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- PDB-2v1w: Crystal structure of human LIM protein RIL (PDLIM4) PDZ domain bo... -

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Basic information

Entry
Database: PDB / ID: 2v1w
TitleCrystal structure of human LIM protein RIL (PDLIM4) PDZ domain bound to the C-terminal peptide of human alpha-actinin-1
ComponentsPDZ AND LIM DOMAIN PROTEIN 4
KeywordsSTRUCTURAL PROTEIN / ACTIN / STRESS / FIBRE DYNAMICS / CYTOSKELETON / LIM DOMAIN / METAL-BINDING / PHOSPHORYLATION
Function / homology
Function and homology information


recycling endosome lumen / muscle structure development / excitatory chemical synaptic transmission / muscle alpha-actinin binding / filamentous actin / alpha-actinin binding / stress fiber / early endosome lumen / adherens junction / Z disc ...recycling endosome lumen / muscle structure development / excitatory chemical synaptic transmission / muscle alpha-actinin binding / filamentous actin / alpha-actinin binding / stress fiber / early endosome lumen / adherens junction / Z disc / recycling endosome membrane / lamellipodium / actin cytoskeleton / heart development / actin binding / actin cytoskeleton organization / early endosome membrane / protein phosphatase binding / dendritic spine / postsynaptic membrane / cytoskeleton / perinuclear region of cytoplasm / protein homodimerization activity / metal ion binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
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 ...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
PDZ and LIM domain protein 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSoundararajan, M. / Shrestha, L. / Pike, A.C.W. / Salah, E. / Burgess-Brown, N. / Elkins, J. / Umeano, C. / Ugochukwu, E. / von Delft, F. / Arrowsmith, C.H. ...Soundararajan, M. / Shrestha, L. / Pike, A.C.W. / Salah, E. / Burgess-Brown, N. / Elkins, J. / Umeano, C. / Ugochukwu, E. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. / Sundstrom, M. / 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.C. / Doyle, D.A.
History
DepositionMay 30, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 28, 2015Group: Database references
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
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 / pdbx_struct_conn_angle / struct_conn / 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 / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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.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_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 PROTEIN 4
B: PDZ AND LIM DOMAIN PROTEIN 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4945
Polymers19,1702
Non-polymers3253
Water2,612145
1
A: PDZ AND LIM DOMAIN PROTEIN 4
B: PDZ AND LIM DOMAIN PROTEIN 4
hetero molecules

A: PDZ AND LIM DOMAIN PROTEIN 4
B: PDZ AND LIM DOMAIN PROTEIN 4
hetero molecules

A: PDZ AND LIM DOMAIN PROTEIN 4
B: PDZ AND LIM DOMAIN PROTEIN 4
hetero molecules

A: PDZ AND LIM DOMAIN PROTEIN 4
B: PDZ AND LIM DOMAIN PROTEIN 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,97720
Polymers76,6798
Non-polymers1,29912
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
crystal symmetry operation2_565-x,-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)87.029, 87.029, 53.917
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-2022-

HOH

21A-2053-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.06158, -0.90199, 0.42735), (-0.97762, -0.1408, -0.15631), (0.20116, -0.40816, -0.89047)
Vector: 39.15546, 48.88204, 48.22211)
DetailsENTITY CRYSTALLISED CONTAINS AN ARTIFICIAL OLIGOMERISATIONC-TERMINAL TAG THAT ALLOWS MODULES TO SELF-ASSOCIATE

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Components

#1: Protein PDZ AND LIM DOMAIN PROTEIN 4 / PDLIM4 / LIM PROTEIN RIL / REVERSION-INDUCED LIM PROTEIN


Mass: 9584.851 Da / Num. of mol.: 2 / Fragment: PDZ DOMAIN, RESIDUES 1-85
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: P50479
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.68 Å3/Da / Density % sol: 54.05 %
Crystal growpH: 8.5
Details: 20% PEG 10000, 0.2M MAGNESIUM CHLORIDE, 0.1M TRIS PH8.5, pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00234
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 22, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00234 Å / Relative weight: 1
ReflectionResolution: 1.9→61.55 Å / Num. obs: 16891 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 9.3 % / Biso Wilson estimate: 21.07 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 18.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 4.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.3.0037refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GQ4

1gq4


Resolution: 1.9→61.55 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.714 / SU ML: 0.074 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.211 853 5.1 %RANDOM
Rwork0.173 ---
obs0.174 16015 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2--0.31 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.9→61.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1300 0 17 145 1462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211353
X-RAY DIFFRACTIONr_bond_other_d0.0020.02916
X-RAY DIFFRACTIONr_angle_refined_deg1.3611.9821835
X-RAY DIFFRACTIONr_angle_other_deg0.86932242
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0255179
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.88722.65349
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.62415208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.1811511
X-RAY DIFFRACTIONr_chiral_restr0.0750.2212
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021513
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02256
X-RAY DIFFRACTIONr_nbd_refined0.20.2203
X-RAY DIFFRACTIONr_nbd_other0.2040.2924
X-RAY DIFFRACTIONr_nbtor_refined0.1630.2635
X-RAY DIFFRACTIONr_nbtor_other0.0830.2747
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.293
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1240.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3230.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4763925
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.4351426
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.3158481
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.5911408
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: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.245 71
Rwork0.196 1145
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)
10.92270.22910.09921.62220.65511.83160.01510.0328-0.06130.02940.0343-0.02560.12550.035-0.0494-0.06350.0231-0.0087-0.0828-0.0189-0.07359.072127.20068.3372
22.11340.07520.28821.0392-0.20622.4264-0.0267-0.1015-0.0622-0.00940.0356-0.12440.08320.2067-0.0088-0.05950.0447-0.0299-0.0433-0.0195-0.087218.373734.845531.7488
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 89
2X-RAY DIFFRACTION2B0 - 89

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