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

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Basic information

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


basal protein localization / ErbB-2 class receptor binding / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / hemidesmosome / neurotransmitter receptor transport postsynaptic membrane to endosome / negative regulation of immature T cell proliferation in thymus / ERBB3:ERBB2 complex / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / immature T cell proliferation in thymus ...basal protein localization / ErbB-2 class receptor binding / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / hemidesmosome / neurotransmitter receptor transport postsynaptic membrane to endosome / negative regulation of immature T cell proliferation in thymus / ERBB3:ERBB2 complex / ERBB2-ERBB4 signaling pathway / GRB7 events in ERBB2 signaling / immature T cell proliferation in thymus / RNA polymerase I core binding / embryo development / neurotransmitter receptor transport, endosome to postsynaptic membrane / intermediate filament cytoskeleton organization / negative regulation of monocyte chemotactic protein-1 production / regulation of microtubule-based process / ErbB-3 class receptor binding / semaphorin receptor complex / Sema4D induced cell migration and growth-cone collapse / establishment or maintenance of epithelial cell apical/basal polarity / motor neuron axon guidance / neurotransmitter receptor localization to postsynaptic specialization membrane / PLCG1 events in ERBB2 signaling / neuromuscular junction development / ERBB2-EGFR signaling pathway / RHOB GTPase cycle / ERBB2 Activates PTK6 Signaling / positive regulation of Rho protein signal transduction / 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 / enzyme-linked receptor protein signaling pathway / negative regulation of NF-kappaB transcription factor activity / positive regulation of transcription by RNA polymerase I / ERBB2-ERBB3 signaling pathway / RHOC GTPase cycle / oligodendrocyte differentiation / receptor clustering / ERBB2 Regulates Cell Motility / response to muramyl dipeptide / semaphorin-plexin signaling pathway / PI3K events in ERBB2 signaling / positive regulation of cell adhesion / RHOG GTPase cycle / basement membrane / RHOA GTPase cycle / positive regulation of protein targeting to membrane / RAC2 GTPase cycle / RAC3 GTPase cycle / protein targeting / regulation of angiogenesis / coreceptor activity / Schwann cell development / Signaling by ERBB2 / cellular response to epidermal growth factor stimulus / cell surface receptor protein tyrosine kinase signaling pathway / RAC1 GTPase cycle / GRB2 events in ERBB2 signaling / myelination / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / Downregulation of ERBB2:ERBB3 signaling / transmembrane receptor protein tyrosine kinase activity / SHC1 events in ERBB2 signaling / Constitutive Signaling by Overexpressed ERBB2 / phosphatidylinositol 3-kinase/protein kinase B signal transduction / neurogenesis / regulation of ERK1 and ERK2 cascade / basal plasma membrane / positive regulation of epithelial cell proliferation / positive regulation of translation / integrin-mediated signaling pathway / adherens junction / Signaling by ERBB2 TMD/JMD mutants / positive regulation of MAP kinase activity / wound healing / Signaling by ERBB2 ECD mutants / neuromuscular junction / neuron differentiation / Signaling by ERBB2 KD Mutants / epidermal growth factor receptor signaling pathway / receptor protein-tyrosine kinase / structural constituent of cytoskeleton / receptor tyrosine kinase binding / cellular response to growth factor stimulus / Downregulation of ERBB2 signaling / ruffle membrane / cell-cell adhesion / peptidyl-tyrosine phosphorylation / transmembrane signaling receptor activity / Constitutive Signaling by Aberrant PI3K in Cancer / cell junction / PIP3 activates AKT signaling / myelin sheath
Similarity search - Function
Leucine-rich repeats, bacterial type / Leucine-rich repeat, SDS22-like subfamily / : / Epidermal growth factor receptor transmembrane-juxtamembrane segment / Tyrosine protein kinase, EGF/ERB/XmrK receptor / Growth factor receptor domain 4 / Growth factor receptor domain IV / PDZ domain / Pdz3 Domain / Receptor L-domain ...Leucine-rich repeats, bacterial type / Leucine-rich repeat, SDS22-like subfamily / : / Epidermal growth factor receptor transmembrane-juxtamembrane segment / 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. / Growth factor receptor cysteine-rich domain superfamily / PDZ domain / 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 / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / 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 / MOLECULAR REPLACEMENT / Resolution: 1.88 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 12, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)11,3772
Polymers11,3772
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area740 Å2
ΔGint-4 kcal/mol
Surface area6030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.526, 56.995, 30.951
Angle α, β, γ (deg.)90.00, 99.16, 90.00
Int Tables number4
Space group name H-MP1211

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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 PHOSPHORYLATED Erb-B2 carboxyl-terminal fragment.


Mass: 1084.113 Da / Num. of mol.: 1 / Fragment: PEPTIDE LDVPV / Source method: obtained synthetically / Details: PEPTIDE SYNTHESIZED CHEMICALLY / References: UniProt: P04626*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.03 Å3/Da / Density % sol: 39.38 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 23-26% PEG 4000, 20% GLYCEROL, 100mM AMMONIUM ACETATE, 100mM SODIUM ACETATE, pH 4.5, 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: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 4, 2002 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.88→30.6 Å / Num. all: 7196 / Num. obs: 7068 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.73 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.028 / Rsym value: 0.028 / Net I/σ(I): 44.7
Reflection shellResolution: 1.88→1.95 Å / Redundancy: 3.34 % / Rmerge(I) obs: 0.096 / Mean I/σ(I) obs: 13.3 / Num. unique all: 660 / Rsym value: 0.096 / % possible all: 90.2
Reflection shell
*PLUS
Lowest resolution: 1.93 Å / % possible obs: 90.2 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.1.19refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MFG

1mfg


Resolution: 1.88→30.57 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.941 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2159 330 4.7 %RANDOM
Rwork0.1668 ---
all0.169 7068 --
obs0.169 6738 95 %-
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: 18.168 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å20 Å2-0.24 Å2
2--0.35 Å20 Å2
3---0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.88→30.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms767 0 0 72 839
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022779
X-RAY DIFFRACTIONr_bond_other_d0.0020.02725
X-RAY DIFFRACTIONr_angle_refined_deg1.5791.9781052
X-RAY DIFFRACTIONr_angle_other_deg0.8331694
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.462598
X-RAY DIFFRACTIONr_chiral_restr0.0880.2120
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02868
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02146
X-RAY DIFFRACTIONr_nbd_refined0.220.2117
X-RAY DIFFRACTIONr_nbd_other0.2580.2805
X-RAY DIFFRACTIONr_nbtor_other0.0870.2460
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.253
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3460.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.29
X-RAY DIFFRACTIONr_mcbond_it0.9771.5497
X-RAY DIFFRACTIONr_mcangle_it1.8282807
X-RAY DIFFRACTIONr_scbond_it3.0333282
X-RAY DIFFRACTIONr_scangle_it5.3234.5245
LS refinement shellResolution: 1.88→1.929 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.297 19
Rwork0.169 451
Refinement
*PLUS
Lowest resolution: 30.6 Å / Num. reflection obs: 6737 / % reflection Rfree: 5 % / Rfactor Rfree: 0.216 / Rfactor Rwork: 0.167
Solvent computation
*PLUS
Displacement parameters
*PLUS

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