[English] 日本語
Yorodumi
- PDB-3dab: Structure of the human Mdmx protein bound to the p53 tumor suppre... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3dab
TitleStructure of the human Mdmx protein bound to the p53 tumor suppressor transactivation domain
Components
  • Cellular tumor antigen p53
  • Mdm4 protein
KeywordsCELL CYCLE / MDMX / MDM4 / HDMX / HDM4 / MDM-4 / MDM-X / MDM2 / HDM2 / P53 / tumor / nucleus / oncogene / apoptosis / disease mutation / DNA-binding / transcription
Function / homology
Function and homology information


atrial septum development / heart valve development / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Activation of NOXA and translocation to mitochondria ...atrial septum development / heart valve development / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / signal transduction by p53 class mediator / negative regulation of G1 to G0 transition / negative regulation of glucose catabolic process to lactate via pyruvate / Transcriptional activation of cell cycle inhibitor p21 / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Activation of NOXA and translocation to mitochondria / negative regulation of pentose-phosphate shunt / ATP-dependent DNA/DNA annealing activity / negative regulation of helicase activity / regulation of cell cycle G2/M phase transition / intrinsic apoptotic signaling pathway in response to hypoxia / regulation of fibroblast apoptotic process / oxidative stress-induced premature senescence / oligodendrocyte apoptotic process / negative regulation of miRNA processing / positive regulation of thymocyte apoptotic process / regulation of tissue remodeling / glucose catabolic process to lactate via pyruvate / positive regulation of mitochondrial membrane permeability / negative regulation of mitophagy / positive regulation of programmed necrotic cell death / mRNA transcription / circadian behavior / bone marrow development / histone deacetylase regulator activity / germ cell nucleus / regulation of mitochondrial membrane permeability involved in apoptotic process / RUNX3 regulates CDKN1A transcription / regulation of DNA damage response, signal transduction by p53 class mediator / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / atrioventricular valve morphogenesis / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / ventricular septum development / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / endocardial cushion morphogenesis / negative regulation of glial cell proliferation / negative regulation of neuroblast proliferation / Regulation of TP53 Activity through Association with Co-factors / mitochondrial DNA repair / T cell lineage commitment / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / ER overload response / negative regulation of DNA replication / B cell lineage commitment / thymocyte apoptotic process / positive regulation of cardiac muscle cell apoptotic process / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / TP53 Regulates Transcription of Caspase Activators and Caspases / cardiac septum morphogenesis / entrainment of circadian clock by photoperiod / PI5P Regulates TP53 Acetylation / Association of TriC/CCT with target proteins during biosynthesis / positive regulation of release of cytochrome c from mitochondria / necroptotic process / Zygotic genome activation (ZGA) / positive regulation of execution phase of apoptosis / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / TFIID-class transcription factor complex binding / rRNA transcription / negative regulation of telomere maintenance via telomerase / SUMOylation of transcription factors / intrinsic apoptotic signaling pathway by p53 class mediator / general transcription initiation factor binding / Transcriptional Regulation by VENTX / DNA damage response, signal transduction by p53 class mediator / replicative senescence / response to X-ray / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / mitophagy / cellular response to UV-C / positive regulation of RNA polymerase II transcription preinitiation complex assembly / hematopoietic stem cell differentiation / neuroblast proliferation / negative regulation of reactive oxygen species metabolic process / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / chromosome organization / T cell proliferation involved in immune response / Pyroptosis / embryonic organ development / glial cell proliferation / viral process / cis-regulatory region sequence-specific DNA binding / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / hematopoietic progenitor cell differentiation / type II interferon-mediated signaling pathway / somitogenesis / cellular response to actinomycin D / core promoter sequence-specific DNA binding / cellular response to glucose starvation / negative regulation of stem cell proliferation / positive regulation of intrinsic apoptotic signaling pathway / negative regulation of fibroblast proliferation / gastrulation / MDM2/MDM4 family protein binding / response to salt stress
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 / Cellular tumor antigen p53, transactivation domain 2 ...MDM4 / : / MDM2 / SWIB/MDM2 domain / p53 negative regulator Mdm2/Mdm4 / SWIB/MDM2 domain / SWIB/MDM2 domain / SWIB/MDM2 domain profile. / SWIB/MDM2 domain superfamily / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / Zn-finger in Ran binding protein and others / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / 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 / p53-like transcription factor, DNA-binding / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein Mdm4 / Cellular tumor antigen p53
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPopowicz, G.M. / Czarna, A. / Holak, T.A.
CitationJournal: Cell Cycle / Year: 2008
Title: Structure of the human Mdmx protein bound to the p53 tumor suppressor transactivation domain.
Authors: Popowicz, G.M. / Czarna, A. / Holak, T.A.
History
DepositionMay 29, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 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.title / _struct_ref_seq_dif.details
Revision 1.4Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mdm4 protein
B: Cellular tumor antigen p53
C: Mdm4 protein
D: Cellular tumor antigen p53
E: Mdm4 protein
F: Cellular tumor antigen p53
G: Mdm4 protein
H: Cellular tumor antigen p53


Theoretical massNumber of molelcules
Total (without water)48,3288
Polymers48,3288
Non-polymers00
Water7,728429
1
A: Mdm4 protein
B: Cellular tumor antigen p53


Theoretical massNumber of molelcules
Total (without water)12,0822
Polymers12,0822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-11.2 kcal/mol
Surface area5850 Å2
MethodPISA
2
C: Mdm4 protein
D: Cellular tumor antigen p53


Theoretical massNumber of molelcules
Total (without water)12,0822
Polymers12,0822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-9.5 kcal/mol
Surface area5770 Å2
MethodPISA
3
E: Mdm4 protein
F: Cellular tumor antigen p53


Theoretical massNumber of molelcules
Total (without water)12,0822
Polymers12,0822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-6.9 kcal/mol
Surface area5770 Å2
MethodPISA
4
G: Mdm4 protein
H: Cellular tumor antigen p53


Theoretical massNumber of molelcules
Total (without water)12,0822
Polymers12,0822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-12.4 kcal/mol
Surface area5860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.730, 58.870, 96.110
Angle α, β, γ (deg.)90.00, 92.00, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

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


Mass: 10274.058 Da / Num. of mol.: 4 / Fragment: 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): BL-21 RIL / References: UniProt: O15151
#2: Protein/peptide
Cellular tumor antigen p53 / Tumor suppressor p53 / Phosphoprotein p53 / Antigen NY-CO-13


Mass: 1807.973 Da / Num. of mol.: 4 / Fragment: UNP residues 15-29 / Source method: obtained synthetically / Details: Synthetic human p53 peptide / References: UniProt: P04637
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.76 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG3350, 0.1M MES, pH6.5, VAPOR DIFFUSION, SITTING DROP, temperature 300K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 8, 2008 / Details: mirrors
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 32474 / Num. obs: 31292 / % possible obs: 96 % / Observed criterion σ(F): 2 / Rmerge(I) obs: 0.055
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 7 / % possible all: 86

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YCR

1ycr


Resolution: 1.9→19.78 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.912 / SU B: 3.93 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.18 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2571 1626 5.1 %RANDOM
Rwork0.19657 ---
obs0.19978 30432 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.327 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å2-0.49 Å2
2--0.04 Å20 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3151 0 0 429 3580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223215
X-RAY DIFFRACTIONr_bond_other_d0.0010.022168
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.9864343
X-RAY DIFFRACTIONr_angle_other_deg1.08935332
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.3655386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.98825144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.74515585
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2421512
X-RAY DIFFRACTIONr_chiral_restr0.1270.2486
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023474
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02598
X-RAY DIFFRACTIONr_nbd_refined0.2070.2702
X-RAY DIFFRACTIONr_nbd_other0.1840.22169
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21501
X-RAY DIFFRACTIONr_nbtor_other0.0850.21582
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2255
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3510.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2690.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.233
X-RAY DIFFRACTIONr_mcbond_it0.851.52036
X-RAY DIFFRACTIONr_mcbond_other0.1611.5788
X-RAY DIFFRACTIONr_mcangle_it1.26123143
X-RAY DIFFRACTIONr_scbond_it1.86131362
X-RAY DIFFRACTIONr_scangle_it2.7224.51200
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 82 -
Rwork0.224 2029 -
obs--89.03 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more