5Y3A Signaling Protein date Jul 28, 2017
title Crystal Structure Of Ragulator Complex (P18 49-161)
authors T.Zhang, J.Ding
compound source
Molecule: Ragulator Complex Protein Lamtor1
Chain: A, F
Fragment: Coiled Coil, Unp Residues 50-161
Synonym: Late Endosomallysosomal Adaptor And Mapk And Mtor 1,Lipid Raft Adaptor Protein P18,Protein Associated With Dr Endosomes,P27kip1-Releasing Factor From Rhoa,P27rf-Rho;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Lamtor1, C11orf59, Pdro, Pp7157
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) Codon Plus
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28sumo

Molecule: Ragulator Complex Protein Lamtor2
Chain: B, G
Fragment: Roadblock Domain
Synonym: Endosomal Adaptor Protein P14,Late Endosomallysos Interacting Protein,Late Endosomallysosomal Adaptor And Ma Mtor Activator 2,Mitogen-Activated Protein-Binding Protein- Interacting Protein,Mapbp-Interacting Protein,Roadblock Dom Containing Protein 3;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Lamtor2, Mapbpip, Robld3, Hspc003
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) Codon Plus
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Petduet

Molecule: Ragulator Complex Protein Lamtor3
Chain: C, H
Fragment: Roadblock Domain
Synonym: Late Endosomallysosomal Adaptor And Mapk And Mtor 3,Mek-Binding Partner 1,Mp1,Mitogen-Activated Protein Kinas 1-Interacting Protein 1,Mitogen-Activated Protein Kinase Sc Protein 1;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Lamtor3, Map2k1ip1, Mapksp1, Pro2783
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) Codon Plus
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a

Molecule: Ragulator Complex Protein Lamtor4
Chain: D, I
Fragment: Roadblock Domain
Synonym: Late Endosomallysosomal Adaptor And Mapk And Mtor 4;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Lamtor4, C7orf59
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) Codon Plus
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Petduet

Molecule: Ragulator Complex Protein Lamtor5
Chain: E, J
Fragment: Roadblock Domain
Synonym: Hepatitis B Virus X-Interacting Protein,Hbx-Intera Protein,Late Endosomallysosomal Adaptor And Mapk And Mtor 5;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Lamtor5, Hbxip, Xip
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3) Codon Plus
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Petduet
symmetry Space Group: P 21 21 21
R_factor 0.246 R_Free 0.288
crystal
cell
length a length b length c angle alpha angle beta angle gamma
71.341 89.626 232.173 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
B, G


D, I


F, A


H, C


J, E


Primary referenceStructural basis for Ragulator functioning as a scaffold in membrane-anchoring of Rag GTPases and mTORC1., Zhang T, Wang R, Wang Z, Wang X, Wang F, Ding J, Nat Commun. 2017 Nov 9;8(1):1394. doi: 10.1038/s41467-017-01567-4. PMID:29123114
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (318 Kb) [Save to disk]
  • Biological Unit Coordinates (5y3a.pdb1.gz) 158 Kb
  • Biological Unit Coordinates (5y3a.pdb2.gz) 155 Kb
  • LPC: Ligand-Protein Contacts for 5Y3A
  • CSU: Contacts of Structural Units for 5Y3A
  • Structure Factors (470 Kb)
  • Retrieve 5Y3A in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5Y3A from S2C, [Save to disk]
  • View 5Y3A 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 5Y3A
  • 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
  • Fold representative 5y3a from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5y3a_E] [5y3a_B] [5y3a_H] [5y3a_I] [5y3a_G] [5y3a_F] [5y3a_C] [5y3a_A] [5y3a_D] [5y3a_J]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5Y3A
  • Community annotation for 5Y3A at PDBWiki (http://pdbwiki.org)

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