1YHN Protein Transport date Jan 10, 2005
title Structure Basis Of Rilp Recruitment By Rab7
authors M.Wu, T.Wang, W.Hong, H.Song
compound source
Molecule: Ras-Related Protein Rab-7
Chain: A
Synonym: Rab7
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rab7
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl-21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-6p-1

Molecule: Rab Interacting Lysosomal Protein
Chain: B
Fragment: Rilp Effector Domain
Synonym: Rilp
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rilp
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl-21
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-6p-1
symmetry Space Group: P 65 2 2
R_factor 0.268 R_Free 0.278
crystal
cell
length a length b length c angle alpha angle beta angle gamma
93.134 93.134 132.826 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.00 Å
ligand GTP, MG enzyme
related structures by homologous chain: 1VG9
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural basis for recruitment of RILP by small GTPase Rab7., Wu M, Wang T, Loh E, Hong W, Song H, EMBO J. 2005 Apr 20;24(8):1491-501. Epub 2005 Mar 31. PMID:15933719
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (47 Kb) [Save to disk]
  • Biological Unit Coordinates (1yhn.pdb1.gz) 83 Kb
  • LPC: Ligand-Protein Contacts for 1YHN
  • CSU: Contacts of Structural Units for 1YHN
  • Likely Quarternary Molecular Structure file(s) for 1YHN
  • Structure Factors (55 Kb)
  • Retrieve 1YHN in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YHN from S2C, [Save to disk]
  • Re-refined 1yhn structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1YHN 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 1YHN
  • 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 1YHN, from MSDmotif at EBI
  • Fold representative 1yhn from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1yhn_B] [1yhn_A] [1yhn]
  • SWISS-PROT database: [P51149] [Q96NA2]
  • Domain organization of [RAB7A_HUMAN] [RILP_HUMAN] by SWISSPFAM
  • Domain found in 1YHN: [RAB ] by SMART
  • Alignments of the sequence of 1YHN with the sequences similar proteins can be viewed for 1YHN's classification [RAB7A_HUMAN] [RILP_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [RAB7A_HUMAN] [RILP_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1YHN
  • Community annotation for 1YHN 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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