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- PDB-2pkt: Crystal structure of the human CLP-36 (PDLIM1) bound to the C-ter... -

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Basic information

Entry
Database: PDB / ID: 2pkt
TitleCrystal structure of the human CLP-36 (PDLIM1) bound to the C-terminal peptide of human alpha-actinin-1
ComponentsPDZ and LIM domain protein 1
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PDZ DOMAIN / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


muscle structure development / establishment or maintenance of actin cytoskeleton polarity / muscle alpha-actinin binding / maintenance of cell polarity / cadherin binding involved in cell-cell adhesion / fibroblast migration / stress fiber assembly / filamentous actin / stress fiber / adherens junction ...muscle structure development / establishment or maintenance of actin cytoskeleton polarity / muscle alpha-actinin binding / maintenance of cell polarity / cadherin binding involved in cell-cell adhesion / fibroblast migration / stress fiber assembly / filamentous actin / stress fiber / adherens junction / Z disc / actin binding / heart development / actin cytoskeleton organization / response to oxidative stress / transcription regulator complex / transcription coactivator activity / cytoskeleton / response to hypoxia / focal adhesion / regulation of transcription by RNA polymerase II / metal ion binding / cytoplasm
Similarity search - Function
PDZ and LIM domain protein 1 / Zasp-like motif / ZASP-like motif / Domain of unknown function DUF4749 / Domain of unknown function (DUF4749) / 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 and LIM domain protein 1 / Zasp-like motif / ZASP-like motif / Domain of unknown function DUF4749 / Domain of unknown function (DUF4749) / 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
ACETATE ION / DI(HYDROXYETHYL)ETHER / PDZ and LIM domain protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsUppenberg, J. / Gileadi, C. / Elkins, J. / Bray, J. / Burgess-Brown, N. / Salah, E. / Gileadi, O. / Bunkoczi, G. / Ugochukwu, E. / Umeano, C. ...Uppenberg, J. / Gileadi, C. / Elkins, J. / Bray, J. / Burgess-Brown, N. / Salah, E. / Gileadi, O. / Bunkoczi, G. / Ugochukwu, E. / Umeano, C. / von Delft, F. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A. / Sundstrom, M. / Doyle, D.A. / Structural Genomics Consortium (SGC)
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 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Jun 23, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 21, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 999 SEQUENCE C-TERMINAL RESIDUES 87-90 (GLU-SER-ASP-LEU) CORRESPOND TO THE C-TERMINAL TAIL OF HUMAN ... SEQUENCE C-TERMINAL RESIDUES 87-90 (GLU-SER-ASP-LEU) CORRESPOND TO THE C-TERMINAL TAIL OF HUMAN ALPHA-ACTININ-1, UNIPROT ENTRY ACTN1_HUMAN, ACCESSION CODE P12814, SEQUENCE POSITION 889-892.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PDZ and LIM domain protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2087
Polymers9,7331
Non-polymers4756
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.740, 38.740, 246.460
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-202-

CA

21A-203-

CL

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PDZ and LIM domain protein 1 / Elfin / LIM domain protein CLP-36 / C-terminal LIM domain protein 1


Mass: 9732.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Heart / Gene: PDLIM1, CLIM1, CLP36 / Plasmid: PNIC28-BSA4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O00151

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Non-polymers , 6 types, 111 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#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.: 105 / 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: 2.74 Å3/Da / Density % sol: 55.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 40% PEG 300, 0.2M Calcium acetate, 0.1M Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.79987 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 11, 2007
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.79987 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 18632 / Num. obs: 18632 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.8 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 14.3
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2617 / % possible all: 89.6

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å14.02 Å
Translation2.5 Å14.02 Å

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Processing

Software
NameVersionClassificationNB
PHASERphasing
REFMAC5.3.0034refinement
PDB_EXTRACT2data extraction
MAR345CCDdata collection
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house model

Resolution: 1.5→41.06 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.157 / SU ML: 0.062 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.077 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.231 960 5.2 %RANDOM
Rwork0.212 ---
all0.213 18632 --
obs0.213 18632 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 7.375 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20.09 Å20 Å2
2--0.17 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.5→41.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms677 0 26 105 808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.021712
X-RAY DIFFRACTIONr_bond_other_d0.0010.02477
X-RAY DIFFRACTIONr_angle_refined_deg0.9191.986959
X-RAY DIFFRACTIONr_angle_other_deg0.76731177
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.118592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.05725.51729
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.28215118
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.39154
X-RAY DIFFRACTIONr_chiral_restr0.0550.2112
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.02785
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02122
X-RAY DIFFRACTIONr_nbd_refined0.1790.2105
X-RAY DIFFRACTIONr_nbd_other0.1740.2489
X-RAY DIFFRACTIONr_nbtor_refined0.1510.2337
X-RAY DIFFRACTIONr_nbtor_other0.0740.2404
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1070.255
X-RAY DIFFRACTIONr_metal_ion_refined0.1040.27
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2130.233
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0730.220
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0540.25
X-RAY DIFFRACTIONr_mcbond_it0.2361.5476
X-RAY DIFFRACTIONr_mcbond_other0.0481.5187
X-RAY DIFFRACTIONr_mcangle_it0.392733
X-RAY DIFFRACTIONr_scbond_it0.6963267
X-RAY DIFFRACTIONr_scangle_it1.0824.5225
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 67 -
Rwork0.339 1123 -
obs-1190 89.01 %
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)
12.71913.98645.357184.014524.174611.50330.2156-0.0925-0.5429-0.41980.0242-1.64110.2860.5124-0.23980.09850.0650.03810.1151-0.01360.217718.5156-15.30159.8475
20.97350.47350.13661.715-0.32231.86670.0758-0.1664-0.01040.1473-0.1096-0.00780.05020.05580.03380.08760.0005-0.00870.0313-0.01540.06579.3454-9.45148.2653
316.4618-11.95492.532115.48410.14623.3485-0.17690.0892-0.18110.37970.17320.7436-0.0805-0.08590.00370.0918-0.02990.0240.02890.0030.141222.223-28.5756-2.6658
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
110 - 91 - 10
2210 - 8411 - 85
3385 - 9086 - 91

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