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- PDB-3pdv: Structure of the PDlim2 PDZ domain in complex with the C-terminal... -

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Basic information

Entry
Database: PDB / ID: 3pdv
TitleStructure of the PDlim2 PDZ domain in complex with the C-terminal 6-peptide extension of NS1
ComponentsPDZ and LIM domain protein 2, C-teminal peptide from Nonstructural protein 1
KeywordsPROTEIN BINDING / PDZ / extension / protein interaction / X-S/T-X-V motif
Function / homology
Function and homology information


muscle structure development / symbiont-mediated suppression of host mRNA processing / filamin binding / symbiont-mediated suppression of host PKR/eIFalpha signaling / muscle alpha-actinin binding / cortical actin cytoskeleton / myosin heavy chain binding / filamentous actin / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / stress fiber ...muscle structure development / symbiont-mediated suppression of host mRNA processing / filamin binding / symbiont-mediated suppression of host PKR/eIFalpha signaling / muscle alpha-actinin binding / cortical actin cytoskeleton / myosin heavy chain binding / filamentous actin / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / stress fiber / adherens junction / protein catabolic process / Z disc / actin binding / heart development / actin cytoskeleton organization / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / ubiquitin protein ligase binding / RNA binding / metal ion binding / nucleus
Similarity search - Function
Domain of unknown function DUF4749 / Domain of unknown function (DUF4749) / Influenza A virus NS1 protein / Influenza A virus NS1, effector domain-like superfamily / Influenza non-structural protein (NS1) / Influenza non-structural protein (NS1) / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type ...Domain of unknown function DUF4749 / Domain of unknown function (DUF4749) / Influenza A virus NS1 protein / Influenza A virus NS1, effector domain-like superfamily / Influenza non-structural protein (NS1) / Influenza non-structural protein (NS1) / 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 / S15/NS1, RNA-binding / Roll / Mainly Beta
Similarity search - Domain/homology
Non-structural protein 1 / PDZ and LIM domain protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLi, X.
CitationJournal: Plos One / Year: 2011
Title: PDlim2 selectively interacts with the PDZ binding motif of highly pathogenic avian H5N1 influenza A virus NS1
Authors: Yu, J. / Li, X. / Wang, Y. / Li, B. / Li, H. / Li, Y. / Zhou, W. / Zhang, C. / Wang, Y. / Rao, Z. / Bartlam, M. / Cao, Y.
History
DepositionOct 25, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_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 2, C-teminal peptide from Nonstructural protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6162
Polymers9,5931
Non-polymers231
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.917, 81.917, 81.917
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein PDZ and LIM domain protein 2, C-teminal peptide from Nonstructural protein 1 / PDZ-LIM protein mystique


Mass: 9592.925 Da / Num. of mol.: 1 / Fragment: PDZ domain
Source method: isolated from a genetically manipulated source
Details: Chimera of PDZ and LIM domain protein 2 and C-teminal peptide from Nonstructural protein 1
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Influenza A virus
Strain: A/chicken/Henan/12/2004(H5N1) / Gene: PDLIM2, NS1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96JY6, UniProt: Q29SJ1
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.39 Å3/Da / Density % sol: 48.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 0.2M NaCl, 0.1M HEPES, 22.5% PEG3350, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 4588 / Num. obs: 4548 / % possible obs: 99.79 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→19.31 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.888 / SU B: 5.825 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2489 215 4.5 %RANDOM
Rwork0.19799 ---
obs0.20009 4548 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.547 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms658 0 1 47 706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022679
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1871.974923
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.731590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.59724.44427
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.93315113
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.008155
X-RAY DIFFRACTIONr_chiral_restr0.0680.2106
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02517
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.2287
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2940.2464
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.253
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1850.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5071.5449
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.9842722
X-RAY DIFFRACTIONr_scbond_it1.3693235
X-RAY DIFFRACTIONr_scangle_it2.5584.5201
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.204→2.261 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 17 -
Rwork0.207 344 -
obs--100 %

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