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- PDB-9cdz: Crystal Structure of MDM2-Peptide Complex -

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Basic information

Entry
Database: PDB / ID: 9cdz
TitleCrystal Structure of MDM2-Peptide Complex
Components
  • E3 ubiquitin-protein ligase Mdm2
  • Peptide
KeywordsONCOPROTEIN / De novo design / Cyclic peptide / Deep learning / AlphaFold / MDM2
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 / fibroblast activation / atrial septum development / 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 / fibroblast activation / atrial septum development / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / negative regulation of signal transduction by p53 class mediator / receptor serine/threonine kinase binding / Trafficking of AMPA receptors / peroxisome proliferator activated receptor binding / positive regulation of vascular associated smooth muscle cell migration / negative regulation of protein processing / SUMO transferase activity / response to iron ion / NEDD8 ligase activity / AKT phosphorylates targets in the cytosol / atrioventricular valve morphogenesis / cellular response to peptide hormone stimulus / response to steroid hormone / 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 / ligase activity / Constitutive Signaling by AKT1 E17K in Cancer / regulation of protein catabolic process / negative regulation of DNA damage response, signal transduction by p53 class mediator / response to magnesium ion / SUMOylation of transcription factors / protein sumoylation / cellular response to UV-C / cellular response to estrogen stimulus / blood vessel remodeling / cellular response to actinomycin D / protein localization to nucleus / 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 / DNA damage response, signal transduction by p53 class mediator / proteolysis involved in protein catabolic process / ubiquitin binding / positive regulation of protein export from nucleus / Stabilization of p53 / response to cocaine / establishment of protein localization / Regulation of RUNX3 expression and activity / cellular response to gamma radiation / protein destabilization / cellular response to growth factor stimulus / RING-type E3 ubiquitin transferase / Oncogene Induced Senescence / Regulation of TP53 Activity through Methylation / centriolar satellite / cellular response to hydrogen peroxide / response to toxic substance / protein polyubiquitination / ubiquitin-protein transferase activity / disordered domain specific binding / p53 binding / endocytic vesicle membrane / ubiquitin protein ligase activity / 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 / protein-containing complex assembly / ubiquitin-dependent protein catabolic process / Oxidative Stress Induced Senescence / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / amyloid fibril formation / proteasome-mediated ubiquitin-dependent protein catabolic process / regulation of cell cycle / postsynaptic density / Ub-specific processing proteases / protein ubiquitination / protein domain specific binding / response to xenobiotic stimulus / response to antibiotic / negative regulation of DNA-templated transcription / apoptotic process / positive regulation of cell population proliferation / ubiquitin protein ligase binding / positive regulation of gene expression / negative regulation of apoptotic process / nucleolus / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsBera, A.K. / Rettie, S. / Bhardwaj, G.
Funding support United States, 2items
OrganizationGrant numberCountry
Defense Advanced Research Projects Agency (DARPA) United States
Defense Threat Reduction Agency (DTRA) United States
CitationJournal: Nat Commun / Year: 2025
Title: Cyclic peptide structure prediction and design using AlphaFold2.
Authors: Rettie, S.A. / Campbell, K.V. / Bera, A.K. / Kang, A. / Kozlov, S. / Bueso, Y.F. / De La Cruz, J. / Ahlrichs, M. / Cheng, S. / Gerben, S.R. / Lamb, M. / Murray, A. / Adebomi, V. / Zhou, G. / ...Authors: Rettie, S.A. / Campbell, K.V. / Bera, A.K. / Kang, A. / Kozlov, S. / Bueso, Y.F. / De La Cruz, J. / Ahlrichs, M. / Cheng, S. / Gerben, S.R. / Lamb, M. / Murray, A. / Adebomi, V. / Zhou, G. / DiMaio, F. / Ovchinnikov, S. / Bhardwaj, G.
History
DepositionJun 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jun 18, 2025Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase Mdm2
B: Peptide
C: E3 ubiquitin-protein ligase Mdm2
D: Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3406
Polymers28,2944
Non-polymers462
Water28816
1
A: E3 ubiquitin-protein ligase Mdm2
B: Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1703
Polymers14,1472
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-21 kcal/mol
Surface area6220 Å2
MethodPISA
2
C: E3 ubiquitin-protein ligase Mdm2
D: Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1703
Polymers14,1472
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1410 Å2
ΔGint-21 kcal/mol
Surface area6050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.775, 48.930, 49.266
Angle α, β, γ (deg.)90.000, 111.643, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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: 12332.134 Da / Num. of mol.: 2 / Mutation: E52A, K53A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MDM2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q00987, RING-type E3 ubiquitin transferase
#2: Protein/peptide Peptide


Mass: 1814.948 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 30 % w/v polyacylate 5100, sodium salt, 10% ethanol and 0.1 M MES-NaOH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97935 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: May 31, 2024
Details: Horizontal pre-focus bimorph mirror & KB bimorph mirrors
RadiationMonochromator: Si(111) DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.72→24.47 Å / Num. obs: 15978 / % possible obs: 91.4 % / Redundancy: 6.8 % / Biso Wilson estimate: 34.8 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.03 / Net I/σ(I): 11.1
Reflection shellResolution: 1.72→1.81 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.65 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2539 / CC1/2: 0.529 / Rpim(I) all: 0.75 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→24.47 Å / SU ML: 0.352 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 37.0878
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2704 1597 10.01 %
Rwork0.2216 14358 -
obs0.2264 15955 91.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.5 Å2
Refinement stepCycle: LAST / Resolution: 1.72→24.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1782 0 2 16 1800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00531834
X-RAY DIFFRACTIONf_angle_d0.69942476
X-RAY DIFFRACTIONf_chiral_restr0.0452280
X-RAY DIFFRACTIONf_plane_restr0.0067308
X-RAY DIFFRACTIONf_dihedral_angle_d21.0441696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.770.45171610.40511437X-RAY DIFFRACTION99.88
1.77-1.840.3791610.35291433X-RAY DIFFRACTION100
1.84-1.90.3831420.3291252X-RAY DIFFRACTION99.93
1.93-20.38391190.30041060X-RAY DIFFRACTION95.85
2-2.10.38051020.2864941X-RAY DIFFRACTION65.89
2.1-2.230.30991580.2611402X-RAY DIFFRACTION99.87
2.27-2.410.30521180.25461058X-RAY DIFFRACTION98.41
2.41-2.650.32091580.26361431X-RAY DIFFRACTION100
2.65-3.030.32171600.23471438X-RAY DIFFRACTION99.94
3.03-3.820.25271590.20861439X-RAY DIFFRACTION99.94
3.82-24.470.2141590.17811467X-RAY DIFFRACTION99.82
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)
15.56104749297-1.178129775922.090247970516.88774523195-1.00737725213.209162706840.1639217875310.1913206610830.124516930472-0.328541265011-0.06537746511750.5934904151050.0231445886768-0.162024327164-0.1122685580480.213452710371-0.0233364383192-0.00528445681990.2431727771610.02923940364990.279187164873-0.2491700313118.05591849705-24.0663573307
26.33880341136-1.61623773086-0.5780426069314.92658327859-1.64647988497.995215064020.166166397617-1.99942108421-0.2137510814412.31517214454-0.245781748537-0.634779133245-0.05784067771420.2797266918850.06379104291560.45170361366-0.1222372876840.0002572205286180.607650524314-0.02803344359070.3959404985936.481200845279.61706835424-13.2310031498
34.47602619562-0.760618114058-0.5751114610617.86359293671-0.7452918612695.168303128050.0877378414992-0.1531904089110.1019747504470.1118525317110.07705256159470.7855782559380.350984488772-0.370059928056-0.135525088180.259139397711-0.02903467923390.01899292053320.29130150210.01807578344850.2615475741348.6994785084810.8989168152-46.8382753256
48.33293210897-4.868627000981.649210110835.00479678417-3.019552276793.00479207666-0.778894944713-1.83114980901-0.08788467958422.232535995070.903079692531-1.036889312-0.145041153247-0.1380261158320.1037053948120.638216697002-0.01975539821570.02085047145740.6321716790650.06177598233470.32019842765616.119288452611.1940791448-35.8940993394
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain A and resseq 13:106)AA13 - 1061 - 94
22(chain B and resseq 1:16)BB1 - 161 - 16
33(chain C and resseq 13:106)CC13 - 1061 - 94
44(chain D and resseq 1:16)DD1 - 161 - 16

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