BMRB Entry 30812

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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/BMR30812
MolProbity Validation Chart

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Title:
Solution NMR structure of CDHR3 extracellular domain EC1
Deposition date:
2020-11-06
Original release date:
2021-01-26
Authors:
Lee, W.; Tonelli, M.; Frederick, R.; Watters, K.; Markley, J.; Palmenberg, A.
Citation:

Citation: Lee, W.; Frederick, R.; Tonelli, M.; Palmenberg, A.. "Solution NMR Determination of the CDHR3 Rhinovirus-C Binding Domain, EC1"  Viruses 13, 159-159 (2021).

Assembly members:

Assembly members:
entity_1, polymer, 126 residues, 13688.275 Da.
entity_CA, non-polymer, 40.078 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

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: MASDYKDDDDKLHLILLPAT GNVAENSPPGTSVHKFSVKL SASLSPVIPGFPQIVNSNPL TEAFRVNWLSGTYFEVVTTG MEQLDFETGPNIFDLQIYVK DEVGVTDLQVLTVQVTDVNE PPGGTK

Data sets:
Data typeCount
13C chemical shifts493
15N chemical shifts113
1H chemical shifts797

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1unit_11
2unit_22
3unit_32
4unit_42

Entities:

Entity 1, unit_1 126 residues - 13688.275 Da.

1   METALASERASPTYRLYSASPASPASPASP
2   LYSLEUHISLEUILELEULEUPROALATHR
3   GLYASNVALALAGLUASNSERPROPROGLY
4   THRSERVALHISLYSPHESERVALLYSLEU
5   SERALASERLEUSERPROVALILEPROGLY
6   PHEPROGLNILEVALASNSERASNPROLEU
7   THRGLUALAPHEARGVALASNTRPLEUSER
8   GLYTHRTYRPHEGLUVALVALTHRTHRGLY
9   METGLUGLNLEUASPPHEGLUTHRGLYPRO
10   ASNILEPHEASPLEUGLNILETYRVALLYS
11   ASPGLUVALGLYVALTHRASPLEUGLNVAL
12   LEUTHRVALGLNVALTHRASPVALASNGLU
13   PROPROGLYGLYTHRLYS

Entity 2, unit_2 - Ca - 40.078 Da.

1   CA

Samples:

sample_1: CDHR3 extracellular domain EC1, [U-100% 13C; U-100% 15N], 0.4 mM; HEPES 50 mM; potassium chloride 300 mM; calcium chloride 10 mM; sodium azide 0.05 % w/v; D2O, [U-100% 2H], 10 % v/v

sample_conditions_1: ionic strength: 380 mM; pH: 7.0; pressure: 1 atm; temperature: 293 K

Experiments:

NameSampleSample stateSample conditions
3D HNCACBsample_1isotropicsample_conditions_1
3D CBCA(CO)NHsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D HN(CA)COsample_1isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HBHA(CO)NHsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D HCCH-TOCSYsample_1isotropicsample_conditions_1
3D HCCH-COSYsample_1isotropicsample_conditions_1
3D NOESY 1H-15N HSQCsample_1isotropicsample_conditions_1
3D NOESY 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
2D 1H-13C HSQC aliphaticsample_1isotropicsample_conditions_1
2D 1H-15N HSQCsample_1isotropicsample_conditions_1

Software:

TopSpin, Bruker Biospin - collection

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

NMRFAM-SPARKY, Lee, Tonelli, Markley - peak picking

I-PINE, Lee, Bahrami, Dashti, Eghbalnia, Tonelli, Westler and Markley - chemical shift assignment

PONDEROSA-C/S, Lee, Petit, Cornilescu, Stark and Markley - structure calculation

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

NMR spectrometers:

  • Bruker AVANCE III 600 MHz
  • Varian VNMR 600 MHz
  • Varian VNMR 800 MHz

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