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- PDB-8ia5: Small peptide enhances the binding of nutline-3a to N-terminal do... -

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Basic information

Entry
Database: PDB / ID: 8ia5
TitleSmall peptide enhances the binding of nutline-3a to N-terminal domain of MdmX
Components
  • 9-mer peptide
  • Protein Mdm4
KeywordsONCOPROTEIN / MdmX / p53 / Nutlin-3a / Enhancement
Function / homology
Function and homology information


atrial septum development / heart valve development / atrioventricular valve morphogenesis / ventricular septum development / endocardial cushion morphogenesis / DNA damage response, signal transduction by p53 class mediator / transcription repressor complex / Stabilization of p53 / Oncogene Induced Senescence / negative regulation of protein catabolic process ...atrial septum development / heart valve development / atrioventricular valve morphogenesis / ventricular septum development / endocardial cushion morphogenesis / DNA damage response, signal transduction by p53 class mediator / transcription repressor complex / Stabilization of p53 / Oncogene Induced Senescence / negative regulation of protein catabolic process / Regulation of TP53 Activity through Methylation / ubiquitin-protein transferase activity / Regulation of TP53 Degradation / cellular response to hypoxia / protein-containing complex assembly / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / protein stabilization / Ub-specific processing proteases / regulation of cell cycle / protein ubiquitination / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / negative regulation of apoptotic process / enzyme binding / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
MDM4 / p53 negative regulator Mdm2/Mdm4 / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SWIB/MDM2 domain superfamily / Zn-finger in Ran binding protein and others / Zinc finger, C3HC4 type (RING finger) / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily ...MDM4 / p53 negative regulator Mdm2/Mdm4 / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SWIB/MDM2 domain superfamily / Zn-finger in Ran binding protein and others / Zinc finger, C3HC4 type (RING finger) / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Chem-NUT / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE / Protein Mdm4
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsCheng, X.Y. / Wei, Q.Y. / Huang, Y. / Su, Z.D.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Small peptide enhances the binding of nutline-3a to N-terminal domain of MdmX
Authors: Cheng, X.Y. / Wei, Q.Y. / Huang, Y. / Su, Z.D.
History
DepositionFeb 7, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein Mdm4
B: 9-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1924
Polymers11,3462
Non-polymers8462
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-5 kcal/mol
Surface area6040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.080, 47.080, 90.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Protein Mdm4 / Double minute 4 protein / Mdm2-like p53-binding protein / Protein Mdmx / p53-binding protein Mdm4


Mass: 10247.978 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MDM4, MDMX / Production host: Escherichia coli (E. coli) / References: UniProt: O15151
#2: Protein/peptide 9-mer peptide


Mass: 1098.163 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: peptide to enhance the binding of nutline-3a to N-terminal domain of MdmX
Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-NUT / 4-({(4S,5R)-4,5-bis(4-chlorophenyl)-2-[4-methoxy-2-(propan-2-yloxy)phenyl]-4,5-dihydro-1H-imidazol-1-yl}carbonyl)piperazin-2-one / Nutlin 3a


Mass: 581.490 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H30Cl2N4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-O4B / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE


Mass: 264.315 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H24O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M HEPES pH6.0, 1.6M Ammonium sulfate / PH range: 6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.93→26.81 Å / Num. obs: 8075 / % possible obs: 98.8 % / Redundancy: 24.1 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 1
Reflection shellResolution: 1.93→5.23 Å / CC1/2: 1

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Processing

Software
NameVersionClassification
REFMACREFMAC5refinement
xia2data scaling
xia2data reduction
MrBUMPphasing
HKL-3000data collection
PDB_EXTRACTdata extraction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→26.81 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.915 / SU B: 5.036 / SU ML: 0.144 / Cross valid method: NONE / ESU R: 0.195 / ESU R Free: 0.192
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2838 430 5.338 %
Rwork0.2101 7626 -
all0.214 --
obs-8056 98.629 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 46.762 Å2
Baniso -1Baniso -2Baniso -3
1--0.067 Å20 Å20 Å2
2---0.067 Å20 Å2
3---0.133 Å2
Refinement stepCycle: LAST / Resolution: 1.93→26.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms767 0 58 62 887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.012852
X-RAY DIFFRACTIONr_bond_other_d0.0010.016822
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.6611145
X-RAY DIFFRACTIONr_angle_other_deg0.51.5741895
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.229595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.54510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.19610148
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.551039
X-RAY DIFFRACTIONr_chiral_restr0.0770.2118
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02946
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02190
X-RAY DIFFRACTIONr_nbd_refined0.3270.2269
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2440.2856
X-RAY DIFFRACTIONr_nbtor_refined0.1980.2410
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.2489
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.258
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.5430.216
X-RAY DIFFRACTIONr_nbd_other0.190.252
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2140.28
X-RAY DIFFRACTIONr_mcbond_it4.4134.58381
X-RAY DIFFRACTIONr_mcbond_other4.4194.575379
X-RAY DIFFRACTIONr_mcangle_it6.1258.192472
X-RAY DIFFRACTIONr_mcangle_other6.138.193473
X-RAY DIFFRACTIONr_scbond_it4.635.226471
X-RAY DIFFRACTIONr_scbond_other4.6265.225472
X-RAY DIFFRACTIONr_scangle_it7.0069.376672
X-RAY DIFFRACTIONr_scangle_other79.373673
X-RAY DIFFRACTIONr_lrange_it15.24256.2891095
X-RAY DIFFRACTIONr_lrange_other15.14255.7691089
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.93-1.980.307340.3155470.3145970.9240.93697.31990.263
1.98-2.0340.296300.35190.35590.930.94698.21110.244
2.034-2.0930.346270.2795120.2825510.920.95497.82210.236
2.093-2.1570.314260.2685060.2715460.9490.95197.43590.217
2.157-2.2270.251280.2564840.2565200.9590.95898.46150.217
2.227-2.3050.205250.234650.2294960.9710.96498.79030.192
2.305-2.3910.273250.2374710.2395050.9360.96398.21780.216
2.391-2.4880.316210.2154480.2194730.8940.97299.15430.187
2.488-2.5970.411180.2454230.2524500.8540.96980.222
2.597-2.7230.317320.2364060.2424410.9430.96699.31970.215
2.723-2.8690.269320.2293760.2334130.960.96498.78930.21
2.869-3.040.278250.2253800.2294070.9620.96799.50860.205
3.04-3.2470.241200.1783450.1813690.9710.97898.9160.174
3.247-3.5030.215190.193430.1923640.9710.97599.45050.203
3.503-3.8310.378140.1863130.1923280.9120.97499.69510.197
3.831-4.2730.234160.1792920.1823080.9710.9781000.205
4.273-4.9130.405100.1542550.1622660.9460.98499.62410.187
4.913-5.9670.205110.2182350.2172460.9810.971000.255
5.967-8.2370.433110.2161820.2271930.9010.9621000.256
8.237-26.810.15560.2331240.231320.9970.96998.48480.31

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