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- PDB-2uzc: Structure of human PDLIM5 in complex with the C-terminal peptide ... -

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Basic information

Entry
Database: PDB / ID: 2uzc
TitleStructure of human PDLIM5 in complex with the C-terminal peptide of human alpha-actinin-1
ComponentsPDZ AND LIM DOMAIN 5
KeywordsSIGNALING PROTEIN / METAL-BINDING / ENIGMA HOMOLOG / PHOSPHORYLATION / LIM DOMAIN / PDZ DOMAIN
Function / homology
Function and homology information


muscle structure development / cell growth involved in cardiac muscle cell development / muscle alpha-actinin binding / cadherin binding involved in cell-cell adhesion / regulation of dendritic spine morphogenesis / actinin binding / Neurexins and neuroligins / regulation of synapse assembly / filamentous actin / stress fiber ...muscle structure development / cell growth involved in cardiac muscle cell development / muscle alpha-actinin binding / cadherin binding involved in cell-cell adhesion / regulation of dendritic spine morphogenesis / actinin binding / Neurexins and neuroligins / regulation of synapse assembly / filamentous actin / stress fiber / protein kinase C binding / cell projection / adherens junction / Z disc / presynapse / actin cytoskeleton / heart development / actin binding / actin cytoskeleton organization / postsynaptic density / metal ion binding / membrane / cytosol
Similarity search - Function
: / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. ...: / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
PDZ and LIM domain protein 5 / PDZ and LIM domain protein 5
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBunkoczi, G. / Elkins, J. / Salah, E. / Burgess-Brown, N. / Papagrigoriou, E. / Pike, A.C.W. / Turnbull, A. / Gileadi, O. / von Delft, F. / Arrowsmith, C.H. ...Bunkoczi, G. / Elkins, J. / Salah, E. / Burgess-Brown, N. / Papagrigoriou, E. / Pike, A.C.W. / Turnbull, A. / Gileadi, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Sundstrom, M. / Weigelt, J. / Doyle, D.
CitationJournal: Protein Sci. / Year: 2010
Title: Unusual binding interactions in PDZ domain crystal structures help explain binding mechanisms.
Authors: Elkins, J.M. / Gileadi, C. / Shrestha, L. / Phillips, C. / Wang, J. / Muniz, J.R. / Doyle, D.A.
History
DepositionApr 27, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 28, 2015Group: Database references / Other
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / citation_author / entity_src_gen
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PDZ AND LIM DOMAIN 5
B: PDZ AND LIM DOMAIN 5
C: PDZ AND LIM DOMAIN 5
D: PDZ AND LIM DOMAIN 5
E: PDZ AND LIM DOMAIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,92513
Polymers46,5885
Non-polymers3378
Water8,287460
1
A: PDZ AND LIM DOMAIN 5


Theoretical massNumber of molelcules
Total (without water)9,3181
Polymers9,3181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PDZ AND LIM DOMAIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4153
Polymers9,3181
Non-polymers982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: PDZ AND LIM DOMAIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3532
Polymers9,3181
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: PDZ AND LIM DOMAIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4514
Polymers9,3181
Non-polymers1333
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: PDZ AND LIM DOMAIN 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3883
Polymers9,3181
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)61.250, 36.474, 88.706
Angle α, β, γ (deg.)90.00, 99.15, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.71731, -0.6454, -0.26254), (0.5981, -0.76365, 0.24314), (-0.35741, 0.01738, 0.93378)20.2177, -15.0469, 22.95777
2given(-0.19437, 0.98072, 0.02022), (0.97218, 0.18985, 0.13717), (0.13068, 0.04632, -0.99034)-13.56198, -36.80161, 32.61575
3given(0.34988, 0.92298, -0.16026), (-0.91094, 0.2953, -0.28809), (-0.21857, 0.24678, 0.9441)6.8579, 12.03168, 39.62221
4given(0.67922, -0.65864, 0.32381), (-0.68185, -0.72953, -0.05365), (0.27157, -0.18435, -0.9446)-31.24924, -15.49909, 12.26183

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Components

#1: Protein
PDZ AND LIM DOMAIN 5 / HUMAN PDLIM5


Mass: 9317.584 Da / Num. of mol.: 5 / Fragment: RESIDUES 1-83
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-BSA4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3 / References: UniProt: Q8WVK0, UniProt: Q96HC4*PLUS
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#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.: 460 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE LAST 4 RESIDUES WERE TAGGED TO THE C-TERMINUS TO PROMOTE CRYSTAL CONTACTS

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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 Å3/Da / Density % sol: 38 %
Crystal growDetails: 20% PEG3350 0.20 M KSCN

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9537
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 3, 2007 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.5→46.4 Å / Num. obs: 49917 / % possible obs: 79.7 % / Observed criterion σ(I): 0 / Redundancy: 2.69 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.2
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 0.83 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.98 / % possible all: 37

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Processing

Software
NameVersionClassification
REFMAC5.3.0034refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PKT

2pkt


Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.312 / SU ML: 0.062 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.215 2527 5.1 %RANDOM
Rwork0.163 ---
obs0.166 47380 79.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.97 Å20 Å2-0.56 Å2
2--0.72 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3188 0 14 460 3662
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223346
X-RAY DIFFRACTIONr_bond_other_d0.0010.022235
X-RAY DIFFRACTIONr_angle_refined_deg1.481.9644523
X-RAY DIFFRACTIONr_angle_other_deg0.9335519
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.815437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92625.786140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.65915591
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0151517
X-RAY DIFFRACTIONr_chiral_restr0.0840.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023754
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02594
X-RAY DIFFRACTIONr_nbd_refined0.2040.2627
X-RAY DIFFRACTIONr_nbd_other0.1940.22313
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21572
X-RAY DIFFRACTIONr_nbtor_other0.0860.21874
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2310
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.241
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2540.291
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.253
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.16932257
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.253499
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.17881236
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.097111023
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: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.34 72
Rwork0.251 1339
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)
12.3815-0.5863-1.47320.5006-0.23282.12220.08450.11730.1840.13550.0102-0.0685-0.2794-0.1072-0.09470.0441-0.01980.0193-0.0552-0.006-0.04329.9072.9667-0.1126
22.10960.68941.04160.89640.32571.82620.0613-0.0393-0.19450.0893-0.0837-0.1714-0.0028-0.07080.0223-0.0283-0.0064-0.0028-0.06370.0008-0.000311.241-11.36319.1072
31.3577-0.09510.57170.51420.18820.8041-0.03740.0702-0.01240.00180.07420.0095-0.0020.0639-0.0368-0.0325-0.0060.0016-0.0068-0.007-0.0207-12.5631-26.538834.2257
41.46950.0226-0.70270.50640.00931.2075-0.0194-0.0584-0.00540.00130.0017-0.0563-0.04520.02980.0177-0.03150.0013-0.0072-0.0212-0.0108-0.013513.16073.749538.0767
52.6005-0.32020.13291.4375-0.66131.9360.0471-0.01460.0076-0.104-0.05810.0053-0.0676-0.21020.011-0.0360.025-0.0116-0.0224-0.0351-0.0465-26.4705-24.486114.6904
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 87
2X-RAY DIFFRACTION2B0 - 87
3X-RAY DIFFRACTION3C0 - 87
4X-RAY DIFFRACTION4D0 - 87
5X-RAY DIFFRACTION5E0 - 87

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