BMRB Entry 31108

Name: Solution structure of ACKR3-targeting nanobody VUN701
Published: 2024-06-20

Click here to enlarge.

PDB ID: 8uek
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR31108
MolProbity Validation Chart

NMR-STAR file interactive viewer.
NMR-STAR v3 text file.
XML gzip file.
RDF gzip file.
All files associated with the entry

Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

Select model:

I am color blind

Download raw data. Direct link to this display. Help

Title:

Solution structure of ACKR3-targeting nanobody VUN701

Deposition date:

2023-10-01

Original release date:

2024-06-20

Authors:

Schlimgen, R.; Peterson, F.; Volkman, B.

Citation:

Citation: Schlimgen, R.; Peterson, F.; Heukers, R.; Smit, M.; McCorvy, J.; Volkman, B.. "Structural basis for selectivity and antagonism in extracellular GPCR-nanobodies" Nat. Commun. 15, 4611-4611 (2024).
PubMed: 38816420

Assembly members:

Assembly members:
entity_1, polymer, 124 residues, 13318.542 Da.

Natural source:

Natural source: Common Name: llama Taxonomy ID: 9844 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Lama glama

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli BL21(DE3) Vector: pET28

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GSGSQVQLVESGGGLVQAGG SLRLSCAASGSTFSLHLMGW YRQAPGKQREVVATSGSGGD TNYADSVKGRFTISRDNDKN TVDLQMNNLKPEDTADYYCR AQQKIGRDTFRDYWGQGTQV TVSS

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	470
15N chemical shifts	139
1H chemical shifts	772

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
Hide all

Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1

Entities:

Entity 1, unit_1 124 residues - 13318.542 Da.

1

GLY

SER

GLY

SER

GLN

VAL

GLN

LEU

VAL

GLU

2

SER

GLY

LEU

VAL

GLN

ALA

GLY

3

SER

LEU

ARG

LEU

SER

CYS

ALA

SER

GLY

4

SER

THR

PHE

SER

LEU

HIS

LEU

MET

GLY

TRP

5

TYR

ARG

GLN

ALA

PRO

GLY

LYS

GLN

ARG

GLU

6

VAL

ALA

THR

SER

GLY

SER

GLY

ASP

7

THR

ASN

TYR

ALA

ASP

SER

VAL

LYS

GLY

ARG

8

PHE

THR

ILE

SER

ARG

ASP

ASN

ASP

LYS

ASN

9

THR

VAL

ASP

LEU

GLN

MET

ASN

LEU

LYS

10

PRO

GLU

ASP

THR

ALA

ASP

TYR

CYS

ARG

11

ALA

GLN

LYS

ILE

GLY

ARG

ASP

THR

PHE

12

ARG

ASP

TYR

TRP

GLY

GLN

GLY

THR

GLN

VAL

13

THR

VAL

SER

Samples:

sample_1: MES, [U-100% 2H], 25 mM; VUN701, [U-98% 13C; U-98% 15N], 0.75 mM; sodium azide 0.02 % v/v

sample_conditions_1: ionic strength: 20 mM; pH: 6.8; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 1H-15N NOESY	sample_1	anisotropic	sample_conditions_1
3D 1H-13C NOESY aliphatic	sample_1	anisotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	sample_1	anisotropic	sample_conditions_1
3D HNCO	sample_1	anisotropic	sample_conditions_1

Software:

TopSpin v3.6, Bruker Biospin - collection

NMRPipe v9.6, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - data analysis

XEASY v1.3.13, Bartels et al. - data analysis

GARANT v2.2, Bartels, Guntert, Billeter and Wuthrich - chemical shift assignment

CYANA v3.0, Guntert, Mumenthaler and Wuthrich - refinement

X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - geometry optimization

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

NMR spectrometers:

Bruker AVANCE III HD 600 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks