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- PDB-6q0u: Structure of the Erbin PDZ variant E-6a with a high-affinity C-te... -

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Basic information

Entry
Database: PDB / ID: 6q0u
TitleStructure of the Erbin PDZ variant E-6a with a high-affinity C-terminal peptide
Components
  • Erbin
  • peptide
KeywordsSIGNALING PROTEIN / peptide-phage display / protein engineering / PDZ domains / 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 / negative regulation of NF-kappaB transcription factor activity / RHOB 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 / negative regulation of monocyte chemotactic protein-1 production / establishment or maintenance of epithelial cell apical/basal polarity / negative regulation of NF-kappaB transcription factor activity / 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 / RHOC GTPase cycle / response to muramyl dipeptide / regulation of postsynaptic membrane neurotransmitter receptor levels / basement membrane / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / 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 / epidermal growth factor receptor signaling pathway / Signaling by ERBB2 KD Mutants / neuromuscular junction / 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 / 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. ...: / Leucine-rich repeats, bacterial type / Leucine-rich repeat, SDS22-like subfamily / 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 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)22,5056
Polymers22,3814
Non-polymers1242
Water2,414134
1
A: Erbin
C: peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3154
Polymers11,1912
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-5 kcal/mol
Surface area5810 Å2
MethodPISA
2
B: Erbin
D: peptide


Theoretical massNumber of molelcules
Total (without water)11,1912
Polymers11,1912
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-6 kcal/mol
Surface area5840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.590, 38.090, 38.450
Angle α, β, γ (deg.)83.04, 74.99, 63.66
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z

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Components

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


Mass: 10273.659 Da / Num. of mol.: 2 / Mutation: S1294R, S1296A, V1351I
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 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: 916.974 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
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: 1.94 Å3/Da / Density % sol: 36.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 14% PEG3350,200 mM MgCl2, 100 mM MES 6.0. Cryoprotected with this condition 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: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 19, 2018 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.89→37.14 Å / Num. obs: 12494 / % possible obs: 91.1 % / Redundancy: 2.4 % / Biso Wilson estimate: 18.78 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.051 / Net I/σ(I): 10.4
Reflection shellResolution: 1.89→1.99 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 4051 / CC1/2: 0.941 / % possible all: 73.2

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Processing

Software
NameClassification
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Swiss-Modeller model of this PDZ

Resolution: 1.89→37.14 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.237 1250 10.01 %
Rwork0.178 --
obs0.184 12486 91.1 %
Displacement parametersBiso mean: 31.92 Å2
Refinement stepCycle: LAST / Resolution: 1.89→37.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1558 0 8 134 1700
LS refinement shellResolution: 1.886→1.9615 Å
RfactorNum. reflection% reflection
Rfree0.369 127 -
Rwork0.2787 1145 -
obs--83 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.31481.1276-0.22285.5477-2.43452.7709-0.02910.1055-0.077-0.07930.2354-0.1985-0.0718-0.1529-0.23710.3330.0198-0.07130.2331-0.01640.15376.753913.13482.706
24.7182-0.4528-5.4972.21420.36777.66470.1404-1.558-0.74110.36830.23580.24210.44420.2041-0.33770.2369-0.0465-0.01040.34350.06630.21012.674.804816.971
37.810.76680.34815.22280.53425.15940.02910.0011-0.3789-0.0653-0.018-0.08370.11260.13150.02930.18680.0384-0.02380.13510.0030.131415.87464.7488.8335
42.5294-2.02390.77775.91212.36548.78410.17810.04140.0613-0.0168-0.2144-0.5795-0.71010.59380.08140.2769-0.0448-0.02490.18030.05570.211615.059617.470811.3253
54.7801-1.2036-1.94982.1376-1.33752.76660.5464-0.9673-0.0770.2501-0.15080.0237-0.55160.739-0.30410.3908-0.0194-0.05340.2803-0.05250.182414.067912.356919.6587
66.22261.7229-0.21435.6061-2.14878.45250.31020.17320.4865-0.07540.1409-0.0204-0.4005-0.4942-0.26320.20840.0558-0.08620.22130.00080.1557.710912.38337.7739
76.15020.91890.26141.8346-3.06055.9061-0.1260.0450.22380.1725-0.081-0.4744-0.050.11360.20470.27210.0568-0.01220.1682-0.06740.16626.4716-8.9527-5.2723
87.99990.0115-0.73925.78180.09664.29110.05090.39130.2283-0.19680.05440.35180.0598-0.0806-0.08610.24830.0328-0.06220.15470.02050.148216.8788-9.6031-12.8191
91.09281.01730.5585.56730.55843.87750.13640.05610.13580.48280.09270.6616-0.1139-0.1671-0.1580.35510.0850.06230.1685-0.01760.270114.995-4.795-1.8368
103.6225-0.3108-0.50756.8155-0.69634.4510.2864-0.2353-0.15031.0047-0.1277-0.55130.0663-0.1284-0.20360.18120.0405-0.04170.2557-0.01440.140623.7888-9.7629-3.5765
115.224-2.6035-1.33261.48890.86660.8778-0.1675-0.5843-0.70760.5338-0.2063-0.31150.21730.28110.08790.19430.0099-0.12650.28020.14180.397517.77272.343216.5936
121.6227-1.9828-2.04372.38372.4282.95560.28240.47760.3072-0.34550.23240.4659-0.4469-1.027-0.4380.2348-0.0056-0.07190.36770.16580.37514.3472-2.2953-15.2749
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 9 )
2X-RAY DIFFRACTION2chain 'A' and (resid 10 through 15 )
3X-RAY DIFFRACTION3chain 'A' and (resid 16 through 55 )
4X-RAY DIFFRACTION4chain 'A' and (resid 56 through 69 )
5X-RAY DIFFRACTION5chain 'A' and (resid 70 through 79 )
6X-RAY DIFFRACTION6chain 'A' and (resid 80 through 92 )
7X-RAY DIFFRACTION7chain 'B' and (resid 0 through 15 )
8X-RAY DIFFRACTION8chain 'B' and (resid 16 through 55 )
9X-RAY DIFFRACTION9chain 'B' and (resid 56 through 79 )
10X-RAY DIFFRACTION10chain 'B' and (resid 80 through 92 )
11X-RAY DIFFRACTION11chain 'C' and (resid -4 through 2 )
12X-RAY DIFFRACTION12chain 'D' and (resid -4 through 2 )

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