BMRB Entry 25564

Click here to enlarge.

PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR25564
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

Title:
Structure of the Third Type III Domain from Human Fibronectin
Deposition date:
2015-04-04
Original release date:
2015-11-09
Authors:
Stine, Jessica; Sun, Yizhi; Armstrong, Geoffrey; Briknarova, Klara
Citation:

Citation: Stine, Jessica; Sun, Yizhi; Armstrong, Geoffrey; Briknarova, Klara. "Structure and Unfolding of the Third Type III Domain from Human Fibronectin"  Biochemistry 54, 6724-6733 (2015).
PubMed: 26517579

Assembly members:

Assembly members:
entity, polymer, 106 residues, 11337.317 Da.

Natural source:

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

Experimental source:

Experimental source:   Production method: recombinant technology   Host organism: Escherichia coli   Vector: pET15b

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity: GSHMGTTTAPDAPPDPTVDQ VDDTSIVVRWSRPQAPITGY RIVYSPSVEGSSTELNLPET ANSVTLSDLQPGVQYNITIY AVEENQESTPVVIQQETTGT PRSDGT

Data sets:
Data typeCount
13C chemical shifts439
15N chemical shifts99
1H chemical shifts681

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1entity1

Entities:

Entity 1, entity 106 residues - 11337.317 Da.

The recombinant protein contains six extraneous amino acids at the N-terminus, residues 808-905 of human fibronectin, and two extraneous amino acids at the C-terminus (gshmgtTTAP...PRSDgt).

1   GLYSERHISMETGLYTHRTHRTHRALAPRO
2   ASPALAPROPROASPPROTHRVALASPGLN
3   VALASPASPTHRSERILEVALVALARGTRP
4   SERARGPROGLNALAPROILETHRGLYTYR
5   ARGILEVALTYRSERPROSERVALGLUGLY
6   SERSERTHRGLULEUASNLEUPROGLUTHR
7   ALAASNSERVALTHRLEUSERASPLEUGLN
8   PROGLYVALGLNTYRASNILETHRILETYR
9   ALAVALGLUGLUASNGLNGLUSERTHRPRO
10   VALVALILEGLNGLNGLUTHRTHRGLYTHR
11   PROARGSERASPGLYTHR

Samples:

sample_1: entity, [U-99% 13C; U-99% 15N], 0.6 mM; sodium phosphate 10 mM; potassium phosphate 1.8 mM; sodium chloride 140 mM; potassium chloride 2.7 mM; H2O 90%; D2O 10%

sample_2: entity, [U-99% 15N], 0.6 mM; sodium phosphate 10 mM; potassium phosphate 1.8 mM; sodium chloride 140 mM; potassium chloride 2.7 mM; H2O 90%; D2O 10%

sample_3: entity 0.6 mM; sodium phosphate 10 mM; potassium phosphate 1.8 mM; sodium chloride 140 mM; potassium chloride 2.7 mM; H2O 90%; D2O 10%

sample_4: entity 0.6 mM; sodium phosphate 10 mM; potassium phosphate 1.8 mM; sodium chloride 140 mM; potassium chloride 2.7 mM; D2O 100%

sample_5: entity, [U-99% 13C; U-99% 15N], 0.9 mM; sodium phosphate 10 mM; potassium phosphate 1.8 mM; sodium chloride 140 mM; potassium chloride 2.7 mM; entity 0.9 mM; H2O 90%; D2O 10%

sample_conditions_1: ionic strength: 0.17 M; pH: 7.5; pressure: 1 atm; temperature: 298.15 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aromaticsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D C(CO)NHsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D CCH-TOCSYsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
2D HBCB(CGCD)HDsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
2D 15N HMQCsample_2isotropicsample_conditions_1
2D DQF-COSYsample_3isotropicsample_conditions_1
2D 1H-1H TOCSYsample_3isotropicsample_conditions_1
2D 1H-1H NOESYsample_3isotropicsample_conditions_1
2D DQF-COSYsample_4isotropicsample_conditions_1
2D 1H-1H TOCSYsample_4isotropicsample_conditions_1
2D 1H-1H NOESYsample_4isotropicsample_conditions_1
2D 13C/15N-filtered 13C/15N-edited NOESYsample_5isotropicsample_conditions_1

Software:

VNMRJ, Agilent - collection

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

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

CcpNmr, CCPN - chemical shift assignment, data analysis, peak picking

ARIA, Linge, O'Donoghue and Nilges - refinement, structure solution

CNS, Brunger, Adams, Clore, Gros, Nilges and Read - refinement, structure solution

TALOS, Cornilescu, Delaglio and Bax - generation of torsion angle restraints

NMR spectrometers:

  • Varian Varian NMR System 600 MHz
  • Varian Varian NMR System 800 MHz

Related Database Links:

UNP P02751
AlphaFold Q9UMK2

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