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- PDB-6q0m: Structure of Erbin PDZ derivative E-14 with a high-affinity peptide -

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Basic information

Entry
Database: PDB / ID: 6q0m
TitleStructure of Erbin PDZ derivative E-14 with a high-affinity peptide
Components
  • Erbin
  • peptide
KeywordsSIGNALING PROTEIN / PDZ domains / peptide-phage display / peptide engineering / C-terminal peptide
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 / negative regulation of monocyte chemotactic protein-1 production / establishment or maintenance of epithelial cell apical/basal polarity / RHOB GTPase cycle / Drug-mediated inhibition of ERBB2 signaling ...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 / negative regulation of monocyte chemotactic protein-1 production / establishment or maintenance of epithelial cell apical/basal polarity / RHOB 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 / RHOC GTPase cycle / regulation of postsynaptic membrane neurotransmitter receptor levels / response to muramyl dipeptide / RHOG GTPase cycle / basement membrane / RHOA GTPase cycle / protein targeting / RAC3 GTPase cycle / RAC2 GTPase cycle / Signaling by ERBB2 / RAC1 GTPase cycle / Constitutive Signaling by Overexpressed ERBB2 / basal plasma membrane / integrin-mediated signaling pathway / Signaling by ERBB2 TMD/JMD mutants / neuromuscular junction / Signaling by ERBB2 ECD mutants / epidermal growth factor receptor signaling pathway / Signaling by ERBB2 KD Mutants / structural constituent of cytoskeleton / Downregulation of ERBB2 signaling / cell junction / cellular response to tumor necrosis factor / basolateral plasma membrane / nuclear membrane / response to lipopolysaccharide / cell adhesion / nuclear speck / signaling receptor binding / glutamatergic synapse / signal transduction / nucleus / plasma membrane / cytoplasm
Similarity search - Function
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. / Leucine-rich repeat / PDZ domain ...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. / Leucine-rich repeat / PDZ domain / 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: 1.2 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,70411
Polymers22,3654
Non-polymers3397
Water3,567198
1
A: Erbin
C: peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3665
Polymers11,1832
Non-polymers1833
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-13 kcal/mol
Surface area6090 Å2
MethodPISA
2
B: Erbin
D: peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3396
Polymers11,1832
Non-polymers1564
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-25 kcal/mol
Surface area5960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.000, 36.040, 38.650
Angle α, β, γ (deg.)84.330, 76.950, 66.660
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

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


Mass: 10207.618 Da / Num. of mol.: 2 / Mutation: L1280I, S1283R, S1285A, Q1308S, H1336L, V1340I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERBIN, ERBB2IP, KIAA1225, LAP2 / Plasmid: pHH0103
Details (production host): 6His plus GST at N-terminus, followed by TEV cleavage site
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q96RT1
#2: Protein/peptide peptide /


Mass: 975.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 205 molecules

#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 1.9 Å3/Da / Density % sol: 35.31 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 9% PEG8K, 200 mM MgCl2, 100 mM NaAc 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 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: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.16→37.45 Å / Num. obs: 48498 / % possible obs: 86.5 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.041 / Net I/σ(I): 15.5
Reflection shellResolution: 1.16→1.18 Å / Redundancy: 3.1 % / Rmerge(I) obs: 1.11 / Mean I/σ(I) obs: 1 / Num. unique obs: 1838 / CC1/2: 0.77 / % possible all: 67

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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 E-14 PDZ

Resolution: 1.2→30.6 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.185 5029 10.98 %
Rwork0.156 --
obs0.159 45815 89.27 %
Displacement parametersBiso mean: 21.61 Å2
Refinement stepCycle: LAST / Resolution: 1.2→30.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1561 0 19 199 1779
LS refinement shellResolution: 1.2→1.2136 Å
RfactorNum. reflection% reflection
Rfree0.1888 177 -
Rwork0.1468 1329 -
obs--89 %

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