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- PDB-2vje: Crystal Structure of the MDM2-MDMX RING Domain Heterodimer -

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Basic information

Entry
Database: PDB / ID: 2vje
TitleCrystal Structure of the MDM2-MDMX RING Domain Heterodimer
Components
  • E3 UBIQUITIN-PROTEIN LIGASE MDM2
  • MDM4 PROTEIN
KeywordsLIGASE / PROTO-ONCOGENE / PHOSPHORYLATION / ALTERNATIVE SPLICING / HOST-VIRUS INTERACTION / UBL CONJUGATION PATHWAY / ZINC-FINGER / POLYMORPHISM / METAL-BINDING / MDM / ZINC / RING / NUCLEUS / CYTOPLASM
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 / heart valve development / 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 / negative regulation of protein catabolic process / 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 / protein stabilization / Ub-specific processing proteases / protein ubiquitination / protein domain specific binding / response to xenobiotic stimulus / negative regulation of cell population proliferation / 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
Similarity search - Function
MDM4 / : / 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 ...MDM4 / : / 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/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / Protein Mdm4 / E3 ubiquitin-protein ligase Mdm2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsMace, P.D. / Linke, K. / Smith, C.A. / Day, C.L.
CitationJournal: Cell Death Differ. / Year: 2008
Title: Structure of the MDM2/MDMX RING domain heterodimer reveals dimerization is required for their ubiquitylation in trans.
Authors: Linke, K. / Mace, P.D. / Smith, C.A. / Vaux, D.L. / Silke, J. / Day, C.L.
History
DepositionDec 10, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 6, 2018Group: Data collection / Database references / Derived calculations
Category: citation / pdbx_struct_assembly ...citation / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E3 UBIQUITIN-PROTEIN LIGASE MDM2
B: MDM4 PROTEIN
C: E3 UBIQUITIN-PROTEIN LIGASE MDM2
D: MDM4 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,15114
Polymers28,3424
Non-polymers80810
Water1,982110
1
A: E3 UBIQUITIN-PROTEIN LIGASE MDM2
B: MDM4 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4336
Polymers14,1712
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-17 kcal/mol
Surface area6670 Å2
MethodPISA
2
C: E3 UBIQUITIN-PROTEIN LIGASE MDM2
D: MDM4 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7188
Polymers14,1712
Non-polymers5476
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-23 kcal/mol
Surface area6880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.562, 40.769, 77.514
Angle α, β, γ (deg.)90.00, 109.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein E3 UBIQUITIN-PROTEIN LIGASE MDM2 / P53-BINDING PROTEIN MDM2 / ONCOPROTEIN MDM2 / DOUBLE MINUTE 2 PROTEIN / HDM2 / MDM2


Mass: 7094.681 Da / Num. of mol.: 2 / Fragment: RESIDUES 383-446
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX6P3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q00987, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein MDM4 PROTEIN / P53-BINDING PROTEIN MDM4 / MDM2-LIKE P53-BINDING PROTEIN / MDMX PROTEIN / DOUBLE MINUTE 4 PROTEIN


Mass: 7076.521 Da / Num. of mol.: 2 / Fragment: RESIDUES 428-490
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX6P3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O15151

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Non-polymers , 4 types, 120 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.6 Å3/Da / Density % sol: 57.1 % / Description: NONE
Crystal growpH: 6.5
Details: 1.8 M NH4(SO4)2, 0.5 M NACL, 0.1 M NA CITRATE, PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.2826
DetectorDate: Dec 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2826 Å / Relative weight: 1
ReflectionResolution: 2.2→35.92 Å / Num. obs: 11282 / % possible obs: 98.2 % / Observed criterion σ(I): 3.2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.9
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.2 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.2→35.92 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.78 / SU ML: 0.146 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE BIOLOGICAL UNIT IS A DIMER. THERE ARE 2 BIOLOGICAL UNITS IN THE ASYMMETRIC UNIT (CHAINS A AND B AND CHAINS C AND D)
RfactorNum. reflection% reflectionSelection details
Rfree0.223 834 5.1 %RANDOM
Rwork0.196 ---
obs0.198 15385 97.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 47.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å20 Å22.56 Å2
2--1.15 Å20 Å2
3----0.73 Å2
Refinement stepCycle: LAST / Resolution: 2.2→35.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1877 0 26 110 2013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221937
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.42722604
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6095241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.0872265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.12415378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6091516
X-RAY DIFFRACTIONr_chiral_restr0.1030.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021396
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.2852
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21314
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2112
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.228
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0950.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8031.51276
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.23421994
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.9033732
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2474.5610
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.276 61
Rwork0.237 1108

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