[English] 日本語
Yorodumi
- PDB-6q9w: X-ray structure of compound 15 bound to HdmX: Structural states o... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6q9w
TitleX-ray structure of compound 15 bound to HdmX: Structural states of Hdm2 and HdmX: X-ray elucidation of adaptations and binding interactions for different chemical compound classes
ComponentsProtein Mdm4
KeywordsAPOPTOSIS / HDMX / MDM4
Function / homology
Function and homology information


atrial septum development / heart valve development / atrioventricular valve morphogenesis / endocardial cushion morphogenesis / ventricular septum development / transcription repressor complex / DNA damage response, signal transduction by p53 class mediator / Stabilization of p53 / Oncogene Induced Senescence / negative regulation of protein catabolic process ...atrial septum development / heart valve development / atrioventricular valve morphogenesis / endocardial cushion morphogenesis / ventricular septum development / transcription repressor complex / DNA damage response, signal transduction by p53 class mediator / 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 / protein-containing complex assembly / Oxidative Stress Induced Senescence / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / regulation of cell cycle / Ub-specific processing proteases / protein stabilization / 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 ...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 superfamily / Zinc finger RanBP2-type signature. / 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
Chem-HRT / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE / Protein Mdm4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsKallen, J.
CitationJournal: Chemmedchem / Year: 2019
Title: Structural States of Hdm2 and HdmX: X-ray Elucidation of Adaptations and Binding Interactions for Different Chemical Compound Classes.
Authors: Kallen, J. / Izaac, A. / Chau, S. / Wirth, E. / Schoepfer, J. / Mah, R. / Schlapbach, A. / Stutz, S. / Vaupel, A. / Guagnano, V. / Masuya, K. / Stachyra, T.M. / Salem, B. / Chene, P. / ...Authors: Kallen, J. / Izaac, A. / Chau, S. / Wirth, E. / Schoepfer, J. / Mah, R. / Schlapbach, A. / Stutz, S. / Vaupel, A. / Guagnano, V. / Masuya, K. / Stachyra, T.M. / Salem, B. / Chene, P. / Gessier, F. / Holzer, P. / Furet, P.
History
DepositionDec 18, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 23, 2019Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.pdbx_CC_half / _reflns.pdbx_Rpim_I_all ..._reflns.pdbx_CC_half / _reflns.pdbx_Rpim_I_all / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_Rpim_I_all
Revision 1.3Jan 24, 2024Group: 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: Protein Mdm4
B: Protein Mdm4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,72810
Polymers22,3742
Non-polymers2,3548
Water3,045169
1
A: Protein Mdm4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3645
Polymers11,1871
Non-polymers1,1774
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein Mdm4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3645
Polymers11,1871
Non-polymers1,1774
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.152, 50.334, 92.377
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11A-395-

HOH

-
Components

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


Mass: 11186.985 Da / Num. of mol.: 2 / Fragment: N-terminal domain, p53 binding domain / Mutation: C17S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MDM4, MDMX / Plasmid: pET28-derived vector / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O15151
#2: Chemical ChemComp-HRT / (4~{S})-4-(4-chlorophenyl)-5-[(1~{S})-1-(3-chlorophenyl)ethyl]-2-(2,4-dimethoxypyrimidin-5-yl)-3-propan-2-yl-4~{H}-pyrrolo[3,4-d]imidazol-6-one


Mass: 552.452 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H27Cl2N5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-O4B / 1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE


Mass: 264.315 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H24O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.45 Å3/Da / Density % sol: 49.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2.25M AmSO4, 4% w/v 18-crown-ether, 0.1M HEPES

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99984 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 16, 2012
RadiationMonochromator: SI 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 1.55→19.38 Å / Num. obs: 32626 / % possible obs: 99.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.069 / Rrim(I) all: 0.062 / Net I/σ(I): 18.1
Reflection shellResolution: 1.55→1.59 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.5 / Rpim(I) all: 0.447 / Rrim(I) all: 0.567 / % possible all: 99.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Q9Q

6q9q


Resolution: 1.55→19.38 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.94 / SU B: 1.503 / SU ML: 0.056 / SU R Cruickshank DPI: 0.0897 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.088
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2404 1632 5 %RANDOM
Rwork0.216 ---
obs0.2172 30991 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 56.31 Å2 / Biso mean: 21.292 Å2 / Biso min: 9.66 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.1 Å20 Å2
3----0.13 Å2
Refinement stepCycle: final / Resolution: 1.55→19.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1359 0 149 169 1677
Biso mean--29.42 33.58 -
Num. residues----170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221545
X-RAY DIFFRACTIONr_angle_refined_deg1.1652.0872066
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5455170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg46.23424.83962
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.25115267
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.074156
X-RAY DIFFRACTIONr_chiral_restr0.0880.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211091
LS refinement shellResolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 119 -
Rwork0.297 2245 -
all-2364 -
obs--99.87 %

+
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