BMRB Entry 36341

Name: N-terminal domain (NTD) Solution structure of aciniform spidroin (AcSpN) from Nephila antipodiana.
Published: 2023-02-23

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PDB ID: 7but
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR36341
MolProbity Validation Chart

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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: N-terminal domain (NTD) Solution structure of aciniform spidroin (AcSpN) from Nephila antipodiana. PubMed: 32586030

Deposition date: 2020-04-08 Original release date: 2023-02-23

Authors: Fan, J.; Yang, D.

Citation: Chakraborty, Rusha; Fan, Jing-Song; Lai, Chong Cheong; Raghuvamsi, Palur Venkata; Chee, Pin Xuan; Anand, Ganesh Srinivasan; Yang, Daiwen. "Structural Basis of Oligomerization of N-Terminal Domain of Spider Aciniform Silk Protein." Int. J. Mol. Sci. 21, 4466-4466 (2020).

Assembly members:
Aciniform Spidroin, polymer, 142 residues, 15318.378 Da.

Natural source: Common Name: Nephila antipodiana Taxonomy ID: 171624 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Nephila antipodiana

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

Entity Sequences (FASTA):
Aciniform Spidroin: GSMSSKSPWANPKKANAFMK CLIQKISVSPVFPQQEKEDM ESIVETMMSAISGVSTSRGS SEATLQAMNMAFASSMAELV IAEDVNNPDSIAEKTEALSQ ALKQCFRSTMGTVNRQFITE IKHLMTMFAAEAAQEAAAGD NE

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	85
15N chemical shifts	144
1H chemical shifts	824

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	entity_1	1

Entities:

Entity 1, entity_1 142 residues - 15318.378 Da.

1

GLY

SER

MET

SER

LYS

SER

PRO

TRP

ALA

2

ASN

PRO

LYS

ALA

ASN

ALA

PHE

MET

LYS

3

CYS

LEU

ILE

GLN

LYS

ILE

SER

VAL

SER

PRO

4

VAL

PHE

PRO

GLN

GLU

LYS

GLU

ASP

MET

5

GLU

SER

ILE

VAL

GLU

THR

MET

SER

ALA

6

ILE

SER

GLY

VAL

SER

THR

SER

ARG

GLY

SER

7

SER

GLU

ALA

THR

LEU

GLN

ALA

MET

ASN

MET

8

ALA

PHE

ALA

SER

MET

ALA

GLU

LEU

VAL

9

ILE

ALA

GLU

ASP

VAL

ASN

PRO

ASP

SER

10

ILE

ALA

GLU

LYS

THR

GLU

ALA

LEU

SER

GLN

11

ALA

LEU

LYS

GLN

CYS

PHE

ARG

SER

THR

MET

12

GLY

THR

VAL

ASN

ARG

GLN

PHE

ILE

THR

GLU

13

ILE

LYS

HIS

LEU

MET

THR

MET

PHE

ALA

14

GLU

ALA

GLN

GLU

ALA

GLY

ASP

15

ASN

GLU

Samples:

sample_1: NTD, [U-100% 13C; U-100% 15N], 1 ± 0.1 mM; H2O 95%; D2O, [U-2H], 5%

sample_conditions_1: ionic strength: 500 mM; pH: 7.0; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
3D CBCA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_1	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_1	isotropic	sample_conditions_1

Software:

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

Sparky, Goddard - chemical shift assignment, peak picking

X-PLOR NIH v2.53, Schwieters, Kuszewski, Tjandra and Clore - refinement, structure calculation

NMR spectrometers:

Bruker AVANCE 800 MHz

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