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- PDB-6q0n: Structure of the Erbin PDB domain in complex with a high-affinity... -

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Basic information

Entry
Database: PDB / ID: 6q0n
TitleStructure of the Erbin PDB domain in complex with a high-affinity peptide
Components
  • Erbin
  • peptide
KeywordsSIGNALING PROTEIN / Complex / high-affinity / specificity
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 / postsynaptic specialization / intermediate filament cytoskeleton organization / establishment or maintenance of epithelial cell apical/basal polarity / negative regulation of monocyte chemotactic protein-1 production / RHOB GTPase cycle / RHOC GTPase cycle ...basal protein localization / ErbB-2 class receptor binding / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / hemidesmosome / postsynaptic specialization / intermediate filament cytoskeleton organization / establishment or maintenance of epithelial cell apical/basal polarity / negative regulation of monocyte chemotactic protein-1 production / RHOB GTPase cycle / 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 / negative regulation of NF-kappaB transcription factor activity / response to muramyl dipeptide / basement membrane / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / regulation of postsynaptic membrane neurotransmitter receptor levels / protein targeting / Signaling by ERBB2 / RAC1 GTPase cycle / Constitutive Signaling by Overexpressed ERBB2 / basal plasma membrane / integrin-mediated signaling pathway / Signaling by ERBB2 TMD/JMD mutants / Signaling by ERBB2 ECD mutants / neuromuscular junction / Signaling by ERBB2 KD Mutants / structural constituent of cytoskeleton / epidermal growth factor receptor signaling pathway / Downregulation of ERBB2 signaling / cell junction / cellular response to tumor necrosis factor / basolateral plasma membrane / nuclear membrane / response to lipopolysaccharide / cell adhesion / intracellular signal transduction / nuclear speck / signaling receptor binding / glutamatergic synapse / signal transduction / nucleus / plasma membrane / cytoplasm
Similarity search - Function
: / : / Leucine-rich repeat region / Leucine-rich repeats, bacterial type / Leucine-rich repeat, SDS22-like subfamily / PDZ domain / Pdz3 Domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily ...: / : / Leucine-rich repeat region / Leucine-rich repeats, bacterial type / Leucine-rich repeat, SDS22-like subfamily / PDZ domain / Pdz3 Domain / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / 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 / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 Å
AuthorsSinger, A.U. / Teyra, J. / Ernst, A. / Sicheri, F. / Sidhu, S.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-93684 Canada
CitationJournal: Protein Sci. / Year: 2020
Title: Comprehensive analysis of all evolutionary paths between two divergent PDZ domain specificities.
Authors: Teyra, J. / Ernst, A. / Singer, A. / Sicheri, F. / Sidhu, S.S.
History
DepositionAug 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 22, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Erbin
B: Erbin
C: peptide
D: peptide


Theoretical massNumber of molelcules
Total (without water)22,0074
Polymers22,0074
Non-polymers00
Water2,864159
1
A: Erbin
C: peptide


Theoretical massNumber of molelcules
Total (without water)11,0032
Polymers11,0032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-6 kcal/mol
Surface area5620 Å2
MethodPISA
2
B: Erbin
D: peptide


Theoretical massNumber of molelcules
Total (without water)11,0032
Polymers11,0032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-7 kcal/mol
Surface area5520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.060, 35.359, 38.676
Angle α, β, γ (deg.)83.880, 75.480, 68.990
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Erbin / Densin-180-like protein / Erbb2-interacting protein / Protein LAP2


Mass: 10148.464 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERBIN, ERBB2IP, KIAA1225, LAP2 / Plasmid: pHH0103
Details (production host): 6-His and GST at N-terminus, followed by TEV cleavage site
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q96RT1
#2: Protein/peptide peptide


Mass: 854.903 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 1.81 Å3/Da / Density % sol: 31.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 6%PEG3350, 100 mM MgCl2, 100 mM Sodium Acetate pH 4.5. Cryoprotection was achieved with the same buffer plus 25% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 18, 2018 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.16→30.04 Å / Num. obs: 47892 / % possible obs: 86.7 % / Redundancy: 3.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.051 / Net I/σ(I): 12.4
Reflection shellResolution: 1.16→1.18 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1996 / CC1/2: 0.856 / % possible all: 71.5

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Processing

Software
NameClassification
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SWISS-MODELLER model of the E-14 variant of the Erbin PDZ

Resolution: 1.18→30.04 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.183 4604 10.11 %Random selection
Rwork0.155 ---
obs0.158 45554 87.55 %-
Displacement parametersBiso mean: 27.9 Å2
Refinement stepCycle: LAST / Resolution: 1.18→30.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1519 0 0 159 1678
LS refinement shellResolution: 1.18→1.1934 Å
RfactorNum. reflection% reflection
Rfree0.2769 156 -
Rwork0.2589 1205 -
obs--81 %

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