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- PDB-4ydp: Crystal structure of N-terminal PDZ domain of ZASP in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4ydp
TitleCrystal structure of N-terminal PDZ domain of ZASP in complex with myotilin C-terminal peptide.
ComponentsLIM domain-binding protein 3
KeywordsSTRUCTURAL PROTEIN / ZASP/LDB3 / myotilin / striated muscle Z-disc / sarcomere
Function / homology
Function and homology information


muscle structure development / muscle alpha-actinin binding / sarcomere organization / filamentous actin / pseudopodium / stress fiber / cytoskeletal protein binding / adherens junction / protein kinase C binding / Z disc ...muscle structure development / muscle alpha-actinin binding / sarcomere organization / filamentous actin / pseudopodium / stress fiber / cytoskeletal protein binding / adherens junction / protein kinase C binding / Z disc / heart development / actin binding / actin cytoskeleton organization / cytoskeleton / perinuclear region of cytoplasm / metal ion binding
Similarity search - Function
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. ...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
GLUTAMIC ACID / LEUCINE / LIM domain-binding protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsGrishkovskaya, I. / Onipe, A. / Kontaxis, G. / Djinovic-Carugo, K.
CitationJournal: To Be Published
Title: Crystal structure of N-terminal PDZ domain of ZASP in complex with myotilin C-terminal peptide.
Authors: Grishkovskaya, I. / Onipe, A. / Kontaxis, G. / Djinovic-Carugo, K.
History
DepositionFeb 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LIM domain-binding protein 3
B: LIM domain-binding protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9778
Polymers18,1272
Non-polymers8516
Water2,612145
1
A: LIM domain-binding protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4894
Polymers9,0631
Non-polymers4253
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: LIM domain-binding protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,4894
Polymers9,0631
Non-polymers4253
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.900, 95.500, 28.900
Angle α, β, γ (deg.)90.000, 120.000, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 1 - 83 / Label seq-ID: 2 - 84

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein LIM domain-binding protein 3 / Protein cypher / Z-band alternatively spliced PDZ-motif protein


Mass: 9063.291 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LDB3, KIAA0613, ZASP / Production host: Escherichia coli (E. coli) / References: UniProt: O75112
#2: Chemical
ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO2
#4: 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: 1.91 Å3/Da / Density % sol: 35.45 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG 6000, imidazole

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.666
11H+L, -K, -L20.334
ReflectionResolution: 1.4→47.75 Å / Num. obs: 24577 / % possible obs: 92.4 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 14.7
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 2 % / Rmerge(I) obs: 0.301 / Mean I/σ(I) obs: 2 / % possible all: 61.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2pkt

2pkt


Resolution: 1.4→47.75 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.656 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.014 / ESU R Free: 0.012 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1565 1195 4.9 %RANDOM
Rwork0.1236 ---
obs0.1252 23381 92.38 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 77.78 Å2 / Biso mean: 13.354 Å2 / Biso min: 6.52 Å2
Baniso -1Baniso -2Baniso -3
1--3.82 Å20 Å21.57 Å2
2--2.02 Å20 Å2
3---1.8 Å2
Refinement stepCycle: final / Resolution: 1.4→47.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1240 0 35 145 1420
Biso mean--26.56 29.71 -
Num. residues----166
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.021309
X-RAY DIFFRACTIONr_bond_other_d0.0030.021257
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.951783
X-RAY DIFFRACTIONr_angle_other_deg0.96132873
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2895177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.53626.08746
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.46515211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.384152
X-RAY DIFFRACTIONr_chiral_restr0.0870.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021489
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02281
X-RAY DIFFRACTIONr_mcbond_it1.1751.196692
X-RAY DIFFRACTIONr_mcbond_other1.1741.194691
X-RAY DIFFRACTIONr_mcangle_it1.5091.797860
X-RAY DIFFRACTIONr_rigid_bond_restr2.32732566
X-RAY DIFFRACTIONr_sphericity_free27.277556
X-RAY DIFFRACTIONr_sphericity_bonded8.65352637
Refine LS restraints NCS

Ens-ID: 1 / Number: 4473 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.402→1.438 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 48 -
Rwork0.18 1053 -
all-1101 -
obs--54.34 %

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