3NVQ Signaling Protein Protein Binding date Jul 08, 2010
title Molecular Mechanism Of Guidance Cue Recognition
authors Z.Juo, H.Liu, A.Shim, P.Focia, X.Chen, C.Garcia, X.He
compound source
Molecule: Semaphorin-7a
Chain: A, E
Fragment: Unp Residues 45-637
Synonym: Semaphorin-L, Sema L, Semaphorin-K1, Sema K1, John Hargen Human Blood Group Ag, Jmh Blood Group Antigen, Cdw10
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Sema7a, Cd108, Semal
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
Expression_system_cell: Hek293s

Molecule: Plexin-C1
Chain: B, F
Fragment: Unp Residues 33-507
Synonym: Virus-Encoded Semaphorin Protein Receptor
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Plxnc1, Vespr
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
Expression_system_cell: Hek293s
symmetry Space Group: P 21 21 21
R_factor 0.248 R_Free 0.277
crystal
cell
length a length b length c angle alpha angle beta angle gamma
99.645 126.078 236.419 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.40 Å
ligand NAG, NDG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, E


F, B


Primary referenceStructural basis of semaphorin-plexin recognition and viral mimicry from Sema7A and A39R complexes with PlexinC1., Liu H, Juo ZS, Shim AH, Focia PJ, Chen X, Garcia KC, He X, Cell. 2010 Sep 3;142(5):749-61. Epub 2010 Aug 19. PMID:20727575
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (363 Kb) [Save to disk]
  • Biological Unit Coordinates (3nvq.pdb1.gz) 355 Kb
  • LPC: Ligand-Protein Contacts for 3NVQ
  • CSU: Contacts of Structural Units for 3NVQ
  • Structure Factors (868 Kb)
  • Retrieve 3NVQ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3NVQ from S2C, [Save to disk]
  • Re-refined 3nvq structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3NVQ 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 3NVQ
  • 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 3NVQ, from MSDmotif at EBI
  • Fold representative 3nvq from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3nvq] [3nvq_B] [3nvq_A] [3nvq_E] [3nvq_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3NVQ: [IG] [PSI] [Sema ] by SMART
  • Other resources with information on 3NVQ
  • Community annotation for 3NVQ at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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