6TTU Ligase date Dec 30, 2019
title Ubiquitin Ligation To Substrate By A Cullin-Ring E3 Ligase A Resolution: Nedd8-Cul1-Rbx1 N98r-Skp1-Monomeric B-Trcp1dd-I Ub~Ube2d2
authors K.Baek, J.R.Prabu, B.A.Schulman
compound source
Molecule: F-Boxwd Repeat-Containing Protein 1a
Chain: T
Synonym: E3rsikappab,Epididymis Tissue Protein Li 2a,F-Box Repeats Protein Beta-Trcp,Pikappabalpha-E3 Receptor Subunit
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Btrc, Btrcp, Fbw1a, Fbxw1a
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: S-Phase Kinase-Associated Protein 1
Chain: S
Synonym: Cyclin-Acdk2-Associated Protein P19,P19a,Organ Of Protein 2,Ocp-2,Organ Of Corti Protein II,Ocp-II,Rna Polyme Elongation Factor-Like Protein,Siii,Transcription Elongatio Polypeptide 1-Like,P19skp1;
Engineered: Yes
Other_details: Skp1 Contains Truncations Of Residues 38-43,

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Skp1, Emc19, Ocp2, Skp1a, Tceb1l
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Cullin-1
Chain: C
Synonym: Cul-1
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cul1
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Nedd8
Chain: N
Synonym: Neddylin,Neural Precursor Cell Expressed Developme Down-Regulated Protein 8,Nedd-8,Ubiquitin-Like Protein Nedd
Engineered: Yes
Other_details: Residue 1, Ser, Comes From The Linker. Nedd8 Starts From Met.;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nedd8
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: E3 Ubiquitin-Protein Ligase Rbx1
Chain: R
Synonym: E3 Ubiquitin-Protein Transferase Rbx1,Protein Zyp, Finger Protein 75,Ring-Box Protein 1,Rbx1,Regulator Of Cull Roc1;
Ec: 2.3.2.27,2.3.2.32
Engineered: Yes
Other_details: Rbx1 Contains Mutation Asn98arg (N98r). Ther Zinc Ions Coordinated Throughout. This Is Not Meant To Alig C-Terminus Of The Protein.;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Rbx1, Rnf75, Roc1
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ubiquitin-Conjugating Enzyme E2 D2
Chain: D
Synonym: (E3-Independent) E2 Ubiquitin-Conjugating Enzyme D Ubiquitin-Conjugating Enzyme D2,Ubiquitin Carrier Protein D Ubiquitin-Conjugating Enzyme E2(17)Kb 2,Ubiquitin-Conjugati E2-17 Kda 2,Ubiquitin-Protein Ligase D2,P53-Regulated Ubiqu Conjugating Enzyme 1;
Ec: 2.3.2.23,2.3.2.24
Engineered: Yes
Other_details: Ube2d2 Contains Mutations Of The Following: Cys107ala, Cys111asp.;

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ube2d2, Pubc1, Ubc4, Ubc5b, Ubch4, Ubch5b
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Polyubiquitin-C
Chain: U
Engineered: Yes

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

Molecule: Cys-Lys-Lys-Ala-Arg-His-Asp-Sep-Gly
Chain: I
Engineered: Yes
Other_details: Phosphorylated Peptide Derived From Ikba.

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 3.70 Å
ligand SEP, ZN enzyme Transferase E.C.2.3.2.27 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
C


D


N


R


S


T


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (239 Kb) [Save to disk]
  • Biological Unit Coordinates (6ttu.pdb1.gz) 231 Kb
  • LPC: Ligand-Protein Contacts for 6TTU
  • CSU: Contacts of Structural Units for 6TTU
  • Retrieve 6TTU in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6TTU from S2C, [Save to disk]
  • View 6TTU 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 6TTU
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6ttu_D] [6ttu_S] [6ttu_T] [6ttu_I] [6ttu_C] [6ttu_N] [6ttu_U] [6ttu_R]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6TTU
  • Community annotation for 6TTU at PDBWiki (http://pdbwiki.org)

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