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- PDB-6ubh: Structure of the MM7 Erbin PDZ variant in complex with a high-aff... -

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Basic information

Entry
Database: PDB / ID: 6ubh
TitleStructure of the MM7 Erbin PDZ variant in complex with a high-affinity peptide
Components
  • Erbin
  • peptide
KeywordsSIGNALING PROTEIN / Phage display / directed evolution / -2 position / specificity / phage library
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 / 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 / negative regulation of NF-kappaB transcription factor activity ...ErbB-2 class receptor binding / basal protein localization / 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 / negative regulation of NF-kappaB transcription factor activity / 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 / response to muramyl dipeptide / basement membrane / RHOG GTPase cycle / RHOA GTPase cycle / RAC2 GTPase cycle / RAC3 GTPase cycle / protein targeting / regulation of postsynaptic membrane neurotransmitter receptor levels / Signaling by ERBB2 / RAC1 GTPase cycle / basal plasma membrane / Constitutive Signaling by Overexpressed ERBB2 / integrin-mediated signaling pathway / neuromuscular junction / Signaling by ERBB2 TMD/JMD mutants / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / structural constituent of cytoskeleton / Downregulation of ERBB2 signaling / epidermal growth factor receptor signaling pathway / cellular response to tumor necrosis factor / cell junction / nuclear membrane / response to lipopolysaccharide / basolateral plasma membrane / 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 / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSinger, A.U. / Teyra, J. / McLaughlin, M. / Ernst, A. / Sicheri, F. / Sidhu, S.S.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-93684 Canada
CitationJournal: J.Mol.Biol. / Year: 2021
Title: Comprehensive Assessment of the Relationship Between Site -2 Specificity and Helix alpha 2 in the Erbin PDZ Domain.
Authors: Teyra, J. / McLaughlin, M. / Singer, A. / Kelil, A. / Ernst, A. / Sicheri, F. / Sidhu, S.S.
History
DepositionSep 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Advisory / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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: Erbin
D: Erbin
E: peptide
F: peptide
G: peptide
H: peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,15611
Polymers45,0878
Non-polymers693
Water5,891327
1
A: Erbin
E: peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2953
Polymers11,2722
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area920 Å2
ΔGint-6 kcal/mol
Surface area5540 Å2
MethodPISA
2
B: Erbin
F: peptide


Theoretical massNumber of molelcules
Total (without water)11,2722
Polymers11,2722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-6 kcal/mol
Surface area5630 Å2
MethodPISA
3
C: Erbin
G: peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2953
Polymers11,2722
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-16 kcal/mol
Surface area5550 Å2
MethodPISA
4
D: Erbin
H: peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2953
Polymers11,2722
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-12 kcal/mol
Surface area5600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.000, 39.010, 58.380
Angle α, β, γ (deg.)72.550, 72.610, 96.060
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: 10315.668 Da / Num. of mol.: 4 / Mutation: H1347M
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: 956.074 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 1.75 Å3/Da / Density % sol: 29.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 7% PEG8K, 100 mM Sodium Acetate pH 4.5 / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 6, 2018 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 26382 / % possible obs: 78.3 % / Redundancy: 2.2 % / Biso Wilson estimate: 14.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.021 / Rpim(I) all: 0.019 / Rrim(I) all: 0.29 / Net I/σ(I): 26.7
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.053 / Mean I/σ(I) obs: 12.9 / Num. unique obs: 6175 / CC1/2: 0.991 / Rpim(I) all: 0.048 / Rrim(I) all: 0.071 / % possible all: 58.7

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Processing

Software
NameClassification
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UBG

6ubg
PDB Unreleased entry


Resolution: 1.8→36.77 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.2251 1674 7.54 %Random selection
Rwork0.1971 ---
obs0.2102 23129 81.54 %-
Displacement parametersBiso mean: 16.76 Å2
Refinement stepCycle: LAST / Resolution: 1.8→36.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2979 0 3 327 3309
LS refinement shellResolution: 1.8→1.853 Å
RfactorNum. reflection% reflection
Rfree0.2748 137 -
Rwork0.2972 1931 -
obs--82.2 %

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