4KNG Signaling Protein, Membrane Protein date May 09, 2013
title Crystal Structure Of Human Lgr5-Rspo1-Rnf43
authors P.H.Chen, X.He
compound source
Molecule: Leucine-Rich Repeat-Containing G-Protein Coupled 5;
Chain: A, B
Fragment: Extracellular Domain
Synonym: G-Protein Coupled Receptor 49, G-Protein Coupled R 67, G-Protein Coupled Receptor Hg38;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Lgr5, Gpr49, Gpr67
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pvlad6

Molecule: R-Spondin-1
Chain: M, P
Fragment: Furin Repeats
Synonym: Roof Plate-Specific Spondin-1, Hrspo1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rspo1
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pvlad6

Molecule: E3 Ubiquitin-Protein Ligase Rnf43
Chain: E, F
Fragment: Pa Domain
Synonym: Ring Finger Protein 43
Ec: 6.3.2.-
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rnf43
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
Expression_system_cell_line: Hek293
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pvlad6
symmetry Space Group: P 21 21 21
R_factor 0.232 R_Free 0.276
crystal
cell
length a length b length c angle alpha angle beta angle gamma
104.575 120.971 181.009 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
ligand NAG, NI enzyme Ligase E.C.6.3.2 BRENDA
Primary referenceThe structural basis of R-spondin recognition by LGR5 and RNF43., Chen PH, Chen X, Lin Z, Fang D, He X, Genes Dev. 2013 Jun 11. PMID:23756651
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (237 Kb) [Save to disk]
  • Biological Unit Coordinates (4kng.pdb1.gz) 229 Kb
  • LPC: Ligand-Protein Contacts for 4KNG
  • CSU: Contacts of Structural Units for 4KNG
  • Structure Factors (1709 Kb)
  • Retrieve 4KNG in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4KNG from S2C, [Save to disk]
  • Re-refined 4kng structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4KNG in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 4KNG
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4KNG, from MSDmotif at EBI
  • Fold representative 4kng from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4kng_E] [4kng] [4kng_B] [4kng_F] [4kng_M] [4kng_A] [4kng_P]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4KNG: [FU] [LRR] [LRRNT] [LRR_TYP ] by SMART
  • Other resources with information on 4KNG
  • Community annotation for 4KNG at PDBWiki (http://pdbwiki.org)

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