245,392
Structures from the PDB archive

1,068,577
Computed Structure Models (CSM)

4R3P|pdb_00004r3p

Crystal structures of EGFR in complex with Mig6

PDB DOI: https://doi.org/10.2210/pdb4R3P/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2014-08-17 Released: 2015-08-12
Deposition Author(s): Park, E.,Kim, N.,Yi, Z.,Cho, A.,Kim, K.,Ficarro, S.B.,Park, A.,Park, W.Y.,Murray, B.,Meyerson, M.,Beroukim, R.,Marto, J.A.,Cho, J.,Eck, M.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.240 (Depositor), 0.248 (DCC)
R-Value Work:
0.208 (Depositor), 0.215 (DCC)
R-Value Observed:
0.211 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Structure and mechanism of activity-based inhibition of the EGF receptor by Mig6.

Park, E., Kim, N., Ficarro, S.B., Zhang, Y., Lee, B.I., Cho, A., Kim, K., Park, A.K., Park, W.Y., Murray, B., Meyerson, M., Beroukhim, R., Marto, J.A., Cho, J., Eck, M.J.

(2015) Nat Struct Mol Biol 22: 703-711

PubMed: 26280531 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/nsmb.3074
Primary Citation of Related Structures:
4R3P,4R3R,4ZJV

PubMed Abstract:
Mig6 is a feedback inhibitor that directly binds, inhibits and drives internalization of ErbB-family receptors. Mig6 selectively targets activated receptors. Here we found that the epidermal growth factor receptor (EGFR) phosphorylates Mig6 on Y394 and that this phosphorylation is primed by prior phosphorylation of an adjacent residue, Y395, by Src. Crystal structures of human EGFR-Mig6 complexes reveal the structural basis for enhanced phosphorylation of primed Mig6 and show how Mig6 rearranges after phosphorylation by EGFR to effectively irreversibly inhibit the same receptor that catalyzed its phosphorylation. This dual phosphorylation site allows Mig6 to inactivate EGFR in a manner that requires activation of the target receptor and that can be modulated by Src. Loss of Mig6 is a driving event in human cancer; analysis of 1,057 gliomas reveals frequent focal deletions of ERRFI1, the gene that encodes Mig6, in EGFR-amplified glioblastomas.

Organizational Affiliation

Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA USA.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA USA.

Samsung Genome Institute, Samsung Medical Center, Seoul, Republic of Korea.

Samsung Advanced Institute for Health Sciences and Technology, SungKyunKwan University, Seoul, Republic of Korea.

Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA USA.

Biomolecular Function Research Branch, Division of Convergence Technology, Research Institute, National Cancer Center, Goyang, Gyeonggi Republic of Korea.

Broad Institute of Harvard and MIT, Cambridge, MA USA.

Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA USA.

Department of Pathology, Harvard Medical School, Boston, MA USA.

Department of Medicine, Harvard Medical School, Boston, MA USA.

Macromolecule Content

Total Structure Weight: 37.92 kDa
Atom Count: 2,559
Modeled Residue Count: 317
Deposited Residue Count: 330
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Epidermal growth factor receptor	A	323	Homo sapiens	Mutation(s): 1 Gene Names: EGFR, ERBB, ERBB1, HER1 EC: 2.7.10.1
UniProt & NIH Common Fund Data Resources
Find proteins for P00533 (Homo sapiens) Explore P00533 Go to UniProtKB: P00533
PHAROS: P00533 GTEx: ENSG00000146648
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00533
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide from ERBB receptor feedback inhibitor 1	B	7	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UJM3 (Homo sapiens) Explore Q9UJM3 Go to UniProtKB: Q9UJM3
PHAROS: Q9UJM3 GTEx: ENSG00000116285
Entity Groups
UniProt Group	Q9UJM3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR Query on PTR	B	L-PEPTIDE LINKING	C₉ H₁₂ N O₆ P		TYR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.240 (Depositor), 0.248 (DCC)
R-Value Work: 0.208 (Depositor), 0.215 (DCC)
R-Value Observed: 0.211 (Depositor)

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.828	α = 90
b = 143.828	β = 90
c = 143.828	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASES	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2015-08-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-08-12
Type: Initial release
Version 1.1: 2015-08-26
Changes: Database references
Version 1.2: 2015-09-16
Changes: Database references
Version 1.3: 2024-11-27
Changes: Data collection, Database references, Derived calculations, Structure summary