BMRB Entry 34628

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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34628
MolProbity Validation Chart

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Title:
NMR solution structure of SNX9 SH3 - EEEV nsP3 peptide complex
Deposition date:
2021-05-14
Original release date:
2022-04-11
Authors:
Tossavainen, H.; Permi, P.
Citation:

Citation: Tossavainen, H.; Ugurlu, H.; Karjalainen, M.; Hellman, M.; Fagerlund, R.; Saksela, K.; Permi, P.. "Structure of SNX9 SH3 in complex with a viral ligand reveals the molecular basis of its unique specificity for alanine-containing class I SH3 motifs"  Structure 30, 828-839 (2022).
PubMed: 35390274

Assembly members:

Assembly members:
entity_1, polymer, 23 residues, 2548.062 Da.
entity_2, polymer, 67 residues, 7179.922 Da.

Natural source:

Natural source:   Common Name: Eastern equine encephalitis virus   Taxonomy ID: 11021   Superkingdom: Viruses   Kingdom: not available   Genus/species: Alphavirus Eastern equine encephalitis virus

Experimental source:

Experimental source:   Production method: chemical synthesis

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: AERLIPRRPAPPVPVPARIP SPR
entity_2: GSHMATKARVMYDFAAEPGN NELTVNEGEIITITNPDVGG GWLEGRNIKGERGLVPTDYV EILPSDG

Data sets:
Data typeCount
13C chemical shifts224
15N chemical shifts66
1H chemical shifts623

Additional metadata:

  • Assembly
  • Samples and Experiments
  • Software
  • Spectrometers
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Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_22

Entities:

Entity 1, unit_1 23 residues - 2548.062 Da.

1   ALAGLUARGLEUILEPROARGARGPROALA
2   PROPROVALPROVALPROALAARGILEPRO
3   SERPROARG

Entity 2, unit_2 67 residues - 7179.922 Da.

1   GLYSERHISMETALATHRLYSALAARGVAL
2   METTYRASPPHEALAALAGLUPROGLYASN
3   ASNGLULEUTHRVALASNGLUGLYGLUILE
4   ILETHRILETHRASNPROASPVALGLYGLY
5   GLYTRPLEUGLUGLYARGASNILELYSGLY
6   GLUARGGLYLEUVALPROTHRASPTYRVAL
7   GLUILELEUPROSERASPGLY

Samples:

sample_1: SNX9 SH3, [U-13C; U-15N], 1 mM; EEEV nsP3 peptide 1 mM; sodium phosphate 20 mM; sodium chloride 50 mM

sample_conditions_1: ionic strength: 0.15 M; pH: 6.5; pressure: 1 atm; temperature: 298 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 HNCOsample_1isotropicsample_conditions_1
3D iHNCOsample_1isotropicsample_conditions_1
3D H(CCO)NHsample_1isotropicsample_conditions_1
3D (H)CC(CO)NHsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-COSYsample_1isotropicsample_conditions_1
3D HCCmHm-TOCSYsample_1isotropicsample_conditions_1
2D (HB)CB(CGCD)HDsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aromaticsample_1isotropicsample_conditions_1
3D 1H-13C NOESY aliphaticsample_1isotropicsample_conditions_1
2D (HB)CB(CGCDCE)HEsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_1isotropicsample_conditions_1
X-filtered-, 13C-edited NOESYsample_1isotropicsample_conditions_1
F1, F2, 15N, 13C-filtered NOESYsample_1isotropicsample_conditions_1
X-filtered NOESYsample_1isotropicsample_conditions_1

Software:

TopSpin, Bruker Biospin - collection, processing

CcpNmr Analysis, CCPN - chemical shift assignment

CYANA, Guntert, Mumenthaler and Wuthrich - structure calculation

Amber, Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman - refinement

NMR spectrometers:

  • Bruker AVANCE III 800 MHz

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