5X6V Protein Binding date Feb 23, 2017
title Crystal Structure Of Human Heteroheptameric Complex
authors R.Yonehara, S.Nada, T.Nakai, M.Nakai, A.Kitamura, A.Ogawa, H.Nakat K.I.Nakayama, S.Li, D.M.Standley, E.Yamashita, A.Nakagawa, M.Oka
compound source
Molecule: Ragulator Complex Protein Lamtor3
Chain: A
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

Molecule: Ragulator Complex Protein Lamtor2
Chain: B
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

Molecule: Ragulator Complex Protein Lamtor5
Chain: C
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

Molecule: Ragulator Complex Protein Lamtor4
Chain: D
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

Molecule: Ragulator Complex Protein Lamtor1
Chain: E
Fragment: Unp Residues 42-161
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
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Lamtor1, C11orf59, Pdro, Pp7157
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ras-Related Gtp-Binding Protein A
Chain: F
Fragment: Unp Residues 183-313
Synonym: Raga,Adenovirus E3 14.7 Kda-Interacting Protein 1,
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rraga
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ras-Related Gtp-Binding Protein C
Chain: G
Fragment: Unp Residues 238-375
Synonym: Ragc,Gtpase-Interacting Protein 2,Tib929
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Rragc
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.193 R_Free 0.243
crystal
cell
length a length b length c angle alpha angle beta angle gamma
74.099 93.476 125.452 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.02 Å
ligand ACT, NA enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


B


C


D


E


F, G


Primary referenceStructural basis for the assembly of the Ragulator-Rag GTPase complex., Yonehara R, Nada S, Nakai T, Nakai M, Kitamura A, Ogawa A, Nakatsumi H, Nakayama KI, Li S, Standley DM, Yamashita E, Nakagawa A, Okada M, Nat Commun. 2017 Nov 20;8(1):1625. doi: 10.1038/s41467-017-01762-3. PMID:29158492
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (270 Kb) [Save to disk]
  • Biological Unit Coordinates (5x6v.pdb1.gz) 263 Kb
  • LPC: Ligand-Protein Contacts for 5X6V
  • CSU: Contacts of Structural Units for 5X6V
  • Structure Factors (2433 Kb)
  • Retrieve 5X6V in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5X6V from S2C, [Save to disk]
  • View 5X6V 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 5X6V
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5x6v from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5x6v_D] [5x6v_G] [5x6v_E] [5x6v_C] [5x6v_F] [5x6v_B] [5x6v_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5X6V
  • Community annotation for 5X6V at PDBWiki (http://pdbwiki.org)

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