4bss

Structure of the ectodomain of LGR5 in complex with R-spondin-1 (Fu1Fu2) in P21 crystal form

Method: X-RAY DIFFRACTION Dmax: 187.3 Å Quality: GOOD

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 Other combination Heteromer Protein × 4 其他Polymer 3 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 22–543 Chain B; UniProt 22–543 Fragment:EXTRACELLULAR LRR DOMAIN, RESIDUES 22-543 R-SPONDIN-1 × 2 (Q2MKA7) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.20 Å R-free 0.290
2 Other combination Heteromer Protein × 4 其他Polymer 1 PDB declaration: tetrameric(4) Consistent with protein copy count Chain E; UniProt 22–543 Chain F; UniProt 22–543 Fragment:EXTRACELLULAR LRR DOMAIN, RESIDUES 22-543 R-SPONDIN-1 × 2 (Q2MKA7) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.20 Å R-free 0.290

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.

6 other PDB entries and 7 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 15–536; UniProt 22–543 Author chain B; PDBConstruct 15–536; UniProt 22–543 Author chain E; PDBConstruct 15–536; UniProt 22–543 Author chain F; PDBConstruct 15–536; UniProt 22–543

R-SPONDIN-1

HOMO SAPIENS

UniProt Q2MKA7

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 4 其他Polymer 3 PDB declaration: tetrameric(4) Consistent with protein copy count Chain C; UniProt 31–146 Chain D; UniProt 31–146 Fragment:FU1FU2, RESIDUES 31-146 LEUCINE-RICH REPEAT-CONTAINING G-PROTEIN COUPLED RECEPTOR 5 × 2 (O75473) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.20 Å R-free 0.290
2 Other combination Heteromer Protein × 4 其他Polymer 1 PDB declaration: tetrameric(4) Consistent with protein copy count Chain G; UniProt 31–146 Chain H; UniProt 31–146 Fragment:FU1FU2, RESIDUES 31-146 LEUCINE-RICH REPEAT-CONTAINING G-PROTEIN COUPLED RECEPTOR 5 × 2 (O75473) 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.20 Å R-free 0.290

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.

11 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RSPO1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 3–118; UniProt 31–146 Author chain D; PDBConstruct 3–118; UniProt 31–146 Author chain G; PDBConstruct 3–118; UniProt 31–146 Author chain H; PDBConstruct 3–118; UniProt 31–146

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 4bss

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id4bss
Deposition date deposition_date2013-06-11
Structure title titleStructure of the ectodomain of LGR5 in complex with R-spondin-1 (Fu1Fu2) in P21 crystal form
Keywords keywords;SIGNALING PROTEIN, ADULT STEM CELL, LEUCINE-RICH REPEAT G-PROTEIN COUPLED RECEPTOR, LEUCINE-RICH REPEAT, FURIN DOMAIN, WNT SIGNALING, CONGENITAL ANONYCHIA ;; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier50.91
Radius of gyration Rg (electron density) rg_electron50.97
Forward intensity I(0) i0949249000.00
Molecular weight molecular_weight255710.0 kDa
Excluded volume excluded_volume320340 ų
Envelope volume envelope_volume456610 ų
Hydration-shell volume shell_volume77614 ų
Envelope diameter envelope_diameter196.0
Shell Rg shell_rg51.13
Envelope Rg envelope_rg51.02
Shape Rg shape_rg50.89
Total Rg total_rg51.25
Total atoms total_atoms17925
Residues n_residues2281
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax187.3
Rg (real space) rg_real51.23
Rg uncertainty (real space) rg_real_error2.49
I(0) (real space) i0_real9.4920e+08
I(0) uncertainty (real space) i0_real_error2.1010e+07
Rg (reciprocal space) rg_reciprocal50.65
I(0) (reciprocal space) i0_reciprocal948500000.0000
Solution quality estimate total_estimate0.8155
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary54.4
Skewness Skewness skewness0.630
Kurtosis Kurtosis kurtosis0.203
Angular range angular_range— – 0.1550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha123800000.0000
Real-space data points n_real_points32
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.674; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.827; Smooth: 0.749

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id4bssA01
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_id4bssB01
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_id4bssC00
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_id4bssD00
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_id4bssE01
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_id4bssF01
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_id4bssG00
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_id4bssH00
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

8. Citations (1)

9. Files and Curves (10)