BMRB Entry 30474

Name: De Novo Design of a Protein Heterodimer with Specificity Mediated by Hydrogen Bond Networks
Published: 2018-12-13

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PDB ID: 6dmp
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30474
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title:

De Novo Design of a Protein Heterodimer with Specificity Mediated by Hydrogen Bond Networks

Deposition date:

2018-06-05

Original release date:

2018-12-13

Authors:

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

Citation:

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).
PubMed: 30568301

Assembly members:

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

Natural source:

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

Experimental source:

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

Entity Sequences (FASTA):

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

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list
- spectral_peak_list_1
- spectral_peak_list_2

Data type	Count
13C chemical shifts	625
15N chemical shifts	146
1H chemical shifts	1028

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1
2	entity_2	2

Entities:

Entity 1, entity_1 77 residues - 9344.792 Da.

1

GLY

THR

LYS

GLU

ASP

ILE

LEU

GLU

ARG

GLN

2

ARG

LYS

ILE

GLU

ARG

ALA

GLN

GLU

ILE

3

HIS

ARG

GLN

GLU

ILE

LEU

GLU

4

LEU

GLU

ARG

ILE

ARG

LYS

PRO

GLY

SER

5

SER

GLU

ALA

MET

LYS

ARG

MET

LEU

LYS

6

LEU

GLU

SER

LEU

ARG

LEU

LYS

7

GLU

LEU

GLU

LEU

SER

GLU

SER

ALA

8

GLN

LEU

TYR

GLU

GLN

ARG

Entity 2, entity_2 82 residues - 9798.264 Da.

1

THR

GLU

LYS

ARG

LEU

GLU

ALA

GLU

2

ARG

ALA

HIS

ARG

GLU

GLN

LYS

GLU

ILE

3

LYS

ALA

GLN

GLU

LEU

HIS

ARG

LEU

4

GLU

ILE

VAL

ARG

GLN

SER

GLY

SER

5

GLU

ALA

LYS

GLU

ALA

LYS

ILE

6

LEU

GLU

ILE

ARG

GLU

LEU

SER

LYS

ARG

7

SER

LEU

GLU

LEU

ARG

GLU

ILE

LEU

TYR

8

LEU

SER

GLN

GLU

GLN

LYS

GLY

SER

LEU

VAL

9

PRO

ARG

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:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_1	isotropic	sample_conditions_1
4D HNCH TOCSY	sample_1	isotropic	sample_conditions_1
4D HNCH NOESY	sample_1	isotropic	sample_conditions_1
4D HCCH NOESY	sample_1	isotropic	sample_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 HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks