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- PDB-1n8y: Crystal structure of the extracellular region of rat HER2 -

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Basic information

Entry
Database: PDB / ID: 1n8y
TitleCrystal structure of the extracellular region of rat HER2
Componentsprotooncoprotein
KeywordsTRANSFERASE / tyrosin kinase receptor / cell surface receptor
Function / homology
Function and homology information


Signaling by ERBB2 / coreceptor activity involved in epidermal growth factor receptor signaling pathway / ERBB2 Activates PTK6 Signaling / Drug-mediated inhibition of ERBB2 signaling / ERBB2 Regulates Cell Motility / GRB2 events in ERBB2 signaling / Downregulation of ERBB2 signaling / PI3K events in ERBB2 signaling / Sema4D induced cell migration and growth-cone collapse / SHC1 events in ERBB2 signaling ...Signaling by ERBB2 / coreceptor activity involved in epidermal growth factor receptor signaling pathway / ERBB2 Activates PTK6 Signaling / Drug-mediated inhibition of ERBB2 signaling / ERBB2 Regulates Cell Motility / GRB2 events in ERBB2 signaling / Downregulation of ERBB2 signaling / PI3K events in ERBB2 signaling / Sema4D induced cell migration and growth-cone collapse / SHC1 events in ERBB2 signaling / PIP3 activates AKT signaling / tongue development / negative regulation of immature T cell proliferation in thymus / ERBB3:ERBB2 complex / glial cell differentiation / ERBB2-ERBB4 signaling pathway / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / ERBB2-ERBB3 signaling pathway / RNA polymerase I core binding / lateral loop / sympathetic nervous system development / mammary gland involution / ErbB-3 class receptor binding / regulation of microtubule-based process / peripheral nervous system development / motor neuron axon guidance / estrous cycle / myelination / positive regulation of Ras protein signal transduction / neuromuscular junction development / RAF/MAP kinase cascade / positive regulation of transcription by RNA polymerase I / transmembrane receptor protein tyrosine kinase activator activity / ERBB2-EGFR signaling pathway / protein tyrosine kinase activator activity / : / regulation of cell differentiation / oligodendrocyte differentiation / microvillus / positive regulation of protein targeting to membrane / positive regulation of cell adhesion / response to axon injury / skeletal muscle tissue development / phosphatidylinositol 3-kinase signaling / response to progesterone / cellular response to epidermal growth factor stimulus / basal plasma membrane / regulation of ERK1 and ERK2 cascade / liver development / positive regulation of translation / positive regulation of epithelial cell proliferation / central nervous system development / Hsp90 protein binding / cellular response to growth factor stimulus / neuron differentiation / receptor protein-tyrosine kinase / transmembrane receptor protein tyrosine kinase activity / wound healing / positive regulation of kinase activity / positive regulation of GTPase activity / transmembrane signaling receptor activity / postsynaptic membrane / positive regulation of MAP kinase activity / peptidyl-tyrosine phosphorylation / nervous system development / regulation of cell population proliferation / positive regulation of phosphatidylinositol 3-kinase signaling / myelin sheath / basolateral plasma membrane / transmembrane receptor protein tyrosine kinase signaling pathway / heart development / positive regulation of cell growth / cytoplasmic vesicle / protein tyrosine kinase activity / protein C-terminus binding / positive regulation of MAPK cascade / protein phosphatase binding / endosome membrane / cell surface receptor signaling pathway / early endosome / receptor complex / apical plasma membrane / intracellular signal transduction / response to xenobiotic stimulus / protein autophosphorylation / protein heterodimerization activity / positive regulation of protein phosphorylation / membrane raft / protein-containing complex binding / ubiquitin protein ligase binding / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / perinuclear region of cytoplasm / signal transduction / plasma membrane => GO:0005886 / DNA binding / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
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 / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Alpha-Beta Horseshoe / Receptor L-domain superfamily / Furin-like cysteine rich region ...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 / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / Alpha-Beta Horseshoe / Receptor L-domain superfamily / Furin-like cysteine rich region / Receptor L domain / Furin-like cysteine-rich domain / Receptor L-domain / Furin-like repeats / Furin-like repeat / Growth factor receptor cysteine-rich domain superfamily / Ribbon / Tyrosine kinase, catalytic domain / Tyrosine-protein kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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
: / Receptor tyrosine-protein kinase erbB-2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCho, H.-S. / Mason, K. / Ramyar, K.X. / Stanley, A.M. / Gabelli, S.B. / Denney Jr., D.W. / Leahy, D.J.
CitationJournal: Nature / Year: 2003
Title: Structure of the Extracellular Region of HER2 Alone and in complex with the Herceptin Fab
Authors: Cho, H.-S. / Mason, K. / Ramyar, K.X. / Stanley, A.M. / Gabelli, S.B. / Denney Jr., D.W. / Leahy, D.J.
History
DepositionNov 21, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 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_validate_close_contact / 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 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: protooncoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4314
Polymers67,3611
Non-polymers1,0703
Water1,51384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.87, 116.40, 55.37
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein protooncoprotein


Mass: 67361.422 Da / Num. of mol.: 1 / Fragment: extracellular region (residues 26-633)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: neu / Plasmid: pSGHV0 / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO(Lec1) / References: GenBank: 22651765, UniProt: P06494*PLUS
#2: 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.: 2
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
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 15-30% PEG4000, 50mM Na citrate pH5.4, 10mM EDTA, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
210 mMTris1droppH7.5
315-30 %PEG40001reservoir
450 mMsodium citrate1reservoirpH5.4
510 mMEDTA1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 20, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 34177 / Num. obs: 33900 / % possible obs: 99.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.7 %
Reflection shellResolution: 2.4→2.49 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.77 / % possible all: 93.9
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 34177 / Redundancy: 3.7 % / Num. measured all: 196228 / Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 93.9 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.1.19refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1M6B
Resolution: 2.4→20 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.898 / SU B: 9.33 / SU ML: 0.215 / Cross valid method: THROUGHOUT / σ(F): 1 / σ(I): 1 / ESU R: 0.364 / ESU R Free: 0.28
RfactorNum. reflection% reflectionSelection details
Rfree0.28246 1568 5 %RANDOM
Rwork0.22375 ---
all0.2266 34177 --
obs0.2237 30022 94.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.924 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å20 Å20 Å2
2---2.57 Å20 Å2
3---1.32 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4578 0 70 84 4732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0214781
X-RAY DIFFRACTIONr_angle_refined_deg1.7241.986509
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.445589
X-RAY DIFFRACTIONr_chiral_restr0.1210.2713
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023644
X-RAY DIFFRACTIONr_nbd_refined0.2270.21883
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2188
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2740.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.25
X-RAY DIFFRACTIONr_mcbond_it0.6751.52952
X-RAY DIFFRACTIONr_mcangle_it1.29524757
X-RAY DIFFRACTIONr_scbond_it2.36431829
X-RAY DIFFRACTIONr_scangle_it3.8024.51752
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.413 -
Rwork0.296 1764
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.282 / Rfactor Rwork: 0.226
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.015
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.72

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