BMRB Entry 30584

Name: Solution structure of human myeloid-derived growth factor
Published: 2019-11-05

Chem Shift validation: AVS_full, LACS
BMRB Entry DOI: doi:10.13018/BMR30584

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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: Solution structure of human myeloid-derived growth factor PubMed: 31819058

Deposition date: 2019-03-07 Original release date: 2019-11-05

Authors: Bortnov, V.; Tonelli, M.; Lee, W.; Markley, J.; Mosher, D.

Citation: Bortnov, Valeriu; Tonelli, Marco; Lee, Woonghee; Lin, Ziqing; Annis, Douglas; Demerdash, Omar; Bateman, Alex; Mitchell, Julie; Ge, Ying; Markley, John; Mosher, Deane. "Solution structure of human myeloid-derived growth factor suggests a conserved function in the endoplasmic reticulum" Nat. Comm. 10, 5612-5612 (2019).

Assembly members:
entity_1, polymer, 147 residues, 16286.207 Da.

Natural source: Common Name: Human Taxonomy ID: 9606 Superkingdom: Eukaryota Kingdom: Metazoa Genus/species: Homo sapiens

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

Entity Sequences (FASTA):
entity_1: GSKGTVSEPTTVAFDVRPGG VVHSFSHNVGPGDKYTCMFT YASQGGTNEQWQMSLGTSED HQHFTCTIWRPQGKSYLYFT QFKAEVRGAEIEYAMAYSKA AFERESDVPLKTEEFEVTKT AVAHRPGAFKAELSKLVIVA KASRTEL

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1
spectral_peak_list

Data type	Count
13C chemical shifts	630
15N chemical shifts	149
1H chemical shifts	972

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_1 147 residues - 16286.207 Da.

1

GLY

SER

LYS

GLY

THR

VAL

SER

GLU

PRO

THR

2

THR

VAL

ALA

PHE

ASP

VAL

ARG

PRO

GLY

3

VAL

HIS

SER

PHE

SER

HIS

ASN

VAL

GLY

4

PRO

GLY

ASP

LYS

TYR

THR

CYS

MET

PHE

THR

5

TYR

ALA

SER

GLN

GLY

THR

ASN

GLU

GLN

6

TRP

GLN

MET

SER

LEU

GLY

THR

SER

GLU

ASP

7

HIS

GLN

HIS

PHE

THR

CYS

THR

ILE

TRP

ARG

8

PRO

GLN

GLY

LYS

SER

TYR

LEU

TYR

PHE

THR

9

GLN

PHE

LYS

ALA

GLU

VAL

ARG

GLY

ALA

GLU

10

ILE

GLU

TYR

ALA

MET

ALA

TYR

SER

LYS

ALA

11

ALA

PHE

GLU

ARG

GLU

SER

ASP

VAL

PRO

LEU

12

LYS

THR

GLU

PHE

GLU

VAL

THR

LYS

THR

13

ALA

VAL

ALA

HIS

ARG

PRO

GLY

ALA

PHE

LYS

14

ALA

GLU

LEU

SER

LYS

LEU

VAL

ILE

VAL

ALA

15

LYS

ALA

SER

ARG

THR

GLU

LEU

Samples:

sample_1: MYDGF, [U-15N; U-13C], 8.25 mg/mL; sodium phosphate 9 mM; sodium chloride 135 mM; DSS 15 uM; sodium azide 0.02 % w/v

sample_conditions_1: ionic strength: 135 mM; pH: 6; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
3D 1H,15N-HSQC NOESY	sample_1	isotropic	sample_conditions_1
3D 1H,13C-HSQC NOESY aliphatic	sample_1	isotropic	sample_conditions_1
3D 1H,13C-HSQC NOESY aromatic	sample_1	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aliphatic	sample_1	isotropic	sample_conditions_1
2D 1H-13C HSQC aromatic	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 HNCO	sample_1	isotropic	sample_conditions_1
3D C(CO)NH	sample_1	isotropic	sample_conditions_1
3D HBHA(CO)NH	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY aliphatic	sample_1	isotropic	sample_conditions_1
3D H(CCO)NH	sample_1	isotropic	sample_conditions_1
2D (HB)CB(CGCD)HD aromatic	sample_1	isotropic	sample_conditions_1
2D (HB)CB(CGCDCE)HDHE aromatic	sample_1	isotropic	sample_conditions_1
3D HCCH-TOCSY aromatic	sample_1	isotropic	sample_conditions_1
3D 1H,15N-HSQC NOESY 1H,13C-HSQC	sample_1	isotropic	sample_conditions_1

Software:

VNMR v4.2, Varian - collection

TopSpin v3.5, Bruker Biospin - collection

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

NMRFAM-SPARKY, W. Lee, M. Tonelli and J.L. Markley - chemical shift assignment, peak picking

I-PINE, W. Lee, A. Bahrami, H. Dashti, H.R. Eghbalnia, M. Tonelli, W.M. Westler, J.L. Markley - chemical shift assignment

PONDEROSA-C/S, W. Lee, J.L. Stark, J.L. Markley - refinement, structure calculation

TALOS-N, Shen and Bax - structure calculation

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

PyMOL, Schroedinger, Inc. - refinement

NMR spectrometers:

Varian VNS 800 MHz
Bruker AvanceIII 600 MHz
Bruker AvanceIII 900 MHz
Varian VNS 600 MHz

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