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- PDB-2h3l: Crystal Structure of ERBIN PDZ -

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Basic information

Entry
Database: PDB / ID: 2h3l
TitleCrystal Structure of ERBIN PDZ
ComponentsLAP2 protein
KeywordsCELL ADHESION / PDZ Domain
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 / neurotransmitter receptor transport postsynaptic membrane to endosome / embryo development / neurotransmitter receptor transport, endosome to postsynaptic membrane / intermediate filament cytoskeleton organization / negative regulation of monocyte chemotactic protein-1 production / establishment or maintenance of epithelial cell apical/basal polarity ...basal protein localization / ErbB-2 class receptor binding / negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / hemidesmosome / neurotransmitter receptor transport postsynaptic membrane to endosome / embryo development / neurotransmitter receptor transport, endosome to postsynaptic membrane / 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 / receptor clustering / response to muramyl dipeptide / RHOG GTPase cycle / basement membrane / 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 / adherens junction / Signaling by ERBB2 TMD/JMD mutants / Signaling by ERBB2 ECD mutants / neuromuscular junction / Signaling by ERBB2 KD Mutants / epidermal growth factor receptor signaling pathway / structural constituent of cytoskeleton / Downregulation of ERBB2 signaling / cell-cell adhesion / cell junction / cellular response to tumor necrosis factor / basolateral plasma membrane / postsynaptic membrane / nuclear membrane / response to lipopolysaccharide / postsynaptic density / 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. / PDZ domain / Leucine-rich repeat ...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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsAppleton, B.A. / Zhang, Y. / Wu, P. / Yin, J.P. / Hunziker, W. / Skelton, N.J. / Sidhu, S.S. / Wiesmann, C.
Citation
Journal: J.Biol.Chem. / Year: 2006
Title: Comparative structural analysis of the Erbin PDZ domain and the first PDZ domain of ZO-1. Insights into determinants of PDZ domain specificity.
Authors: Appleton, B.A. / Zhang, Y. / Wu, P. / Yin, J.P. / Hunziker, W. / Skelton, N.J. / Sidhu, S.S. / Wiesmann, C.
#1: Journal: J.Biol.Chem. / Year: 2006
Title: Convergent and Divergent Ligand Specificity Amongst the PDZ Domains of the LAP and ZO Families
Authors: Zhang, Y. / Yeh, S. / Appleton, B.A. / Held, H.A. / Kausalya, J.P. / Phua, D.C.Y. / Wong, W.L. / Lasky, L.A. / Wiesmann, C. / Hunziker, W. / Sidhu, S.S.
History
DepositionMay 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LAP2 protein
B: LAP2 protein


Theoretical massNumber of molelcules
Total (without water)22,3932
Polymers22,3932
Non-polymers00
Water4,828268
1
A: LAP2 protein


Theoretical massNumber of molelcules
Total (without water)11,1971
Polymers11,1971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LAP2 protein


Theoretical massNumber of molelcules
Total (without water)11,1971
Polymers11,1971
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.864, 44.032, 57.265
Angle α, β, γ (deg.)90.00, 106.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 11196.597 Da / Num. of mol.: 2 / Fragment: PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERBIN / Plasmid: pET22d / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q96RT1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.1 Å3/Da / Density % sol: 41.44 %
Crystal growTemperature: 292 K / pH: 7.5
Details: 0.1 M TRIS-HCL, 35% PEG 4000, pH 7.5-8.5, vapor diffusion, temperature 292K, pH 7.50

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.849
DetectorType: MARRESEARCH / Detector: CCD / Date: May 2, 2002
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelengthWavelength: 0.849 Å / Relative weight: 1
ReflectionResolution: 1→30 Å / Num. obs: 100042 / % possible obs: 99.4 % / Redundancy: 3.2 % / Rsym value: 0.071 / Net I/σ(I): 19.5
Reflection shellResolution: 1→1.04 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.517 / % possible all: 97.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 1MFG

1mfg


Resolution: 1→30 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.66 / SU ML: 0.016 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.024 / ESU R Free: 0.025 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.169 4711 5 %RANDOM
Rwork0.148 ---
all0.14872 100218 --
obs-94642 94.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20 Å2-0.04 Å2
2--0.11 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1543 0 0 268 1811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221570
X-RAY DIFFRACTIONr_bond_other_d0.0010.021450
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.972118
X-RAY DIFFRACTIONr_angle_other_deg0.82133384
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.325199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.20724.53375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.96315272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2971512
X-RAY DIFFRACTIONr_chiral_restr0.0970.2232
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021769
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02303
X-RAY DIFFRACTIONr_nbd_refined0.2280.2254
X-RAY DIFFRACTIONr_nbd_other0.190.21403
X-RAY DIFFRACTIONr_nbtor_refined0.1690.2766
X-RAY DIFFRACTIONr_nbtor_other0.080.2947
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2151
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0930.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2130.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7072.51271
X-RAY DIFFRACTIONr_mcbond_other1.3572.5419
X-RAY DIFFRACTIONr_mcangle_it4.36551599
X-RAY DIFFRACTIONr_scbond_it4.2392.5633
X-RAY DIFFRACTIONr_scangle_it5.9985519
X-RAY DIFFRACTIONr_rigid_bond_restr2.03533505
X-RAY DIFFRACTIONr_sphericity_free15.0685268
X-RAY DIFFRACTIONr_sphericity_bonded6.65952993
LS refinement shellResolution: 1→1.02 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.222 231 -
Rwork0.228 4732 -
obs--83.85 %

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