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- PDB-6aaw: Mdm2 in complex with a D amino Acid Containing Stapled Peptide -

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Basic information

Entry
Database: PDB / ID: 6aaw
TitleMdm2 in complex with a D amino Acid Containing Stapled Peptide
Components
  • ACE-LEU-THR-PHE-STQ-GLU-TYR-DTR-GLN-LEU-CBA-MK8-SER-ALA-ALA
  • E3 ubiquitin-protein ligase Mdm2
KeywordsLIGASE / E3 ligase
Function / homology
Function and homology information


cellular response to vitamin B1 / response to formaldehyde / response to water-immersion restraint stress / response to ether / traversing start control point of mitotic cell cycle / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / 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 / response to ether / traversing start control point of mitotic cell cycle / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / 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 / response to iron ion / peroxisome proliferator activated receptor binding / negative regulation of protein processing / response to steroid hormone / NEDD8 ligase activity / SUMO transferase activity / AKT phosphorylates targets in the cytosol / cellular response to peptide hormone stimulus / atrioventricular valve morphogenesis / 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 / negative regulation of DNA damage response, signal transduction by p53 class mediator / response to magnesium ion / ligase activity / protein sumoylation / SUMOylation of transcription factors / protein localization to nucleus / cellular response to actinomycin D / cellular response to UV-C / blood vessel remodeling / protein autoubiquitination / cellular response to estrogen stimulus / ribonucleoprotein complex binding / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / positive regulation of vascular associated smooth muscle cell proliferation / NPAS4 regulates expression of target genes / transcription repressor complex / regulation of heart rate / positive regulation of mitotic cell cycle / proteolysis involved in protein catabolic process / positive regulation of protein export from nucleus / response to cocaine / ubiquitin binding / Stabilization of p53 / Regulation of RUNX3 expression and activity / protein destabilization / cellular response to gamma radiation / 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 hydrogen peroxide / cellular response to growth factor stimulus / protein polyubiquitination / ubiquitin-protein transferase activity / endocytic vesicle membrane / ubiquitin protein ligase activity / disordered domain specific binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Regulation of TP53 Degradation / p53 binding / negative regulation of neuron projection development / 5S rRNA binding / ubiquitin-dependent protein catabolic process / cellular response to hypoxia / proteasome-mediated ubiquitin-dependent protein catabolic process / regulation of gene expression / protein-containing complex assembly / Oxidative Stress Induced Senescence / Regulation of TP53 Activity through Phosphorylation / amyloid fibril formation / protein ubiquitination / regulation of cell cycle / Ub-specific processing proteases / 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 / negative regulation of transcription by RNA polymerase II / enzyme binding / protein-containing complex / zinc ion binding / nucleoplasm / identical protein binding
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
E3 ubiquitin-protein ligase Mdm2
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage M13 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBrown, C.J. / Partridge, A.W.
CitationJournal: To Be Published
Title: A Model System to Explore Macrocyclic Peptide Structural and Chirality Relationships: Tolerance of helix-breaking residues within the context of a stapled peptide.
Authors: Partridge, A.W. / Hung, Y.K.K. / Juang, Y. / Sadruddin, A. / Lim, S. / Brown, C.J. / Ng, S. / Thean, D. / Ferrer, F. / Johannes, C. / Yuen, T.Y. / Kannan, S. / Aronica, P. / Tan, Y.S. / ...Authors: Partridge, A.W. / Hung, Y.K.K. / Juang, Y. / Sadruddin, A. / Lim, S. / Brown, C.J. / Ng, S. / Thean, D. / Ferrer, F. / Johannes, C. / Yuen, T.Y. / Kannan, S. / Aronica, P. / Tan, Y.S. / Mohan, P.R. / Verma, C.S. / Hichman, J. / Chen, S. / Wan, H. / Lane, D.P. / Sawyer, T.K.
History
DepositionJul 19, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 2.0Apr 5, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_src_syn / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_torsion / struct_conn / struct_ref_seq
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.details / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _pdbx_entity_src_syn.pdbx_end_seq_num / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 3.1Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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: ACE-LEU-THR-PHE-STQ-GLU-TYR-DTR-GLN-LEU-CBA-MK8-SER-ALA-ALA


Theoretical massNumber of molelcules
Total (without water)15,5242
Polymers15,5242
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-11 kcal/mol
Surface area5930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.946, 43.378, 34.542
Angle α, β, γ (deg.)90.00, 94.82, 90.00
Int Tables number5
Space group name H-MC121

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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: 13749.694 Da / Num. of mol.: 1 / Fragment: UNP residues 6-125
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MDM2 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q00987, RING-type E3 ubiquitin transferase
#2: Protein/peptide ACE-LEU-THR-PHE-STQ-GLU-TYR-DTR-GLN-LEU-CBA-MK8-SER-ALA-ALA


Mass: 1774.130 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Chemically synthesized Helically Stabilized Peptide Designed to disrupt the Mdm2/p53 protein:protein interaction. Template sequence before incorporation of non natural amino acids was ...Details: Chemically synthesized Helically Stabilized Peptide Designed to disrupt the Mdm2/p53 protein:protein interaction. Template sequence before incorporation of non natural amino acids was derived from M13 phage display.
Source: (synth.) Enterobacteria phage M13 (virus)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 1.93 Å3/Da / Density % sol: 36.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20 % w/v Polyethylene glycol 8,000, 100 mM HEPES pH 7.5, 200 mM Ammonium sulfate, 10 % v/v 2-Propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95372 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 2→40.33 Å / Num. obs: 8132 / % possible obs: 99.3 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.246 / Rpim(I) all: 0.105 / Rrim(I) all: 0.267 / Net I/σ(I): 5.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 5.8 % / Rmerge(I) obs: 1.211 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 1118 / Rpim(I) all: 0.528 / Rrim(I) all: 1.324 / % possible all: 95.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XDSdata scaling
PARROTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4umn

4umn


Resolution: 2→40.33 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.524 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.172 / ESU R Free: 0.154 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22336 422 5.2 %RANDOM
Rwork0.18412 ---
obs0.18637 7710 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.041 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å2-1.4 Å2
2--0.08 Å2-0 Å2
3---0.7 Å2
Refinement stepCycle: 1 / Resolution: 2→40.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms839 0 0 34 873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02864
X-RAY DIFFRACTIONr_bond_other_d0.0020.02852
X-RAY DIFFRACTIONr_angle_refined_deg2.2022.0621170
X-RAY DIFFRACTIONr_angle_other_deg1.08731973
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.947595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.02323.52934
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54115157
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.467154
X-RAY DIFFRACTIONr_chiral_restr0.3470.2133
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02902
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02172
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_it1.7532.436395
X-RAY DIFFRACTIONr_mcbond_other1.7472.427393
X-RAY DIFFRACTIONr_mcangle_it2.7943.627491
X-RAY DIFFRACTIONr_mcangle_other2.7933.626491
X-RAY DIFFRACTIONr_scbond_it2.1262.68469
X-RAY DIFFRACTIONr_scbond_other2.1242.683470
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6083.922676
X-RAY DIFFRACTIONr_long_range_B_refined5.76827.625961
X-RAY DIFFRACTIONr_long_range_B_other5.70127.582960
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 24 -
Rwork0.209 536 -
obs--90.47 %

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