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- PDB-7aye: Crystal structure of the computationally designed chemically disr... -

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Basic information

Entry
Database: PDB / ID: 7aye
TitleCrystal structure of the computationally designed chemically disruptable heterodimer LD6-MDM2
Components
  • Isoform 11 of E3 ubiquitin-protein ligase Mdm2
  • Thiol:disulfide interchange protein DsbD
KeywordsPROTEIN BINDING / chemically disruptable heterodimer (CDH) / protein-protein interaction / gene and cell therapy / protein switches
Function / homology
Function and homology information


protein-disulfide reductase / protein-disulfide reductase [NAD(P)H] activity / cellular response to vitamin B1 / response to formaldehyde / cytochrome complex assembly / response to water-immersion restraint stress / response to ether / traversing start control point of mitotic cell cycle / atrial septum development / regulation of protein catabolic process at postsynapse, modulating synaptic transmission ...protein-disulfide reductase / protein-disulfide reductase [NAD(P)H] activity / cellular response to vitamin B1 / response to formaldehyde / cytochrome complex assembly / response to water-immersion restraint stress / response to ether / traversing start control point of mitotic cell cycle / atrial septum development / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / fibroblast activation / Trafficking of AMPA receptors / receptor serine/threonine kinase binding / peroxisome proliferator activated receptor binding / negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator / positive regulation of vascular associated smooth muscle cell migration / negative regulation of protein processing / SUMO transferase activity / response to steroid hormone / AKT phosphorylates targets in the cytosol / response to iron ion / NEDD8 ligase activity / atrioventricular valve morphogenesis / cellular response to peptide hormone stimulus / endocardial cushion morphogenesis / ventricular septum development / positive regulation of muscle cell differentiation / cardiac septum morphogenesis / regulation of postsynaptic neurotransmitter receptor internalization / blood vessel development / SUMOylation of ubiquitinylation proteins / ligase activity / cellular response to alkaloid / Constitutive Signaling by AKT1 E17K in Cancer / regulation of protein catabolic process / negative regulation of signal transduction by p53 class mediator / negative regulation of DNA damage response, signal transduction by p53 class mediator / SUMOylation of transcription factors / response to magnesium ion / cellular response to UV-C / protein sumoylation / cellular response to actinomycin D / cellular response to estrogen stimulus / blood vessel remodeling / 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 / proteolysis involved in protein catabolic process / positive regulation of protein export from nucleus / ubiquitin binding / response to cocaine / DNA damage response, signal transduction by p53 class mediator / Stabilization of p53 / establishment of protein localization / Regulation of RUNX3 expression and activity / cellular response to gamma radiation / Oncogene Induced Senescence / RING-type E3 ubiquitin transferase / protein destabilization / Regulation of TP53 Activity through Methylation / cellular response to growth factor stimulus / response to toxic substance / centriolar satellite / cellular response to hydrogen peroxide / protein polyubiquitination / ubiquitin-protein transferase activity / disordered domain specific binding / p53 binding / ubiquitin protein ligase activity / endocytic vesicle membrane / 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 / electron transfer activity / regulation of cell cycle / Ub-specific processing proteases / postsynaptic density / protein ubiquitination / response to xenobiotic stimulus / protein domain specific binding / response to antibiotic / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / apoptotic process / ubiquitin protein ligase binding / positive regulation of gene expression
Similarity search - Function
Thiol:disulphide interchange protein DsbD / Thiol:disulfide interchange protein DsbD, N-terminal domain superfamily / DsbD gamma / Thiol:disulfide interchange protein DsbD, N-terminal domain / Thiol:disulfide interchange protein DsbD, N-terminal / Cytochrome C biogenesis protein, transmembrane domain / Cytochrome C biogenesis protein transmembrane domain / Thioredoxin-like domain / E3 ubiquitin-protein ligase Mdm2 / MDM2, modified RING finger, HC subclass ...Thiol:disulphide interchange protein DsbD / Thiol:disulfide interchange protein DsbD, N-terminal domain superfamily / DsbD gamma / Thiol:disulfide interchange protein DsbD, N-terminal domain / Thiol:disulfide interchange protein DsbD, N-terminal / Cytochrome C biogenesis protein, transmembrane domain / Cytochrome C biogenesis protein transmembrane domain / Thioredoxin-like domain / E3 ubiquitin-protein ligase Mdm2 / MDM2, modified RING finger, HC subclass / MDM2 / SWIB/MDM2 domain / Thioredoxin-like fold / 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 / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Zinc finger RING-type profile. / Zinc finger, RING-type / Thioredoxin-like superfamily / Zinc finger, RING/FYVE/PHD-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
E3 ubiquitin-protein ligase Mdm2 / Thiol:disulfide interchange protein DsbD
Similarity search - Component
Biological speciesHomo sapiens (human)
Shigella dysenteriae Sd197 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsYang, C. / Lau, K. / Pojer, F. / Correia, B.E.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Commission716058European Union
CitationJournal: Nat Commun / Year: 2021
Title: A rational blueprint for the design of chemically-controlled protein switches.
Authors: Shui, S. / Gainza, P. / Scheller, L. / Yang, C. / Kurumida, Y. / Rosset, S. / Georgeon, S. / Di Roberto, R.B. / Castellanos-Rueda, R. / Reddy, S.T. / Correia, B.E.
History
DepositionNov 12, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
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.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 11 of E3 ubiquitin-protein ligase Mdm2
B: Thiol:disulfide interchange protein DsbD


Theoretical massNumber of molelcules
Total (without water)28,7232
Polymers28,7232
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-10 kcal/mol
Surface area10700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.238, 73.238, 92.262
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein Isoform 11 of 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: 13185.105 Da / Num. of mol.: 1
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 Thiol:disulfide interchange protein DsbD / Protein-disulfide reductase / Disulfide reductase


Mass: 15537.526 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella dysenteriae Sd197 (bacteria) / Gene: dsbD, SDY_4441 / Production host: Escherichia coli (E. coli) / References: UniProt: Q328D2, protein-disulfide reductase
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

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1.5 M Ammonium sulfate, 0.1 M Sodium cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.95→45.2 Å / Num. obs: 5646 / % possible obs: 99.8 % / Redundancy: 6.9 % / CC1/2: 0.99 / Net I/σ(I): 22.18
Reflection shellResolution: 2.95→3.13 Å / Mean I/σ(I) obs: 2.19 / Num. unique obs: 872 / CC1/2: 0.67 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AFG

5afg


Resolution: 2.95→45.2 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.931 / SU B: 21.452 / SU ML: 0.383 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.434 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2599 285 5 %RANDOM
Rwork0.1971 ---
obs0.2006 5361 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 174.21 Å2 / Biso mean: 86.097 Å2 / Biso min: 52.11 Å2
Baniso -1Baniso -2Baniso -3
1-1.95 Å20 Å20 Å2
2--1.95 Å20 Å2
3----3.9 Å2
Refinement stepCycle: final / Resolution: 2.95→45.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1656 0 0 0 1656
Num. residues----205
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131693
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171638
X-RAY DIFFRACTIONr_angle_refined_deg1.611.6422294
X-RAY DIFFRACTIONr_angle_other_deg1.2161.5823763
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8585203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.78123.29485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.78315300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.692157
X-RAY DIFFRACTIONr_chiral_restr0.0620.2216
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021884
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02390
LS refinement shellResolution: 2.954→3.031 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 18 -
Rwork0.327 382 -
all-400 -
obs--99.5 %

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