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- PDB-1mfg: The Structure of ERBIN PDZ domain bound to the Carboxy-terminal t... -

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Basic information

Entry
Database: PDB / ID: 1mfg
TitleThe Structure of ERBIN PDZ domain bound to the Carboxy-terminal tail of the ErbB2 Receptor
Components
  • Erb-B2 INTERACTING PROTEIN
  • Erb-B2 carboxyl-terminal fragment
KeywordsSIGNALING PROTEIN / PDZ DOMAIN / PROTEIN-PEPTIDE COMPLEX / ERB-B2 / ERBIN.
Function / homology
Function and homology information


ErbB-2 class receptor binding / basal protein localization / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / hemidesmosome / negative regulation of immature T cell proliferation in thymus / ERBB3:ERBB2 complex / postsynaptic specialization / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / RNA polymerase I core binding ...ErbB-2 class receptor binding / basal protein localization / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / hemidesmosome / negative regulation of immature T cell proliferation in thymus / ERBB3:ERBB2 complex / postsynaptic specialization / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / RNA polymerase I core binding / immature T cell proliferation in thymus / intermediate filament cytoskeleton organization / semaphorin receptor complex / negative regulation of monocyte chemotactic protein-1 production / establishment or maintenance of epithelial cell apical/basal polarity / regulation of microtubule-based process / ErbB-3 class receptor binding / motor neuron axon guidance / Sema4D induced cell migration and growth-cone collapse / PLCG1 events in ERBB2 signaling / RHOB GTPase cycle / ERBB2-EGFR signaling pathway / negative regulation of NF-kappaB transcription factor activity / ERBB2 Activates PTK6 Signaling / enzyme-linked receptor protein signaling pathway / neurotransmitter receptor localization to postsynaptic specialization membrane / neuromuscular junction development / positive regulation of Rho protein signal transduction / ERBB2-ERBB3 signaling pathway / RHOC GTPase cycle / Drug-mediated inhibition of ERBB2 signaling / Resistance of ERBB2 KD mutants to trastuzumab / Resistance of ERBB2 KD mutants to sapitinib / Resistance of ERBB2 KD mutants to tesevatinib / Resistance of ERBB2 KD mutants to neratinib / Resistance of ERBB2 KD mutants to osimertinib / Resistance of ERBB2 KD mutants to afatinib / Resistance of ERBB2 KD mutants to AEE788 / Resistance of ERBB2 KD mutants to lapatinib / Drug resistance in ERBB2 TMD/JMD mutants / positive regulation of transcription by RNA polymerase I / positive regulation of MAP kinase activity / response to muramyl dipeptide / ERBB2 Regulates Cell Motility / semaphorin-plexin signaling pathway / oligodendrocyte differentiation / basement membrane / PI3K events in ERBB2 signaling / RHOG GTPase cycle / RHOA GTPase cycle / positive regulation of protein targeting to membrane / RAC2 GTPase cycle / RAC3 GTPase cycle / regulation of angiogenesis / regulation of ERK1 and ERK2 cascade / protein targeting / Schwann cell development / regulation of postsynaptic membrane neurotransmitter receptor levels / coreceptor activity / Signaling by ERBB2 / RAC1 GTPase cycle / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / myelination / transmembrane receptor protein tyrosine kinase activity / GRB2 events in ERBB2 signaling / positive regulation of cell adhesion / SHC1 events in ERBB2 signaling / Downregulation of ERBB2:ERBB3 signaling / cell surface receptor protein tyrosine kinase signaling pathway / basal plasma membrane / Constitutive Signaling by Overexpressed ERBB2 / cellular response to epidermal growth factor stimulus / peptidyl-tyrosine phosphorylation / positive regulation of translation / positive regulation of epithelial cell proliferation / integrin-mediated signaling pathway / neuromuscular junction / phosphatidylinositol 3-kinase/protein kinase B signal transduction / wound healing / Signaling by ERBB2 TMD/JMD mutants / receptor protein-tyrosine kinase / Signaling by ERBB2 ECD mutants / receptor tyrosine kinase binding / Signaling by ERBB2 KD Mutants / cellular response to growth factor stimulus / structural constituent of cytoskeleton / ruffle membrane / Downregulation of ERBB2 signaling / epidermal growth factor receptor signaling pathway / neuron differentiation / Constitutive Signaling by Aberrant PI3K in Cancer / cellular response to tumor necrosis factor / cell junction / transmembrane signaling receptor activity / PIP3 activates AKT signaling / myelin sheath / heart development / presynaptic membrane / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade
Similarity search - Function
: / : / Leucine-rich repeat region / Leucine-rich repeats, bacterial type / : / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Leucine-rich repeat, SDS22-like subfamily / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV ...: / : / Leucine-rich repeat region / Leucine-rich repeats, bacterial type / : / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Leucine-rich repeat, SDS22-like subfamily / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / PDZ domain / Pdz3 Domain / 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 / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / PDZ domain / Growth factor receptor cysteine-rich domain superfamily / : / Leucine-rich repeat / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Leucine-rich repeat domain superfamily / 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 / Roll / 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
Similarity search - Domain/homology
Receptor tyrosine-protein kinase erbB-2 / Erbin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.25 Å
AuthorsBirrane, G. / Chung, J. / Ladias, J.A.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Novel mode of ligand recognition by the erbin PDZ domain
Authors: Birrane, G. / Chung, J. / Ladias, J.A.
#1: Journal: NAT.CELL BIOL. / Year: 2000
Title: BIN: A BASOLATERAL PDZ PROTEIN THAT INTERACTS WITH THE MAMMALIAN ERBB2/HER2 RECEPTOR
Authors: BORG, J.P. / MARCHETTO, S. / LEBIVIC, A. / OLLENDORFF, V. / JAULIN-BASTARD, F. / SAITO, H. / FOURNIER, E. / ADELAIDE, J. / MARGOLIS, B. / BIRNBAUM, D.
#2: Journal: J.Biol.Chem. / Year: 2002
Title: THE ERBIN PDZ DOMAIN BINDS WITH HIGH AFFINITY AND SPECIFICITY TO THE CARBOXYL TERMINI OF DELTA-CATENIN AND ARVCF
Authors: LAURA, R.P. / WITT, A.S. / HELD, H.A. / GERSTNER, R. / DESHAYES, K. / KOEHLER, M.F. / KOSIK, K.S. / SIDHU, S.S. / LASKY, L.A.
#3: Journal: J.Biol.Chem. / Year: 2001
Title: ERBIN IS A PROTEIN CONCENTRATED AT POSTSYNAPTIC MEMBRANES THAT INTERACTS WITH PSD-95
Authors: HUANG, Y.Z. / WANG, Q. / XIONG, W.C. / MEI, L.
#4: Journal: J.Biol.Chem. / Year: 2001
Title: THE ERBB2/HER2 RECEPTOR DIFFERENTIALLY INTERACTS WITH ERBIN AND PICK1 PSD-95/DLG/ZO-1 DOMAIN PROTEINS
Authors: JAULIN-BASTARD, F. / SAITO, H. / LEBIVIC, A. / OLLENDORFF, V. / MARCHETTO, S. / BIRNBAUM, D. / BORG, J.P.
History
DepositionAug 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Erb-B2 INTERACTING PROTEIN
B: Erb-B2 carboxyl-terminal fragment


Theoretical massNumber of molelcules
Total (without water)11,2972
Polymers11,2972
Non-polymers00
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-5 kcal/mol
Surface area6170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.605, 57.417, 30.439
Angle α, β, γ (deg.)90.00, 100.59, 90.00
Int Tables number4
Space group name H-MP1211
DetailsCOORDINATES REPRESENT THE COMPLETE BIOLOGICAL ASSEMBLY

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Components

#1: Protein Erb-B2 INTERACTING PROTEIN


Mass: 10292.593 Da / Num. of mol.: 1 / Fragment: PDZ DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PGEX-KT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q96RT1
#2: Protein/peptide Erb-B2 carboxyl-terminal fragment


Mass: 1004.134 Da / Num. of mol.: 1 / Fragment: PEPTIDE EYLGLDVPV / Source method: obtained synthetically / Details: PEPTIDE SYNTHESIZED CHEMICALLY / References: UniProt: P04626*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 1.71 Å3/Da / Density % sol: 39.16 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 12-15%PEG 4000, 100mM Ammonium Acetate, 100mM Sodium Acetate, 10% Glycerol, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
119 mg/mlprotein1drop
2500 mM1dropNaCl
350 mMTris-HCl1droppH8.3
412-15 %PEG40001reservoir
510 %glycerol1reservoir
6100 mMammonium acetate1reservoir
7100 mMsodium acetate1reservoirpH4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.97861 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 10, 2002 / Details: DUAL SLITS
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 1.25→25 Å / Num. all: 24313 / Num. obs: 24313 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.25→1.29 Å / % possible all: 91.4
Reflection
*PLUS
% possible obs: 92.7 % / Rmerge(I) obs: 0.025
Reflection shell
*PLUS
% possible obs: 91.4 % / Rmerge(I) obs: 0.037 / Mean I/σ(I) obs: 16.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.01phasing
SHELXL-97refinement
RefinementMethod to determine structure: MAD / Resolution: 1.25→25 Å / Num. parameters: 8637 / Num. restraintsaints: 10570 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY 2.6% Water molecules 131, 132 and 133 occupy the site where the disordered component of HIS1347 with alternate conformer B is modeled.
RfactorNum. reflection% reflectionSelection details
Rfree0.1648 1240 5.4 %RANDOM
Rwork0.1282 ---
all0.1297 24313 --
obs0.1297 23073 92.7 %-
Refine analyzeNum. disordered residues: 8 / Occupancy sum hydrogen: 766 / Occupancy sum non hydrogen: 929.08
Refinement stepCycle: LAST / Resolution: 1.25→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms824 0 0 134 958
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0274
X-RAY DIFFRACTIONs_zero_chiral_vol0.085
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.077
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.015
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.084
X-RAY DIFFRACTIONs_approx_iso_adps0.103
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 25 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.164 / Rfactor Rwork: 0.128
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_plane_restr0.027
X-RAY DIFFRACTIONs_chiral_restr0.085

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