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- PDB-2w4f: CRYSTAL STRUCTURE OF THE FIRST PDZ DOMAIN OF HUMAN SCRIB1 -

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Basic information

Entry
Database: PDB / ID: 2w4f
TitleCRYSTAL STRUCTURE OF THE FIRST PDZ DOMAIN OF HUMAN SCRIB1
ComponentsPROTEIN LAP4
KeywordsSTRUCTURAL PROTEIN / PHOSPHOPROTEIN / UBL CONJUGATION / LEUCINE-RICH REPEAT / ALTERNATIVE SPLICING / CYTOPLASM / CIRCLETAIL / COILED COIL / POLYMORPHISM / LAP4 / CRIB1 / SCRB1 / VARTUL / MEMBRANE
Function / homology
Function and homology information


extrinsic component of postsynaptic density membrane / neurotransmitter receptor transport postsynaptic membrane to endosome / establishment of T cell polarity / apoptotic process involved in morphogenesis / establishment of apical/basal cell polarity / cochlear nucleus development / synaptic vesicle targeting / Scrib-APC-beta-catenin complex / astrocyte cell migration / polarized epithelial cell differentiation ...extrinsic component of postsynaptic density membrane / neurotransmitter receptor transport postsynaptic membrane to endosome / establishment of T cell polarity / apoptotic process involved in morphogenesis / establishment of apical/basal cell polarity / cochlear nucleus development / synaptic vesicle targeting / Scrib-APC-beta-catenin complex / astrocyte cell migration / polarized epithelial cell differentiation / protein localization to adherens junction / myelin sheath abaxonal region / neurotransmitter receptor transport, endosome to postsynaptic membrane / cell-cell contact zone / mammary gland duct morphogenesis / post-anal tail morphogenesis / establishment or maintenance of epithelial cell apical/basal polarity / activation of GTPase activity / regulation of postsynaptic neurotransmitter receptor internalization / auditory receptor cell stereocilium organization / RND2 GTPase cycle / RND3 GTPase cycle / positive regulation of receptor recycling / positive chemotaxis / RHOJ GTPase cycle / RHOQ GTPase cycle / receptor clustering / negative regulation of activated T cell proliferation / CDC42 GTPase cycle / immunological synapse / synaptic vesicle endocytosis / negative regulation of mitotic cell cycle / signaling adaptor activity / Asymmetric localization of PCP proteins / neural tube closure / adherens junction / wound healing / cell-cell adhesion / positive regulation of type II interferon production / cell-cell junction / cell migration / presynapse / lamellipodium / cell junction / basolateral plasma membrane / cell population proliferation / postsynaptic density / cadherin binding / positive regulation of apoptotic process / glutamatergic synapse / extracellular exosome / nucleoplasm / plasma membrane
Similarity search - Function
Leucine Rich Repeat / Leucine-rich repeats, bacterial type / 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 Repeat / Leucine-rich repeats, bacterial type / 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
Protein scribble homolog
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsHozjan, V. / Pilka, E.S. / Roos, A.K. / W Yue, W. / Phillips, C. / Bray, J. / Cooper, C. / Salah, E. / Elkins, J.M. / Muniz, J.R.C. ...Hozjan, V. / Pilka, E.S. / Roos, A.K. / W Yue, W. / Phillips, C. / Bray, J. / Cooper, C. / Salah, E. / Elkins, J.M. / Muniz, J.R.C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A.M. / von Delft, F. / Bountra, C. / Doyle, D.A. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure of the First Pdz Domain of Human Scrib1
Authors: Hozjan, V. / Pilka, E.S. / Roos, A.K. / W Yue, W. / Phillips, C. / Bray, J. / Cooper, C. / Salah, E. / Elkins, J.M. / Muniz, J.R.C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A.M. / von ...Authors: Hozjan, V. / Pilka, E.S. / Roos, A.K. / W Yue, W. / Phillips, C. / Bray, J. / Cooper, C. / Salah, E. / Elkins, J.M. / Muniz, J.R.C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A.M. / von Delft, F. / Bountra, C. / Doyle, D.A. / Oppermann, U.
History
DepositionNov 25, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN LAP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4024
Polymers10,2151
Non-polymers1863
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)38.216, 41.829, 49.897
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTEIN LAP4 / PDZ DOMAIN OF SCRIB1 VARIANT N1 / PROTEIN SCRIBBLE HOMOLOG / HSCRIB


Mass: 10215.452 Da / Num. of mol.: 1 / Fragment: RESIDUES 725-815
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q14160
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE LAST FOUR RESIDUES (816-819) IN THIS ENTRY DO NOT MATCH THE UNIPROT SEQUENCE DATABASE CROSS- ...THE LAST FOUR RESIDUES (816-819) IN THIS ENTRY DO NOT MATCH THE UNIPROT SEQUENCE DATABASE CROSS-REFERENCE. THESE RESIDUES WERE INTRODUCED IN ORDER TO ENHANCE CRYSTALLIZATION.

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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: 1.95 Å3/Da / Density % sol: 37.1 % / Description: NONE
Crystal growpH: 6.3
Details: 0.15 M AMMONIUM CL PH 6.3, 20 % PEG 1000, 15% ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99988
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99988 Å / Relative weight: 1
ReflectionResolution: 1.3→41.81 Å / Num. obs: 71804 / % possible obs: 99.8 % / Observed criterion σ(I): 4.6 / Redundancy: 3.5 % / Biso Wilson estimate: 14.4 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.5
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 4.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0055refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1X5Q

1x5q


Resolution: 1.3→24.94 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.725 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.221 1028 5.1 %RANDOM
Rwork0.173 ---
obs0.175 19190 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.24 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.3→24.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms689 0 12 94 795
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.021729
X-RAY DIFFRACTIONr_bond_other_d0.0010.02508
X-RAY DIFFRACTIONr_angle_refined_deg1.381.97977
X-RAY DIFFRACTIONr_angle_other_deg0.87831232
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.586596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.6152230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.45615126
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.021159
X-RAY DIFFRACTIONr_chiral_restr0.0760.2111
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02819
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02149
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2933465
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.5565740
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.1328264
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.4711236
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.3→1.33 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.255 73
Rwork0.178 1386

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