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- PDB-1ivo: Crystal Structure of the Complex of Human Epidermal Growth Factor... -

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Basic information

Entry
Database: PDB / ID: 1ivo
TitleCrystal Structure of the Complex of Human Epidermal Growth Factor and Receptor Extracellular Domains.
Components
  • Epidermal Growth Factor Receptor
  • Epidermal growth factor
KeywordsTRANSFERASE/SIGNALING PROTEIN / Transmembrane / Glycoprotein / Receptor / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics / TRANSFERASE-SIGNALING PROTEIN COMPLEX
Function / homology
Function and homology information


Inhibition of Signaling by Overexpressed EGFR / EGFR interacts with phospholipase C-gamma / negative regulation of secretion / negative regulation of cholesterol efflux / positive regulation of hyaluronan biosynthetic process / PLCG1 events in ERBB2 signaling / positive regulation of cerebellar granule cell precursor proliferation / cerebellar granule cell precursor proliferation / ERBB2-EGFR signaling pathway / positive regulation of epithelial tube formation ...Inhibition of Signaling by Overexpressed EGFR / EGFR interacts with phospholipase C-gamma / negative regulation of secretion / negative regulation of cholesterol efflux / positive regulation of hyaluronan biosynthetic process / PLCG1 events in ERBB2 signaling / positive regulation of cerebellar granule cell precursor proliferation / cerebellar granule cell precursor proliferation / ERBB2-EGFR signaling pathway / positive regulation of epithelial tube formation / ERBB2 Activates PTK6 Signaling / regulation of calcium ion import / positive regulation of protein localization to early endosome / regulation of protein localization to cell surface / Signaling by EGFR / transmembrane receptor protein tyrosine kinase activator activity / Signaling by ERBB4 / positive regulation of ubiquitin-dependent protein catabolic process / ERBB2 Regulates Cell Motility / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / PI3K events in ERBB2 signaling / regulation of receptor signaling pathway via JAK-STAT / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / NFE2L2 regulating tumorigenic genes / epidermal growth factor receptor binding / branching morphogenesis of an epithelial tube / positive regulation of DNA binding / GAB1 signalosome / positive regulation of phosphorylation / positive regulation of receptor internalization / Signaling by ERBB2 / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / Complex I biogenesis / mammary gland alveolus development / GRB2 events in ERBB2 signaling / Respiratory electron transport / SHC1 events in ERBB2 signaling / epithelial cell proliferation / positive regulation of endothelial cell proliferation / ERK1 and ERK2 cascade / NOTCH3 Activation and Transmission of Signal to the Nucleus / positive regulation of endothelial cell migration / positive regulation of mitotic nuclear division / EGFR downregulation / Signaling by ERBB2 TMD/JMD mutants / platelet alpha granule lumen / guanyl-nucleotide exchange factor activity / : / positive regulation of peptidyl-threonine phosphorylation / Constitutive Signaling by EGFRvIII / clathrin-coated endocytic vesicle membrane / mitochondrial electron transport, NADH to ubiquinone / Signaling by ERBB2 ECD mutants / proton motive force-driven mitochondrial ATP synthesis / Signaling by ERBB2 KD Mutants / epidermal growth factor receptor signaling pathway / NADH dehydrogenase (ubiquinone) activity / Downregulation of ERBB2 signaling / growth factor activity / aerobic respiration / Constitutive Signaling by Aberrant PI3K in Cancer / positive regulation of canonical Wnt signaling pathway / Cargo recognition for clathrin-mediated endocytosis / positive regulation of peptidyl-tyrosine phosphorylation / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / PIP3 activates AKT signaling / Clathrin-mediated endocytosis / Platelet degranulation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / angiogenesis / Extra-nuclear estrogen signaling / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor ligand activity / electron transfer activity / mitochondrial inner membrane / positive regulation of cell migration / lysosomal membrane / positive regulation of cell population proliferation / calcium ion binding / positive regulation of gene expression / positive regulation of DNA-templated transcription / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Pro-epidermal growth factor / 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A / Receptor L-domain / : / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / Growth factor receptor domain IV / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat ...Pro-epidermal growth factor / 24 nucleotide stem-loop, u2 snrnp hairpin iv. U2 a'; Chain A / Receptor L-domain / : / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A domain 2 / Hormone Receptor, Insulin-like Growth Factor Receptor 1; Chain A, domain 2 / Growth factor receptor domain IV / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / : / Calcium-binding EGF domain / Furin-like cysteine rich region / Receptor L domain / Alpha-Beta Horseshoe / Six-bladed beta-propeller, TolB-like / Laminin / Coagulation Factor Xa inhibitory site / Laminin / EGF-like domain / NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Zinc finger, CHCC-type / Zinc-finger domain / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Growth factor receptor cysteine-rich domain superfamily / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Ribbon / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
NADH dehydrogenase [ubiquinone] iron-sulfur protein 6, mitochondrial / Pro-epidermal growth factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.3 Å
AuthorsOgiso, H. / Ishitani, R. / Nureki, O. / Fukai, S. / Yamanaka, M. / Kim, J.H. / Saito, K. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Cell(Cambridge,Mass.) / Year: 2002
Title: Crystal Structure of the Complex of Human Epidermal Growth Factor and Receptor Extracellular Domains.
Authors: Ogiso, H. / Ishitani, R. / Nureki, O. / Fukai, S. / Yamanaka, M. / Kim, J.H. / Saito, K. / Inoue, M. / Shirouzu, M. / Yokoyama, S.
History
DepositionMar 28, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
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_unobs_or_zero_occ_residues / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _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 / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _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 2.1Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_residues
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Epidermal Growth Factor Receptor
C: Epidermal growth factor
D: Epidermal growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,21313
Polymers150,0194
Non-polymers2,1949
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11490 Å2
ΔGint-9 kcal/mol
Surface area52390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)220.164, 220.164, 113.121
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Epidermal Growth Factor Receptor


Mass: 68780.328 Da / Num. of mol.: 2 / Fragment: extracellular domains I, II, II and IV
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pcDNA-sEGFR / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): LEC8 / References: UniProt: P00533, EC: 2.7.1.112
#2: Protein Epidermal growth factor / EGF


Mass: 6229.027 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-53
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01133
#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.: 1
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: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 5.28 Å3/Da / Density % sol: 76.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: PEG4000, PEG6000, sodium acetate, sodium chloride, TRIS, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 %PEG40001reservoir
21 %PEG60001reservoir
375 mMTris-HCl1reservoirpH8.4
475 mMsodium acetate1reservoir
5200 mM1reservoirNaCl
610 mg/mlprotein1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU11
SYNCHROTRONSPring-8 BL41XU20.9795, 0.9798, 0.9733, 0.9839
Detector
TypeIDDetectorDetailsDate
MARRESEARCH1CCDmirrors
MARRESEARCH2CCDmirrorsJan 1, 2001
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97951
30.97981
40.97331
50.98391
ReflectionResolution: 3.5→50 Å / Num. all: 293584 / Num. obs: 293584 / % possible obs: 99 % / Biso Wilson estimate: 71.3 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 25.6
Reflection shellResolution: 3.5→3.71 Å / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 5.1 / Rsym value: 0.27 / % possible all: 98.6
Reflection
*PLUS
Highest resolution: 3.3 Å / Lowest resolution: 50 Å / Num. obs: 46667 / % possible obs: 98.2 % / Num. measured all: 320883 / Rmerge(I) obs: 0.078
Reflection shell
*PLUS
% possible obs: 92.6 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 3.3→10 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.326 2239 5 %RANDOM
Rwork0.255 ---
obs0.258 44854 98 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.4363 Å2 / ksol: 0.166501 e/Å3
Displacement parametersBiso mean: 82.5 Å2
Baniso -1Baniso -2Baniso -3
1--9.51 Å215.74 Å20 Å2
2---9.51 Å20 Å2
3---19.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.75 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 3.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8673 0 140 79 8892
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.3→3.5 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.37 360 5.2 %
Rwork0.31 6616 -
obs-6103 91.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
Refinement
*PLUS
Highest resolution: 3.3 Å / Lowest resolution: 10 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.39
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.781

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