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- PDB-5wb8: Crystal structure of the epidermal growth factor receptor extrace... -

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Basic information

Entry
Database: PDB / ID: 5wb8
TitleCrystal structure of the epidermal growth factor receptor extracellular region in complex with epigen
Components
  • Epidermal growth factor receptor
  • Epigen
KeywordsSIGNALING PROTEIN / Receptor tyrosine kinase / growth factor / signaling / membrane protein
Function / homology
Function and homology information


transmembrane receptor protein tyrosine kinase activator activity / multivesicular body, internal vesicle lumen / negative regulation of cardiocyte differentiation / epidermal growth factor receptor binding / Shc-EGFR complex / positive regulation of protein kinase C signaling / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity / EGFR interacts with phospholipase C-gamma / regulation of peptidyl-tyrosine phosphorylation ...transmembrane receptor protein tyrosine kinase activator activity / multivesicular body, internal vesicle lumen / negative regulation of cardiocyte differentiation / epidermal growth factor receptor binding / Shc-EGFR complex / positive regulation of protein kinase C signaling / Inhibition of Signaling by Overexpressed EGFR / epidermal growth factor receptor activity / EGFR interacts with phospholipase C-gamma / regulation of peptidyl-tyrosine phosphorylation / epidermal growth factor binding / response to UV-A / PLCG1 events in ERBB2 signaling / ERBB2-EGFR signaling pathway / morphogenesis of an epithelial fold / PTK6 promotes HIF1A stabilization / ERBB2 Activates PTK6 Signaling / digestive tract morphogenesis / Signaling by EGFR / intracellular vesicle / negative regulation of epidermal growth factor receptor signaling pathway / eyelid development in camera-type eye / cerebral cortex cell migration / protein insertion into membrane / ERBB2 Regulates Cell Motility / protein tyrosine kinase activator activity / Respiratory syncytial virus (RSV) attachment and entry / Signaling by ERBB4 / PI3K events in ERBB2 signaling / positive regulation of phosphorylation / positive regulation of peptidyl-serine phosphorylation / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / hair follicle development / MAP kinase kinase kinase activity / GAB1 signalosome / positive regulation of G1/S transition of mitotic cell cycle / embryonic placenta development / salivary gland morphogenesis / Signaling by ERBB2 / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / transmembrane receptor protein tyrosine kinase activity / EGFR Transactivation by Gastrin / positive regulation of mitotic nuclear division / GRB2 events in ERBB2 signaling / ossification / SHC1 events in ERBB2 signaling / basal plasma membrane / positive regulation of DNA repair / cellular response to epidermal growth factor stimulus / positive regulation of DNA replication / epithelial cell proliferation / positive regulation of epithelial cell proliferation / Signal transduction by L1 / positive regulation of protein localization to plasma membrane / NOTCH3 Activation and Transmission of Signal to the Nucleus / cellular response to amino acid stimulus / growth factor activity / phosphatidylinositol 3-kinase/protein kinase B signal transduction / cellular response to estradiol stimulus / EGFR downregulation / clathrin-coated endocytic vesicle membrane / Signaling by ERBB2 TMD/JMD mutants / Constitutive Signaling by EGFRvIII / cell-cell adhesion / receptor protein-tyrosine kinase / Signaling by ERBB2 ECD mutants / negative regulation of protein catabolic process / Signaling by ERBB2 KD Mutants / positive regulation of miRNA transcription / kinase binding / ruffle membrane / Downregulation of ERBB2 signaling / epidermal growth factor receptor signaling pathway / positive regulation of protein phosphorylation / cell morphogenesis / positive regulation of fibroblast proliferation / neuron differentiation / HCMV Early Events / Constitutive Signaling by Aberrant PI3K in Cancer / actin filament binding / cell junction / transmembrane signaling receptor activity / positive regulation of canonical Wnt signaling pathway / Cargo recognition for clathrin-mediated endocytosis / PIP3 activates AKT signaling / MAPK cascade / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / Clathrin-mediated endocytosis / virus receptor activity / ATPase binding / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / positive regulation of cell growth / double-stranded DNA binding / protein tyrosine kinase activity / early endosome membrane / angiogenesis / protein phosphatase binding
Similarity search - Function
Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A / Receptor L-domain / : / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Alpha-Beta Horseshoe / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV ...Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A / Receptor L-domain / : / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Alpha-Beta Horseshoe / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Receptor L-domain / Furin-like cysteine-rich domain / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like repeat / Furin-like repeats / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / : / EGF-like domain / Ribbon / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Epidermal growth factor receptor / Epigen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBessman, N.J. / Freed, D.M. / Moore, J.O. / Ferguson, K.M. / Lemmon, M.A.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA198164 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)U54 CA193417 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM008275 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA112552 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32 GM109688 United States
CitationJournal: Cell / Year: 2017
Title: EGFR Ligands Differentially Stabilize Receptor Dimers to Specify Signaling Kinetics.
Authors: Freed, D.M. / Bessman, N.J. / Kiyatkin, A. / Salazar-Cavazos, E. / Byrne, P.O. / Moore, J.O. / Valley, C.C. / Ferguson, K.M. / Leahy, D.J. / Lidke, D.S. / Lemmon, M.A.
History
DepositionJun 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 1, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.grant_number
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 23, 2022Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_audit_support / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Epidermal growth factor receptor
B: Epigen
C: Epigen
D: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,97110
Polymers126,7764
Non-polymers3,1956
Water1,22568
1
A: Epidermal growth factor receptor
C: Epigen
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9855
Polymers63,3882
Non-polymers1,5973
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint13 kcal/mol
Surface area25430 Å2
MethodPISA
2
B: Epigen
D: Epidermal growth factor receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9855
Polymers63,3882
Non-polymers1,5973
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint19 kcal/mol
Surface area26210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.050, 104.050, 285.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322

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Components

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Protein , 2 types, 4 molecules ADBC

#1: Protein Epidermal growth factor receptor / Proto-oncogene c-ErbB-1 / Receptor tyrosine-protein kinase erbB-1


Mass: 56522.199 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EGFR, ERBB, ERBB1, HER1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9
References: UniProt: P00533, receptor protein-tyrosine kinase
#2: Protein Epigen / Epithelial mitogen / EPG


Mass: 6865.699 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPGN, UNQ3072/PRO9904 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 / References: UniProt: Q6UW88

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Sugars , 3 types, 6 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE

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Non-polymers , 1 types, 68 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.71 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 magnesium formate, 15% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 3→49.04 Å / Num. obs: 31787 / % possible obs: 97.19 % / Redundancy: 5.3 % / Biso Wilson estimate: 25.29 Å2 / Rmerge(I) obs: 0.28 / Rpim(I) all: 0.141 / Net I/σ(I): 6.7
Reflection shellResolution: 3→3.11 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.655 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3148 / CC1/2: 0.604 / Rpim(I) all: 0.29 / % possible all: 98.75

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
PHENIXdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: EGFR domains I and III from PDB entry 3NJP

3njp


Resolution: 3→48.889 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.17 / Phase error: 30.45
RfactorNum. reflection% reflection
Rfree0.3116 1993 6.34 %
Rwork0.2653 --
obs0.2683 31435 96.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 137.98 Å2 / Biso mean: 53.7908 Å2 / Biso min: 0 Å2
Refinement stepCycle: final / Resolution: 3→48.889 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8020 0 212 69 8301
Biso mean--82.03 24.7 -
Num. residues----1073
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028438
X-RAY DIFFRACTIONf_angle_d0.65411501
X-RAY DIFFRACTIONf_chiral_restr0.0451335
X-RAY DIFFRACTIONf_plane_restr0.0031478
X-RAY DIFFRACTIONf_dihedral_angle_d3.7485006
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0001-3.07510.40961430.38942110225399
3.0751-3.15830.35051410.32052087222899
3.1583-3.25120.381430.30222099224299
3.2512-3.35610.31871420.2922098224099
3.3561-3.4760.34241410.30062085222698
3.476-3.61520.3671390.2952054219396
3.6152-3.77960.33061330.26442003213694
3.7796-3.97880.29641420.2512083222597
3.9788-4.2280.28891420.23552093223597
4.228-4.55420.26291410.20692086222796
4.5542-5.01210.2431430.2052114225797
5.0121-5.73640.2861450.23582134227997
5.7364-7.22350.251450.27722149229496
7.2235-48.89530.30721530.24552247240094
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.224-0.29230.81122.610.35651.6362-0.11660.2563-0.2834-0.2484-0.1063-0.34040.25010.41180.03610.19880.04620.11220.285-0.06170.4988-18.701933.23443.6354
20.4572-0.35510.37240.6707-0.34040.8707-0.0052-0.17430.0995-0.04070.05550.08410.07450.2865-0.07680.3161-0.0339-0.00760.2444-0.09160.2802-28.512445.238420.4127
31.31580.3323-0.89422.52960.44991.9147-0.03070.0699-0.0690.09140.1042-0.06910.25330.083-0.02260.1936-0.0213-0.03340.2285-0.02170.202-30.52047.544124.0236
48.8184-0.24661.71213.8738-1.92071.23860.0364-1.2450.30310.70330.00730.364-0.0152-0.5814-0.37650.5504-0.2188-0.00530.61310.19530.4228-48.022-0.542429.7154
50.6856-0.8041-0.61823.06220.8512.3268-0.31050.28360.67050.24490.4817-0.62860.36250.08870.09250.27010.0238-0.02410.30380.06620.3328-14.031611.32148.0558
63.7680.3062-0.34912.34441.40471.84280.1094-0.06030.4924-0.06060.0615-0.7085-0.09280.2041-0.1610.3336-0.0167-0.02880.20760.03750.3521-31.6034-21.0948-0.5059
70.44010.1173-0.27180.14080.4812.46890.23430.17460.056-0.066-0.1094-0.22950.34830.4282-0.07930.24210.0962-0.05980.2493-0.07220.2842-45.2928-27.4453-17.6197
82.5580.03061.73051.69360.02012.4943-0.27470.36940.3046-0.15850.2905-0.3174-0.06280.3366-0.00180.3969-0.00980.10310.3711-0.00630.3201-30.40017.522-20.3769
93.2471-0.7813-2.12243.1402-2.18283.8413-0.0729-0.59230.22341.2630.0126-0.0676-1.20770.51550.59480.77760.0243-0.23460.23220.00920.5553-47.654720.8826-25.9738
100.2398-0.224-0.65870.69630.38235.33740.248-0.6138-0.30510.31980.2936-1.027-0.07131.87-0.27290.4607-0.0556-0.0940.7076-0.10380.9796-15.62121.6543-5.8083
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 164 )A3 - 164
2X-RAY DIFFRACTION2chain 'A' and (resid 165 through 311 )A165 - 311
3X-RAY DIFFRACTION3chain 'A' and (resid 312 through 479 )A312 - 479
4X-RAY DIFFRACTION4chain 'A' and (resid 480 through 504 )A480 - 504
5X-RAY DIFFRACTION5chain 'C' and (resid 44 through 79 )C44 - 79
6X-RAY DIFFRACTION6chain 'D' and (resid 1 through 164 )D1 - 164
7X-RAY DIFFRACTION7chain 'D' and (resid 165 through 311 )D165 - 311
8X-RAY DIFFRACTION8chain 'D' and (resid 312 through 479 )D312 - 479
9X-RAY DIFFRACTION9chain 'D' and (resid 480 through 506 )D480 - 506
10X-RAY DIFFRACTION10chain 'B' and (resid 38 through 79 )B38 - 79

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