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- PDB-7kjn: CRYSTAL STRUCTURE OF HUMAN MDMX IN COMPLEX WITH D-PEPTIDE INHIBIT... -

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Basic information

Entry
Database: PDB / ID: 7kjn
TitleCRYSTAL STRUCTURE OF HUMAN MDMX IN COMPLEX WITH D-PEPTIDE INHIBITOR (DPMI-OMEGA)
Components
  • D-PMI-omega
  • Protein Mdm4
KeywordsLIGASE/LIGASE INHIBITOR / MDMX / MDM2-LIKE P53 BINDING PROTEIN / P53-BINDING PROTEIN MDM4 / D-PEPTIDE ACTIVATOR OF MDMX / MDMX-D-PEPTIDE COMPLEX / HOST-VIRUS INTERACTION / LIGASE / METAL-BINDING / NUCLEUS / PHOSPHOPROTEIN / PROTO-ONCOGENE / UBL CONJUGATION PATHWAY / ZINC-FINGER / LIGASE-LIGASE INHIBITOR COMPLEX
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 / Regulation of TP53 Activity through Methylation ...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 / Regulation of TP53 Activity through Methylation / negative regulation of protein catabolic process / 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 / protein ubiquitination / regulation of cell cycle / Ub-specific processing proteases / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / enzyme binding / 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
: / polypeptide(D) / polypeptide(D) (> 10) / Protein Mdm4
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsTolbert, W.D. / Pazgier, M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI116274 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01AI120756 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI129769 United States
CitationJournal: To Be Published
Title: CRYSTAL STRUCTURE OF HUMAN MDMX IN COMPLEX WITH D-PEPTIDE INHIBITOR (DPMI-OMEGA)
Authors: Tolbert, W.D. / Pazgier, M.
History
DepositionOct 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein Mdm4
B: D-PMI-omega
C: D-PMI-omega


Theoretical massNumber of molelcules
Total (without water)12,9643
Polymers12,9643
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-16 kcal/mol
Surface area6430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.849, 48.849, 90.116
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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: 9575.293 Da / Num. of mol.: 1 / Mutation: Q68A, Q69A, E70A / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O15151
#2: Polypeptide(D) D-PMI-omega


Type: Peptide-like / Class: Inhibitor / Mass: 1694.346 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: BIRD: PRD_002455
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: 2.39 Å3/Da / Density % sol: 48.63 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 4M sodium chloride, 5% isopropanol, 0.1M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 19, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 3311 / % possible obs: 98.8 % / Redundancy: 4.5 % / CC1/2: 0.989 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.078 / Net I/σ(I): 11.5
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 1.35 / Num. unique obs: 158 / CC1/2: 0.729 / Rpim(I) all: 0.516 / % possible all: 95.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PHENIX1.17refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UML

5uml


Resolution: 2.8→42.3 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.926 / SU B: 40.007 / SU ML: 0.311 / Cross valid method: FREE R-VALUE / ESU R Free: 0.378 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24366 184 5.6 %RANDOM
Rwork0.20769 ---
obs0.2097 3108 98.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.08 Å2
Baniso -1Baniso -2Baniso -3
1-2.18 Å21.09 Å20 Å2
2--2.18 Å2-0 Å2
3----7.06 Å2
Refinement stepCycle: 1 / Resolution: 2.8→42.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms910 0 0 0 910
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.014927
X-RAY DIFFRACTIONr_bond_other_d0.0260.018884
X-RAY DIFFRACTIONr_angle_refined_deg2.8971.7981243
X-RAY DIFFRACTIONr_angle_other_deg3.1051.7682053
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0485102
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.07222.90331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.74915127
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.585153
X-RAY DIFFRACTIONr_chiral_restr0.1780.2107
X-RAY DIFFRACTIONr_gen_planes_refined0.030.021020
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02197
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.1724.904429
X-RAY DIFFRACTIONr_mcbond_other3.1714.904429
X-RAY DIFFRACTIONr_mcangle_it5.0227.328524
X-RAY DIFFRACTIONr_mcangle_other5.0197.331525
X-RAY DIFFRACTIONr_scbond_it3.6375.33498
X-RAY DIFFRACTIONr_scbond_other3.6345.333499
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8947.875719
X-RAY DIFFRACTIONr_long_range_B_refined8.58792.9953430
X-RAY DIFFRACTIONr_long_range_B_other8.58692.9823431
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.802→2.874 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 16 -
Rwork0.358 222 -
obs--93.7 %
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)
10.91730.97950.39591.09220.21511.2242-0.0229-0.01630.04820.0122-0.02280.03430.0427-0.08320.04570.03480.02070.00060.0682-0.01330.040425.307-15.2831.106
21.11910.23130.5295.009-3.95713.59370.0622-0.1148-0.0663-0.1093-0.1312-0.1770.16280.04280.0690.07480.0363-0.00780.0723-0.02880.046628.303-21.778-11.435
35.34310.92885.78452.72531.80456.7798-0.36890.45060.3758-0.28820.0078-0.1049-0.41830.40120.36110.0614-0.048-0.0010.07130.0230.04532.216-6.306-9.288
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 108
2X-RAY DIFFRACTION2B1 - 12
3X-RAY DIFFRACTION3C1 - 12

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