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- PDB-3fdo: Structure of human MDMX in complex with high affinity peptide -

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Basic information

Entry
Database: PDB / ID: 3fdo
TitleStructure of human MDMX in complex with high affinity peptide
Components
  • Protein Mdm4
  • Synthetic high affinity peptide
KeywordsCELL CYCLE / MDMX / MDM4 / MDM-X / MDM-4 / p53 / MDM2
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 / regulation of cell cycle / protein ubiquitination / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsCzarna, A.L. / Popowicz, G.M. / Holak, T.A.
CitationJournal: Cell Cycle / Year: 2009
Title: High affinity interaction of the p53 peptide-analogue with human Mdm2 and Mdmx.
Authors: Czarna, A. / Popowicz, G.M. / Pecak, A. / Wolf, S. / Dubin, G. / Holak, T.A.
History
DepositionNov 26, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Nov 6, 2019Group: Data collection / Database references / Category: citation / struct_ref_seq_dif
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI ..._citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_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_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: Protein Mdm4
B: Synthetic high affinity peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8927
Polymers11,7712
Non-polymers1225
Water2,972165
1
A: Protein Mdm4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,3474
Polymers10,2741
Non-polymers733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Synthetic high affinity peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,5453
Polymers1,4971
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA, PQS
3
A: Protein Mdm4
B: Synthetic high affinity peptide
hetero molecules

A: Protein Mdm4
B: Synthetic high affinity peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,78414
Polymers23,5414
Non-polymers24310
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5160 Å2
ΔGint-115 kcal/mol
Surface area10080 Å2
MethodPISA
4
A: Protein Mdm4
hetero molecules

A: Protein Mdm4
hetero molecules

B: Synthetic high affinity peptide
hetero molecules

B: Synthetic high affinity peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,78414
Polymers23,5414
Non-polymers24310
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
crystal symmetry operation3_545x+1/2,y-1/2,z1
crystal symmetry operation4_445-x-1/2,y-1/2,-z1
Buried area3550 Å2
ΔGint-88 kcal/mol
Surface area11690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.230, 30.950, 50.420
Angle α, β, γ (deg.)90.00, 124.41, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 10274.058 Da / Num. of mol.: 1 / Fragment: p53 binding domain, UNP residues 23-111
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MDM4, MDMX / Plasmid: pET-46 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O15151
#2: Protein/peptide Synthetic high affinity peptide


Mass: 1496.641 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic peptide designed to bind MDMX
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 1.89 Å3/Da / Density % sol: 35.02 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 4.3M NaCl, 100mM Hepes, pH7.3, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 15, 2008 / Details: monochromator
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. all: 17646 / Num. obs: 14843 / % possible obs: 84.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.4→1.5 Å / % possible all: 46.2

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0066refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DAB

3dab


Resolution: 1.4→15 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.915 / SU B: 2.973 / SU ML: 0.054 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.118 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24708 768 5.2 %RANDOM
Rwork0.17936 ---
all0.1881 17646 --
obs0.18286 13765 84.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.143 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å20 Å2-0.29 Å2
2--1.37 Å20 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms818 0 5 165 988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022835
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.9731129
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.0285100
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.04924.59537
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.86915150
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.448153
X-RAY DIFFRACTIONr_chiral_restr0.110.2127
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021618
X-RAY DIFFRACTIONr_mcbond_it0.9161.5506
X-RAY DIFFRACTIONr_mcangle_it1.5522813
X-RAY DIFFRACTIONr_scbond_it2.2923329
X-RAY DIFFRACTIONr_scangle_it3.4934.5316
X-RAY DIFFRACTIONr_rigid_bond_restr1.313835
X-RAY DIFFRACTIONr_sphericity_free3.273170
X-RAY DIFFRACTIONr_sphericity_bonded2.8233818
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 23 -
Rwork0.188 469 -
obs--39.2 %

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