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- PDB-3eqy: Crystal structure of human MDMX in complex with a 12-mer peptide ... -

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Basic information

Entry
Database: PDB / ID: 3eqy
TitleCrystal structure of human MDMX in complex with a 12-mer peptide inhibitor
Components
  • 12-mer peptide inhibitor
  • Mdm4 protein
KeywordsONCOPROTEIN / MDM4 / MDMX / MDMX-peptide inhibitor complex / Metal-binding / Nucleus / Zinc-finger
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 / protein ubiquitination / regulation of cell cycle / 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 / MDM2 / SWIB/MDM2 domain / p53 negative regulator Mdm2/Mdm4 / SWIB/MDM2 domain / 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) ...MDM4 / MDM2 / SWIB/MDM2 domain / p53 negative regulator Mdm2/Mdm4 / SWIB/MDM2 domain / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
GUANIDINE / PHOSPHATE ION / Protein Mdm4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsPazgier, M. / Lu, W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structural basis for high-affinity peptide inhibition of p53 interactions with MDM2 and MDMX.
Authors: Pazgier, M. / Liu, M. / Zou, G. / Yuan, W. / Li, C. / Li, C. / Li, J. / Monbo, J. / Zella, D. / Tarasov, S.G. / Lu, W.
History
DepositionOct 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 2, 2014Group: Source and taxonomy
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mdm4 protein
B: Mdm4 protein
C: 12-mer peptide inhibitor
D: 12-mer peptide inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,50410
Polymers22,0064
Non-polymers4986
Water4,684260
1
A: Mdm4 protein
C: 12-mer peptide inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2525
Polymers11,0032
Non-polymers2493
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-23 kcal/mol
Surface area5720 Å2
MethodPISA
2
B: Mdm4 protein
D: 12-mer peptide inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2525
Polymers11,0032
Non-polymers2493
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-23 kcal/mol
Surface area5720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.627, 75.627, 35.181
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
/ NCS ensembles :
ID
1
2

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Components

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


Mass: 9575.293 Da / Num. of mol.: 2 / Fragment: UNP residues residues 24-108 / Mutation: Q68A, Q69A, E70A / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: O15151
#2: Protein/peptide 12-mer peptide inhibitor


Mass: 1427.557 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: peptide identified by screening a duodecimal peptide library displayed on M13 phage
#3: Chemical ChemComp-GAI / GUANIDINE / Guanidine


Mass: 59.070 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH5N3
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 2.64 Å3/Da / Density % sol: 53.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 0.8 M sodium phosphate, 0.8 M potassium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 27, 2008 / Details: confocal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.63→65.51 Å / Num. all: 27997 / Num. obs: 27972 / % possible obs: 99.9 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.045 / Rsym value: 0.049 / Net I/σ(I): 64.3
Reflection shellResolution: 1.63→1.69 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.101 / Mean I/σ(I) obs: 20.2 / Rsym value: 0.098 / % possible all: 94.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.4.0077refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2Z5T

2z5t


Resolution: 1.63→15 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.5 / SU ML: 0.041 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16874 1401 5 %RANDOM
Rwork0.1548 ---
obs0.15551 26538 99.92 %-
all-27939 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.887 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.09 Å20 Å2
2--0.18 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.63→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1528 0 28 260 1816
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221697
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7462.0012324
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4825222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.05124.93375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.6715309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.427156
X-RAY DIFFRACTIONr_chiral_restr0.120.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211288
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.9881.51019
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.56521644
X-RAY DIFFRACTIONr_scbond_it2.4883678
X-RAY DIFFRACTIONr_scangle_it3.9344.5661
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A685tight positional0.010.05
22B102tight positional0.210.05
11A685tight thermal0.110.5
22B102tight thermal0.180.5
LS refinement shellResolution: 1.63→1.674 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 82 -
Rwork0.193 1971 -
obs--99.13 %
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)
11.40550.5191-0.48441.1216-0.13890.95130.0140.0624-0.019-0.0381-0.01840.10680.0325-0.06210.00440.04620.003-0.00690.0429-0.01070.035-10.031318.29843.9288
20.746-0.1463-0.10591.8277-0.49340.9516-0.01770.0543-0.0983-0.04840.01570.0420.0767-0.00650.0020.0425-0.00050.00560.0484-0.01210.0342-20.953744.09439.915
310.59330.8319-0.16561.56991.10013.0812-0.1292-0.2119-0.03880.2035-0.05560.22630.1662-0.1840.18490.0437-0.01520.02060.0144-0.00730.0407-16.196317.828514
43.84954.4404-1.23419.96290.43913.2341-0.0766-0.2541-0.24650.2331-0.15060.0350.24620.04560.22720.04310.02090.02110.01550.0170.042-23.522838.525119.8481
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 108
2X-RAY DIFFRACTION2B25 - 108
3X-RAY DIFFRACTION3C1 - 12
4X-RAY DIFFRACTION4D1 - 12

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