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- PDB-9gfc: HDM2 complexed with stapled peptide-like ligand -

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Basic information

Entry
Database: PDB / ID: 9gfc
TitleHDM2 complexed with stapled peptide-like ligand
Components
  • E3 ubiquitin-protein ligase Mdm2
  • Stapled peptide-like ligand
KeywordsPEPTIDE BINDING PROTEIN / Stapled peptide / HDM2
Function / homology
Function and homology information


cellular response to vitamin B1 / response to formaldehyde / response to water-immersion restraint stress / traversing start control point of mitotic cell cycle / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / response to ether / atrial septum development / fibroblast activation / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / negative regulation of signal transduction by p53 class mediator ...cellular response to vitamin B1 / response to formaldehyde / response to water-immersion restraint stress / traversing start control point of mitotic cell cycle / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / response to ether / atrial septum development / fibroblast activation / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / negative regulation of signal transduction by p53 class mediator / Trafficking of AMPA receptors / receptor serine/threonine kinase binding / peroxisome proliferator activated receptor binding / positive regulation of vascular associated smooth muscle cell migration / SUMO transferase activity / negative regulation of protein processing / response to steroid hormone / response to iron ion / NEDD8 ligase activity / cellular response to peptide hormone stimulus / AKT phosphorylates targets in the cytosol / atrioventricular valve morphogenesis / ventricular septum development / endocardial cushion morphogenesis / positive regulation of muscle cell differentiation / cellular response to alkaloid / SUMOylation of ubiquitinylation proteins / regulation of postsynaptic neurotransmitter receptor internalization / cardiac septum morphogenesis / blood vessel development / regulation of protein catabolic process / ligase activity / Constitutive Signaling by AKT1 E17K in Cancer / negative regulation of DNA damage response, signal transduction by p53 class mediator / response to magnesium ion / SUMOylation of transcription factors / protein sumoylation / blood vessel remodeling / protein localization to nucleus / cellular response to UV-C / cellular response to estrogen stimulus / cellular response to actinomycin D / ribonucleoprotein complex binding / protein autoubiquitination / positive regulation of vascular associated smooth muscle cell proliferation / : / NPAS4 regulates expression of target genes / transcription repressor complex / positive regulation of mitotic cell cycle / regulation of heart rate / positive regulation of protein export from nucleus / ubiquitin binding / proteolysis involved in protein catabolic process / Stabilization of p53 / response to cocaine / establishment of protein localization / Regulation of RUNX3 expression and activity / RING-type E3 ubiquitin transferase / protein destabilization / Oncogene Induced Senescence / cellular response to gamma radiation / Regulation of TP53 Activity through Methylation / cellular response to growth factor stimulus / cellular response to hydrogen peroxide / response to toxic substance / protein polyubiquitination / ubiquitin-protein transferase activity / disordered domain specific binding / endocytic vesicle membrane / ubiquitin protein ligase activity / p53 binding / Signaling by ALK fusions and activated point mutants / Regulation of TP53 Degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of neuron projection development / 5S rRNA binding / regulation of gene expression / ubiquitin-dependent protein catabolic process / protein-containing complex assembly / cellular response to hypoxia / Oxidative Stress Induced Senescence / proteasome-mediated ubiquitin-dependent protein catabolic process / Regulation of TP53 Activity through Phosphorylation / amyloid fibril formation / regulation of cell cycle / postsynaptic density / Ub-specific processing proteases / protein ubiquitination / response to xenobiotic stimulus / protein domain specific binding / response to antibiotic / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / nucleolus / apoptotic process / glutamatergic synapse / enzyme binding
Similarity search - Function
E3 ubiquitin-protein ligase Mdm2 / MDM2, modified RING finger, HC subclass / 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. ...E3 ubiquitin-protein ligase Mdm2 / MDM2, modified RING finger, HC subclass / 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 superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
E3 ubiquitin-protein ligase Mdm2
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.501 Å
AuthorsPerdriau, C. / Luton, A. / Zimmeter, K. / Neuville, M. / Saragaglia, C. / Peluso-lltis, C. / Osz, J. / Kauffmann, B. / Collie, G. / Rochel, N. ...Perdriau, C. / Luton, A. / Zimmeter, K. / Neuville, M. / Saragaglia, C. / Peluso-lltis, C. / Osz, J. / Kauffmann, B. / Collie, G. / Rochel, N. / Guichard, G. / Pasco, M.
Funding support France, 3items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-15-CE07-0010 France
Agence Nationale de la Recherche (ANR)ANR-17-CE07-0020 France
Agence Nationale de la Recherche (ANR)ANR-20-CE18-0038 France
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: Guanidinium-Stapled Helical Peptides for Targeting Protein-Protein Interactions.
Authors: Perdriau, C. / Luton, A. / Zimmeter, K. / Neuville, M. / Saragaglia, C. / Peluso-Iltis, C. / Osz, J. / Kauffmann, B. / Collie, G.W. / Rochel, N. / Guichard, G. / Pasco, M.
History
DepositionAug 8, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase Mdm2
B: E3 ubiquitin-protein ligase Mdm2
C: E3 ubiquitin-protein ligase Mdm2
D: E3 ubiquitin-protein ligase Mdm2
E: Stapled peptide-like ligand
F: Stapled peptide-like ligand
G: Stapled peptide-like ligand


Theoretical massNumber of molelcules
Total (without water)45,2257
Polymers45,2257
Non-polymers00
Water82946
1
A: E3 ubiquitin-protein ligase Mdm2
E: Stapled peptide-like ligand


Theoretical massNumber of molelcules
Total (without water)11,6942
Polymers11,6942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-10 kcal/mol
Surface area5990 Å2
MethodPISA
2
B: E3 ubiquitin-protein ligase Mdm2
F: Stapled peptide-like ligand


Theoretical massNumber of molelcules
Total (without water)11,6942
Polymers11,6942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1220 Å2
ΔGint-10 kcal/mol
Surface area5840 Å2
MethodPISA
3
C: E3 ubiquitin-protein ligase Mdm2
G: Stapled peptide-like ligand


Theoretical massNumber of molelcules
Total (without water)11,6942
Polymers11,6942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-11 kcal/mol
Surface area6050 Å2
MethodPISA
4
D: E3 ubiquitin-protein ligase Mdm2


Theoretical massNumber of molelcules
Total (without water)10,1441
Polymers10,1441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.628, 40.736, 78.177
Angle α, β, γ (deg.)90, 95.86, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
E3 ubiquitin-protein ligase Mdm2 / Double minute 2 protein / Hdm2 / Oncoprotein Mdm2 / RING-type E3 ubiquitin transferase Mdm2 / p53- ...Double minute 2 protein / Hdm2 / Oncoprotein Mdm2 / RING-type E3 ubiquitin transferase Mdm2 / p53-binding protein Mdm2


Mass: 10144.020 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MDM2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q00987, RING-type E3 ubiquitin transferase
#2: Protein/peptide Stapled peptide-like ligand


Mass: 1549.792 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.16 Å3/Da / Density % sol: 42.95 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: Ammonium Sulfate 2.5M + Tris 0.1M pH8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54178 Å
DetectorType: DECTRIS EIGER2 R 1M / Detector: PIXEL / Date: Sep 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.5→28.13 Å / Num. obs: 13311 / % possible obs: 97.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 5.69
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.3674 / Num. unique obs: 1375

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
CrysalisProv171.42data reduction
CrysalisProv171.42data scaling
PHASERv2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.501→28.13 Å / Cor.coef. Fo:Fc: 0.85 / Cor.coef. Fo:Fc free: 0.803 / SU R Cruickshank DPI: 1.536 / Cross valid method: THROUGHOUT / SU R Blow DPI: 1.314 / SU Rfree Blow DPI: 0.381 / SU Rfree Cruickshank DPI: 0.39
RfactorNum. reflection% reflectionSelection details
Rfree0.3175 644 -RANDOM
Rwork0.2632 ---
obs0.2659 13311 97.5 %-
Displacement parametersBiso mean: 33.5 Å2
Baniso -1Baniso -2Baniso -3
1--3.5104 Å20 Å2-2.222 Å2
2--12.627 Å20 Å2
3----9.1166 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å
Refinement stepCycle: LAST / Resolution: 2.501→28.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2816 0 318 46 3180
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0063205HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.894321HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1223SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes507HARMONIC5
X-RAY DIFFRACTIONt_it3205HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion399SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact2505SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.76
X-RAY DIFFRACTIONt_other_torsion19.54
LS refinement shellResolution: 2.501→2.53 Å
RfactorNum. reflection% reflection
Rfree0.318 17 -
Rwork0.263 --
obs--89.62 %

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