BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Entry 30584

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 typeCount
13C chemical shifts630
15N chemical shifts149
1H chemical shifts972

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity_11

Entities:

Entity 1, entity_1 147 residues - 16286.207 Da.

1   GLYSERLYSGLYTHRVALSERGLUPROTHR
2   THRVALALAPHEASPVALARGPROGLYGLY
3   VALVALHISSERPHESERHISASNVALGLY
4   PROGLYASPLYSTYRTHRCYSMETPHETHR
5   TYRALASERGLNGLYGLYTHRASNGLUGLN
6   TRPGLNMETSERLEUGLYTHRSERGLUASP
7   HISGLNHISPHETHRCYSTHRILETRPARG
8   PROGLNGLYLYSSERTYRLEUTYRPHETHR
9   GLNPHELYSALAGLUVALARGGLYALAGLU
10   ILEGLUTYRALAMETALATYRSERLYSALA
11   ALAPHEGLUARGGLUSERASPVALPROLEU
12   LYSTHRGLUGLUPHEGLUVALTHRLYSTHR
13   ALAVALALAHISARGPROGLYALAPHELYS
14   ALAGLULEUSERLYSLEUVALILEVALALA
15   LYSALASERARGTHRGLULEU

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:

NameSampleSample stateSample conditions
3D 1H,15N-HSQC NOESYsample_1isotropicsample_conditions_1
3D 1H,13C-HSQC NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H,13C-HSQC NOESY aromaticsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSY aliphaticsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
2D (HB)CB(CGCD)HD aromaticsample_1isotropicsample_conditions_1
2D (HB)CB(CGCDCE)HDHE aromaticsample_1isotropicsample_conditions_1
3D HCCH-TOCSY aromaticsample_1isotropicsample_conditions_1
3D 1H,15N-HSQC NOESY 1H,13C-HSQCsample_1isotropicsample_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