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- PDB-7lul: Structure of the MM2 Erbin PDZ variant in complex with a high-aff... -

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Basic information

Entry
Database: PDB / ID: 7lul
TitleStructure of the MM2 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


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 / RAC2 GTPase cycle / RAC3 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 / 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. ...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
DI(HYDROXYETHYL)ETHER / Erbin
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 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
DepositionFeb 22, 2021Deposition site: RCSB / Processing site: RCSB
SupersessionJul 28, 2021ID: 6UBG
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Advisory / Database references / Category: database_2 / pdbx_database_PDB_obs_spr
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Apr 3, 2024Group: 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: peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0447
Polymers11,5952
Non-polymers4485
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.200, 69.200, 49.200
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-397-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

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


Mass: 10498.855 Da / Num. of mol.: 1 / Mutation: E88R, H89L, G90E, Q91E, V93E, S94R
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: 1096.241 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 145 molecules

#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.52 Å3/Da / Density % sol: 51.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 12% PEG 8000, 100 mM MES pH 6.0

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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: Jan 26, 2018 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→59.93 Å / Num. obs: 18361 / % possible obs: 91.3 % / Redundancy: 8.9 % / Biso Wilson estimate: 17.84 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.033 / Net I/σ(I): 34.9
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 298 / CC1/2: 0.531 / % possible all: 30.4

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SWISS-MODELLER MODEL

Resolution: 1.65→38.03 Å / SU ML: 0.1364 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.8305
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1897 1642 9.98 %
Rwork0.1799 14819 -
obs0.1809 16461 98.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.77 Å2
Refinement stepCycle: LAST / Resolution: 1.65→38.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms804 0 28 140 972
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072923
X-RAY DIFFRACTIONf_angle_d0.87351251
X-RAY DIFFRACTIONf_chiral_restr0.0661130
X-RAY DIFFRACTIONf_plane_restr0.0073168
X-RAY DIFFRACTIONf_dihedral_angle_d15.6282364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.70.23391170.22051062X-RAY DIFFRACTION87.01
1.7-1.750.21491270.20751186X-RAY DIFFRACTION96.19
1.75-1.820.2991410.24961239X-RAY DIFFRACTION99.93
1.82-1.890.24211380.19861238X-RAY DIFFRACTION99.93
1.89-1.970.20511370.1721246X-RAY DIFFRACTION100
1.97-2.080.1961380.16721222X-RAY DIFFRACTION100
2.08-2.210.20611390.18421245X-RAY DIFFRACTION100
2.21-2.380.19331320.17791256X-RAY DIFFRACTION100
2.38-2.620.18651430.18481248X-RAY DIFFRACTION100
2.62-30.22091400.17771269X-RAY DIFFRACTION100
3-3.780.1771450.17311272X-RAY DIFFRACTION100
3.78-38.030.1431450.16721336X-RAY DIFFRACTION100

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