BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
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BMRB Entry 30474

Title: De Novo Design of a Protein Heterodimer with Specificity Mediated by Hydrogen Bond Networks   PubMed: 30568301

Deposition date: 2018-06-05 Original release date: 2018-12-13

Authors: Chen, Z.; Flores-Solis, D.; Sgourakis, N.; Baker, D.

Citation: Chen, Zibo; Boyken, Scott; Jia, Mengxuan; Busch, Florian; Flores-Solis, David; Bick, Matthew; Lu, Peilong; VanAernum, Zachary; Sahasrabuddhe, Aniruddha; Langan, Robert; Bermeo, Sherry; Brunette, T; Mulligan, Vikram Khipple; Carter, Lauren; DiMaio, Frank; Sgourakis, Nikolaos; Wysocki, Vicki; Baker, David. "Programmable design of orthogonal protein heterodimers."  Nature 565, 106-111 (2019).

Assembly members:
entity_1, polymer, 77 residues, 9344.792 Da.
entity_2, polymer, 82 residues, 9798.264 Da.

Natural source:   Common Name: not available   Taxonomy ID: 32630   Superkingdom: not available   Kingdom: not available   Genus/species: not available not available

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli

Entity Sequences (FASTA):
entity_1: GTKEDILERQRKIIERAQEI HRRQQEILEELERIIRKPGS SEEAMKRMLKLLEESLRLLK ELLELSEESAQLLYEQR
entity_2: TEKRLLEEAERAHREQKEII KKAQELHRRLEEIVRQSGSS EEAKKEAKKILEEIRELSKR SLELLREILYLSQEQKGSLV PR

Data sets:
Data typeCount
13C chemical shifts625
15N chemical shifts146
1H chemical shifts1028

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
  • Hide all

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11
2entity_22

Entities:

Entity 1, entity_1 77 residues - 9344.792 Da.

1   GLYTHRLYSGLUASPILELEUGLUARGGLN
2   ARGLYSILEILEGLUARGALAGLNGLUILE
3   HISARGARGGLNGLNGLUILELEUGLUGLU
4   LEUGLUARGILEILEARGLYSPROGLYSER
5   SERGLUGLUALAMETLYSARGMETLEULYS
6   LEULEUGLUGLUSERLEUARGLEULEULYS
7   GLULEULEUGLULEUSERGLUGLUSERALA
8   GLNLEULEUTYRGLUGLNARG

Entity 2, entity_2 82 residues - 9798.264 Da.

1   THRGLULYSARGLEULEUGLUGLUALAGLU
2   ARGALAHISARGGLUGLNLYSGLUILEILE
3   LYSLYSALAGLNGLULEUHISARGARGLEU
4   GLUGLUILEVALARGGLNSERGLYSERSER
5   GLUGLUALALYSLYSGLUALALYSLYSILE
6   LEUGLUGLUILEARGGLULEUSERLYSARG
7   SERLEUGLULEULEUARGGLUILELEUTYR
8   LEUSERGLNGLUGLNLYSGLYSERLEUVAL
9   PROARG

Samples:

sample_1: entity_1, [U-13C; U-15N], 1.0 ± 0.1 mM; entity_2, [U-13C; U-15N], 1.0 ± 0.1 mM; NaCl 50 mM; NaPO4 20 mM

sample_conditions_1: ionic strength: 0.1 M; pH: 7.2; pressure: 1 atm; temperature: 308 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQCsample_1isotropicsample_conditions_1
4D HNCH TOCSYsample_1isotropicsample_conditions_1
4D HNCH NOESYsample_1isotropicsample_conditions_1
4D HCCH NOESYsample_1isotropicsample_conditions_1

Software:

CS-Rosetta v3.0, Shen, Vernon, Baker and Bax - refinement, structure calculation

SPARKY, Goddard - chemical shift assignment, peak picking

NMRPipe, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMR spectrometers:

  • Bruker AvanceIII 800 MHz

Download simulated HSQC data in one of the following formats:
CSV: Backbone or all simulated shifts
SPARKY: Backbone or all simulated shifts