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4ufr

Structure of the ectodomain of LGR5 in complex with R-spondin-2 (Fu1Fu2)

Method: X-RAY DIFFRACTION Dmax: 139.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

LEUCINE-RICH REPEAT-CONTAINING G-PROTEIN COUPLED RECEPTOR 5

HOMO SAPIENS

UniProt O75473

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 32–487 Chain A； UniProt 538–544 Chain C； UniProt 32–487 Chain C； UniProt 538–544 Fragment：ECTODOMAIN, RESIDUES 32-487 AND RESIDUES 538-544 R-SPONDIN-2 × 2 （Q8BFU0） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CL CHLORIDE ION × 6 X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.5；25 %W/V PEG3350, 0.200 M LITHIUM SULPHATE, 0.100 M BIS-TRIS PH 5.5 Resolution 2.20 Å R-free 0.262

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 4UFR Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4BSR Structure of the ectodomain of LGR5 in complex with R-spondin-1 (Fu1Fu2) in P22121 crystal form Deposited 2013-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 22–543（522 aa） Fragment：EXTRACELLULAR LRR DOMAIN, RESIDUES 22-543
Chain B 22–543（522 aa） Fragment：EXTRACELLULAR LRR DOMAIN, RESIDUES 22-543
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.20 Å R-free 0.258
4BSS Structure of the ectodomain of LGR5 in complex with R-spondin-1 (Fu1Fu2) in P21 crystal form Deposited 2013-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 22–543（522 aa） Fragment：EXTRACELLULAR LRR DOMAIN, RESIDUES 22-543
Chain B 22–543（522 aa） Fragment：EXTRACELLULAR LRR DOMAIN, RESIDUES 22-543
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.20 Å R-free 0.290
4BSS Structure of the ectodomain of LGR5 in complex with R-spondin-1 (Fu1Fu2) in P21 crystal form Deposited 2013-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 22–543（522 aa） Fragment：EXTRACELLULAR LRR DOMAIN, RESIDUES 22-543
Chain F 22–543（522 aa） Fragment：EXTRACELLULAR LRR DOMAIN, RESIDUES 22-543
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.20 Å R-free 0.290
4BST Structure of the ectodomain of LGR5 in complex with R-spondin-1 (Fu1Fu2) in P6122 crystal form Deposited 2013-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 22–543（522 aa） Fragment：EXTRACELLULAR LRR DOMAIN, RESIDUES 22-543
Chain B 22–543（522 aa） Fragment：EXTRACELLULAR LRR DOMAIN, RESIDUES 22-543
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 4.30 Å R-free 0.268
4BSU Structure of the ectodomain of LGR5 in complex with R-spondin-1 (Fu1Fu2) in C2 crystal form Deposited 2013-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 22–543（522 aa）
Chain F 22–543（522 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.20 Å R-free 0.287
4BSU Structure of the ectodomain of LGR5 in complex with R-spondin-1 (Fu1Fu2) in C2 crystal form Deposited 2013-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 22–543（522 aa）
Chain B 22–543（522 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.20 Å R-free 0.287
4KNG Crystal structure of human LGR5-RSPO1-RNF43 Deposited 2013-05-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 32–557（526 aa） Fragment：extracellular domain
Chain B 32–557（526 aa） Fragment：extracellular domain
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NI NICKEL (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；10% PEG4000, 0.2M ammonium sulfate, 7% Sucrose and 0.1 M TRIS pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.50 Å R-free 0.276
4UFS Low resolution structure R-spondin-2 (Fu1Fu2) in complex with the ectodomains of LGR5 and ZNRF3 Deposited 2015-03-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 32–487（456 aa） Fragment：ECTODOMAIN, RESIDUES 32-487 AND RESIDUES 538-544
Chain A 538–544（7 aa） Fragment：ECTODOMAIN, RESIDUES 32-487 AND RESIDUES 538-544
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；0.100 M AMMONIUM ACETATE, 0.600 M SODIUM CHLORIDE, 0.050 M MES PH 6.0, 0.005 M MAGNESIUM SULPHATE
Resolution 4.80 Å R-free 0.313

6 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name LGR5_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–458； UniProt 32–487 Author chain A； PDBConstruct 466–472； UniProt 538–544 Author chain C； PDBConstruct 4–458； UniProt 32–487 Author chain C； PDBConstruct 466–472； UniProt 538–544

R-SPONDIN-2

HOMO SAPIENS

UniProt Q8BFU0

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain B； UniProt 39–144 Chain D； UniProt 39–144 Fragment：FU1-FU2, RESIDUES 39-144 LEUCINE-RICH REPEAT-CONTAINING G-PROTEIN COUPLED RECEPTOR 5 × 2 （O75473） NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CL CHLORIDE ION × 6 X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.5；25 %W/V PEG3350, 0.200 M LITHIUM SULPHATE, 0.100 M BIS-TRIS PH 5.5 Resolution 2.20 Å R-free 0.262

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 4UFR Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4C99 Mouse ZNRF3 ectodomain in complex with mouse RSPO2 Fu1-Fu2 crystal form I Deposited 2013-10-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 37–144（108 aa） Fragment：FU1-FU2, RESIDUES 37-144
Chain D 37–144（108 aa） Fragment：FU1-FU2, RESIDUES 37-144
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.80 Å R-free 0.323
4UFS Low resolution structure R-spondin-2 (Fu1Fu2) in complex with the ectodomains of LGR5 and ZNRF3 Deposited 2015-03-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 39–144（106 aa） Fragment：FU1-FU2, RESIDUES 39-144
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；0.100 M AMMONIUM ACETATE, 0.600 M SODIUM CHLORIDE, 0.050 M MES PH 6.0, 0.005 M MAGNESIUM SULPHATE
Resolution 4.80 Å R-free 0.313
8XFP the pentamerA complex of LGR4-RSPO2-ZNRF3(delta RING) Deposited 2023-12-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain G 41–141（101 aa）
Chain J 41–141（101 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.21 Å
8XFS LGR4-RSPO2-ZNRF3 RING domain (1:2:2) Deposited 2023-12-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 41–141（101 aa）
Chain D 41–141（101 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8Y69 LGR4-RSPO2-ZNRF3 (2:2:2) Deposited 2024-02-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain G 41–141（101 aa）
Chain J 41–141（101 aa）
Not recorded CLR CHOLESTEROL × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.38 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RSPO2_MOUSE
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 4–109； UniProt 39–144 Author chain D； PDBConstruct 4–109； UniProt 39–144

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.

SAXS scattering curve SAXS Profile

SAXS profile for 4ufr

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4ufr
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4ufr
Deposition date deposition_date2015-03-18
Structure title titleStructure of the ectodomain of LGR5 in complex with R-spondin-2 (Fu1Fu2)
Keywords keywordsSIGNALING PROTEIN, WNT, LGR, RSPO; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier39.59 Å
Radius of gyration Rg (electron density) rg_electron39.94 Å
Forward intensity I(0) i0240904000.00
Molecular weight molecular_weight124950.0 kDa
Excluded volume excluded_volume155930 ų
Envelope volume envelope_volume212250 ų
Hydration-shell volume shell_volume47263 ų
Envelope diameter envelope_diameter139.8 Å
Shell Rg shell_rg42.28 Å
Envelope Rg envelope_rg39.83 Å
Shape Rg shape_rg39.91 Å
Total Rg total_rg40.16 Å
Total atoms total_atoms8756
Residues n_residues1121
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax139.5 Å
Rg (real space) rg_real40.11 Å
Rg uncertainty (real space) rg_real_error1.45 Å
I(0) (real space) i0_real2.4090e+08
I(0) uncertainty (real space) i0_real_error4.6720e+06
Rg (reciprocal space) rg_reciprocal39.80 Å
I(0) (reciprocal space) i0_reciprocal240800000.0000
Solution quality estimate total_estimate0.8021
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary34.9 Å
Skewness Skewness skewness0.581
Kurtosis Kurtosis kurtosis-0.312
Angular range angular_range— – 0.2000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha50840000.0000
Real-space data points n_real_points41
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.656; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.722; Smooth: 0.733
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd4ufrb_
Class classg — Small proteins
Fold Fold foldg.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamilyg.3.9 — Growth factor receptor domain
Family Family familyg.3.9.0 — automated matches
Domain ID domain_idd4ufrd_
Class classg — Small proteins
Fold Fold foldg.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamilyg.3.9 — Growth factor receptor domain
Family Family familyg.3.9.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id4ufrA01
Class class3 — Alpha Beta
Architecture architecture80 — Alpha-Beta Horseshoe
Topology topology10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily10 — Ribonuclease Inhibitor
Domain ID domain_id4ufrB00
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology220 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2
Homologous superfamily homologous superfamily10 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2
Domain ID domain_id4ufrC01
Class class3 — Alpha Beta
Architecture architecture80 — Alpha-Beta Horseshoe
Topology topology10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily10 — Ribonuclease Inhibitor
Domain ID domain_id4ufrD00
Class class2 — Mainly Beta
Architecture architecture10 — Ribbon
Topology topology220 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2
Homologous superfamily homologous superfamily10 — Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2
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8. Citations (1)

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9. Files and Curves (10)