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- PDB-3eqs: Crystal structure of human MDM2 in complex with a 12-mer peptide ... -

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Basic information

Entry
Database: PDB / ID: 3eqs
TitleCrystal structure of human MDM2 in complex with a 12-mer peptide inhibitor
Components
  • 12-mer peptide inhibitor
  • E3 ubiquitin-protein ligase Mdm2
KeywordsLIGASE / MDM2 / MDM2-peptide inhibitor complex / oncoprotein / Host-virus interaction / Metal-binding / Nucleus / Phosphoprotein / Proto-oncogene / Ubl conjugation pathway / Zinc-finger
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 / negative regulation of signal transduction by p53 class mediator / fibroblast activation / atrial septum development / receptor serine/threonine kinase binding ...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 / negative regulation of signal transduction by p53 class mediator / fibroblast activation / atrial septum development / receptor serine/threonine kinase binding / Trafficking of AMPA receptors / positive regulation of vascular associated smooth muscle cell migration / peroxisome proliferator activated receptor binding / SUMO transferase activity / negative regulation of protein processing / response to iron ion / response to steroid hormone / NEDD8 ligase activity / AKT phosphorylates targets in the cytosol / atrioventricular valve morphogenesis / cellular response to peptide hormone stimulus / ventricular septum development / endocardial cushion morphogenesis / positive regulation of muscle cell differentiation / SUMOylation of ubiquitinylation proteins / cellular response to alkaloid / blood vessel development / regulation of protein catabolic process / cardiac septum morphogenesis / Constitutive Signaling by AKT1 E17K in Cancer / ligase activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / response to magnesium ion / SUMOylation of transcription factors / protein sumoylation / protein localization to nucleus / cellular response to UV-C / blood vessel remodeling / cellular response to estrogen stimulus / protein autoubiquitination / cellular response to actinomycin D / ribonucleoprotein complex binding / positive regulation of vascular associated smooth muscle cell proliferation / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / NPAS4 regulates expression of target genes / transcription repressor complex / regulation of heart rate / positive regulation of mitotic cell cycle / positive regulation of protein export from nucleus / response to cocaine / proteolysis involved in protein catabolic process / ubiquitin binding / Stabilization of p53 / Regulation of RUNX3 expression and activity / protein destabilization / RING-type E3 ubiquitin transferase / establishment of protein localization / Oncogene Induced Senescence / Regulation of TP53 Activity through Methylation / response to toxic substance / cellular response to gamma radiation / cellular response to growth factor stimulus / cellular response to hydrogen peroxide / protein polyubiquitination / ubiquitin-protein transferase activity / endocytic vesicle membrane / ubiquitin protein ligase activity / disordered domain specific binding / Signaling by ALK fusions and activated point mutants / Regulation of TP53 Degradation / p53 binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of neuron projection development / cellular response to hypoxia / 5S rRNA binding / ubiquitin-dependent protein catabolic process / regulation of gene expression / protein-containing complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / amyloid fibril formation / Ub-specific processing proteases / regulation of cell cycle / protein ubiquitination / response to xenobiotic stimulus / protein domain specific binding / response to antibiotic / negative regulation of DNA-templated transcription / apoptotic process / ubiquitin protein ligase binding / positive regulation of cell population proliferation / positive regulation of gene expression / nucleolus / negative regulation of apoptotic process / enzyme binding / negative regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm
Similarity search - Function
MDM2 / SWIB/MDM2 domain / 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 ...MDM2 / SWIB/MDM2 domain / 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 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 / E3 ubiquitin-protein ligase Mdm2
Similarity search - Component
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 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 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase Mdm2
B: 12-mer peptide inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5323
Polymers11,4722
Non-polymers591
Water2,108117
1
A: E3 ubiquitin-protein ligase Mdm2
B: 12-mer peptide inhibitor
hetero molecules

A: E3 ubiquitin-protein ligase Mdm2
B: 12-mer peptide inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0636
Polymers22,9454
Non-polymers1182
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4320 Å2
ΔGint-30 kcal/mol
Surface area9920 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-11 kcal/mol
Surface area5880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.517, 43.274, 35.036
Angle α, β, γ (deg.)90.00, 116.51, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
12B
22B

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / Refine code: 6

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALAA26 - 1082 - 84
21VALVALAA26 - 1082 - 84
12SERSERBB1 - 111 - 11
22SERSERBB1 - 111 - 11

NCS ensembles :
ID
1
2

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Components

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


Mass: 10044.889 Da / Num. of mol.: 1 / Fragment: UNP residues 25-109 / Source method: obtained synthetically / Details: this sequence occurs naturally in Homo sapiens
References: UniProt: Q00987, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide 12-mer peptide inhibitor


Mass: 1427.557 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: peptide identified by screening a duodecimal peptide library displayed on M13 phage
#3: Chemical ChemComp-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH5N3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.11 Å3/Da / Density % sol: 41.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2 M Ammonium acetate, 0.1M Sodium citrate, 30% PEG 4000, pH 5.6, 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: Jun 14, 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→35.85 Å / Num. all: 12051 / Num. obs: 11993 / % possible obs: 99.5 % / Redundancy: 7 % / Rmerge(I) obs: 0.058 / Rsym value: 0.064 / Net I/σ(I): 46.9
Reflection shellResolution: 1.63→1.69 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 13.6 / Rsym value: 0.238 / % possible all: 95.1

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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 1YCR

1ycr


Resolution: 1.65→15 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.515 / SU ML: 0.055 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19276 553 4.8 %RANDOM
Rwork0.15435 ---
obs0.1561 11009 99.6 %-
all-12004 --
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: 17.703 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å20 Å2-0.04 Å2
2--0.02 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.65→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms791 0 4 117 912
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022916
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5242.0071256
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6895120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.67323.33339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33815190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.415155
X-RAY DIFFRACTIONr_chiral_restr0.0980.2144
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021675
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_it0.8791.5524
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5172864
X-RAY DIFFRACTIONr_scbond_it2.3313392
X-RAY DIFFRACTIONr_scangle_it3.6574.5378
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 / Rms dev position: 0 Å

Ens-IDDom-IDAuth asym-IDNumberTypeWeight position
11A778loose positional5
22B94loose positional5
11A778loose thermal10
22B94loose thermal10
LS refinement shellResolution: 1.65→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 35 -
Rwork0.182 775 -
obs--98.54 %
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)
10.8687-0.1521-0.08190.91040.51141.23550.00670.0665-0.0049-0.03480.0178-0.01660.0793-0.0534-0.02450.0283-0.0095-0.00230.02790.0070.0207-10.32520.0637-5.0347
23.89482.23261.39724.91980.04984.50290.0186-0.2491-0.22510.17850.026-0.2190.1801-0.1571-0.04460.00940.0030.01160.02740.01080.0228-7.09521.85627.504
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 108
2X-RAY DIFFRACTION2B1 - 12

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