0.2452
R_free r_free	0.3338

Mouse ZNRF3 ectodomain in complex with Xenopus RSPO2 Fu1-Fu2 (Seleno Met) crystal form II

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

E3 UBIQUITIN-PROTEIN LIGASE ZNRF3

State in the Current Structure

Other States of the Same Protein in the Database

R-SPONDIN-2

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

4c9e__assembly_1__model_1

4c9e__assembly_1__model_1 | I(q)

4c9e__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Mouse ZNRF3 ectodomain in complex with Xenopus RSPO2 Fu1-Fu2 (Seleno Met) crystal form II

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

E3 UBIQUITIN-PROTEIN LIGASE ZNRF3

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-2

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

4c9e__assembly_1__model_1

4c9e__assembly_1__model_1 | I(q)

4c9e__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)