BMRB Entry 18888

Name: EGFR transmembrane - juxtamembrane (TM-JM) segment in bicelles: MD guided NMR refined structure.
Published: 2013-02-14

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PDB ID: 2m20
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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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Title: EGFR transmembrane - juxtamembrane (TM-JM) segment in bicelles: MD guided NMR refined structure. PubMed: 23374349

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: 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).

Assembly members:
EGFR_TM-JM, polymer, 60 residues, 6779.323 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):
EGFR_TM-JM: KIPSIATGLVGALLLLLVVA LGIGLFIRRRHIVRKRTLRR LLQERELVEPLTPSGEKLWS

Data sets:

assigned_chemical_shifts
- assigned_chem_shift_list_1

Data type	Count
13C chemical shifts	215
15N chemical shifts	55
1H chemical shifts	287

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	EGFR transmembrane - juxtamembrane (TM-JM) segment, 1	1
2	EGFR transmembrane - juxtamembrane (TM-JM) segment, 2	1

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	LYS	ILE	PRO	SER	ILE	ALA	THR	GLY	LEU	VAL
2	GLY	ALA	LEU	LEU	LEU	LEU	LEU	VAL	VAL	ALA
3	LEU	GLY	ILE	GLY	LEU	PHE	ILE	ARG	ARG	ARG
4	HIS	ILE	VAL	ARG	LYS	ARG	THR	LEU	ARG	ARG
5	LEU	LEU	GLN	GLU	ARG	GLU	LEU	VAL	GLU	PRO
6	LEU	THR	PRO	SER	GLY	GLU	LYS	LEU	TRP	SER

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:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_1
3D HNCO	sample_1	isotropic	sample_conditions_1
3D HNCA	sample_1	isotropic	sample_conditions_1
3D HNCACB	sample_1	isotropic	sample_conditions_1
3D HN(CO)CA	sample_1	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_2	isotropic	sample_conditions_1
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_1
3D HCCH-COSY	sample_2	isotropic	sample_conditions_1
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_1
3D 15N-13C F1 filtered/F3 edited NOESY-HSQC	sample_3	isotropic	sample_conditions_1
2D 1H-15N TROSY	sample_1	isotropic	sample_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

UNP	P00533
PDB	2M20
REF	XP_009241058

Biological Magnetic Resonance Data Bank