BMRB Entry 18888

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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/BMR18888
MolProbity Validation Chart

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Title:
EGFR transmembrane - juxtamembrane (TM-JM) segment in bicelles: MD guided NMR refined structure.
Deposition date:
2012-12-11
Original release date:
2013-02-14
Authors:
Endres, Nicolas; Das, Rahul; Smith, Adam; Arkhipov, Anton; Kovacs, Erika; Huang, Yongjian; Pelton, Jeffrey; Shan, Yibing; Shaw, David; Wemmer, David; Groves, Jay; Kuriyan, John
Citation:

Citation: Endres, Nicolas; Das, Rahul; Smith, Adam; Arkhipov, Anton; Kovacs, Erika; Huang, Yongjian; Pelton, Jeffrey; Shan, Yibing; Shaw, David; Wemmer, David; Groves, Jay; Kuriyan, John. "Conformational Coupling across the Plasma Membrane in Activation of the EGF Receptor"  Cell 152, 543-556 (2013).
PubMed: 23374349

Assembly members:

Assembly members:
EGFR_TM-JM, polymer, 60 residues, 6779.323 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: pMMHb

Entity Sequences (FASTA):

Entity Sequences (FASTA):
EGFR_TM-JM: KIPSIATGLVGALLLLLVVA LGIGLFIRRRHIVRKRTLRR LLQERELVEPLTPSGEKLWS

Data sets:
Data typeCount
13C chemical shifts215
15N chemical shifts55
1H chemical shifts287

Additional metadata:

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

Assembly:

Entity Assembly IDEntity NameEntity ID
1EGFR transmembrane - juxtamembrane (TM-JM) segment, 11
2EGFR transmembrane - juxtamembrane (TM-JM) segment, 21

Entities:

Entity 1, EGFR transmembrane - juxtamembrane (TM-JM) segment, 1 60 residues - 6779.323 Da.

Residues at the C-terminus(KLWS)represent a non-native tag

1   LYSILEPROSERILEALATHRGLYLEUVAL
2   GLYALALEULEULEULEULEUVALVALALA
3   LEUGLYILEGLYLEUPHEILEARGARGARG
4   HISILEVALARGLYSARGTHRLEUARGARG
5   LEULEUGLNGLUARGGLULEUVALGLUPRO
6   LEUTHRPROSERGLYGLULYSLEUTRPSER

Samples:

sample_1: EGFR TM-JM, [U-100% 13C; U-100% 15N; U-80% 2H], 0.300 mM; MES 50 mM; TCEP 5 mM; EDTA 1 mM; AMESF 0.05 mM; D2O, [U-2H], 10%; sodium azide 0.02%; DMPC (D54), [U-99% 2H], 9.4 mM; DHPC (D22), [U-99% 2H], 37.98 mM; H2O 90%

sample_2: EGFR TM-JM, [U-100% 13C; U-100% 15N], 0.300 mM; MES 50 mM; TCEP 5 mM; EDTA 1 mM; AMESF 0.05 mM; D2O, [U-2H], 10%; sodium azide 0.02%; DMPC (D54), [U-99% 2H], 9.4 mM; DHPC (D22), [U-99% 2H], 37.98 mM; H2O 90%

sample_3: EGFR TM-JM 0.300 mM; MES 50 mM; TCEP 5 mM; EDTA 1 mM; AMESF 0.05 mM; D2O, [U-2H], 10%; sodium azide 0.02%; DMPC (D54), [U-99% 2H], 18.8 mM; DHPC (D22), [U-99% 2H], 77.86 mM; EGFR TM-JM 0.300 mM; H2O 90%

sample_conditions_1: ionic strength: 0.05 M; pH: 6.2; pressure: 1 atm; temperature: 312 K

Experiments:

NameSampleSample stateSample conditions
2D 1H-15N HSQCsample_2isotropicsample_conditions_1
2D 1H-13C HSQCsample_2isotropicsample_conditions_1
3D HNCOsample_1isotropicsample_conditions_1
3D HNCAsample_1isotropicsample_conditions_1
3D HNCACBsample_1isotropicsample_conditions_1
3D HN(CO)CAsample_1isotropicsample_conditions_1
3D 1H-15N NOESYsample_2isotropicsample_conditions_1
3D 1H-13C NOESYsample_2isotropicsample_conditions_1
3D HCCH-COSYsample_2isotropicsample_conditions_1
3D HCCH-TOCSYsample_2isotropicsample_conditions_1
3D 15N-13C F1 filtered/F3 edited NOESY-HSQCsample_3isotropicsample_conditions_1
2D 1H-15N TROSYsample_1isotropicsample_conditions_1

Software:

TOPSPIN vv1.3, Bruker Biospin - collection

NMRDraw vv3.0, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

NMRPipe vv3.0, Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax - processing

SPARKY vv3.114, Goddard - chemical shift assignment, peak picking

TALOS+, Yang Shen, Frank Delaglio, Gabriel Cornilescu, and Ad Bax, - data analysis

CNS vv1.3, Brunger, Adams, Clore, Gros, Nilges and Read - refinement, structure solution

ProcheckNMR, Laskowski and MacArthur - data analysis

PSVS, Bhattacharya and Montelione - data analysis

Molmol, Koradi, Billeter and Wuthrich - data analysis

NMR spectrometers:

  • Bruker Avance-II 900 MHz
  • Bruker Avance 800 MHz
  • Bruker Avance 600 MHz

Related Database Links:

UNP P00533
PDB
REF XP_009241058
AlphaFold Q9UMG5

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