[English] 日本語
Yorodumi
- PDB-5wts: Green fluorescent protein linked MTide-02 inhibitor in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wts
TitleGreen fluorescent protein linked MTide-02 inhibitor in complex with mdm2
Components
  • E3 ubiquitin-protein ligase Mdm2
  • Green fluorescent protein linked MTide-02
KeywordsFLUORESCENT PROTEIN/INHIBITOR / FLUORESCENT PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


cellular response to vitamin B1 / response to formaldehyde / response to water-immersion restraint stress / traversing start control point of mitotic cell cycle / response to ether / 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 / traversing start control point of mitotic cell cycle / response to ether / 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 / peroxisome proliferator activated receptor binding / SUMO transferase activity / negative regulation of protein processing / response to iron ion / response to steroid hormone / NEDD8 ligase activity / cellular response to peptide hormone stimulus / AKT phosphorylates targets in the cytosol / atrioventricular valve morphogenesis / ventricular septum development / endocardial cushion morphogenesis / positive regulation of muscle cell differentiation / cellular response to alkaloid / SUMOylation of ubiquitinylation proteins / regulation of protein catabolic process / blood vessel development / cardiac septum morphogenesis / ligase activity / Constitutive Signaling by AKT1 E17K in Cancer / response to magnesium ion / negative regulation of DNA damage response, signal transduction by p53 class mediator / SUMOylation of transcription factors / protein sumoylation / protein localization to nucleus / cellular response to UV-C / blood vessel remodeling / cellular response to estrogen stimulus / protein autoubiquitination / cellular response to actinomycin D / ribonucleoprotein complex binding / positive regulation of vascular associated smooth muscle cell proliferation / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / transcription repressor complex / NPAS4 regulates expression of target genes / regulation of heart rate / positive regulation of mitotic cell cycle / positive regulation of protein export from nucleus / ubiquitin binding / proteolysis involved in protein catabolic process / response to cocaine / Stabilization of p53 / protein destabilization / Regulation of RUNX3 expression and activity / establishment of protein localization / RING-type E3 ubiquitin transferase / cellular response to growth factor stimulus / Oncogene Induced Senescence / Regulation of TP53 Activity through Methylation / cellular response to gamma radiation / response to toxic substance / cellular response to hydrogen peroxide / protein polyubiquitination / ubiquitin-protein transferase activity / disordered domain specific binding / endocytic vesicle membrane / ubiquitin protein ligase activity / p53 binding / Signaling by ALK fusions and activated point mutants / Regulation of TP53 Degradation / negative regulation of neuron projection development / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / 5S rRNA binding / cellular response to hypoxia / ubiquitin-dependent protein catabolic process / regulation of gene expression / protein-containing complex assembly / Oxidative Stress Induced Senescence / proteasome-mediated ubiquitin-dependent protein catabolic process / Regulation of TP53 Activity through Phosphorylation / amyloid fibril formation / regulation of cell cycle / Ub-specific processing proteases / protein ubiquitination / response to xenobiotic stimulus / protein domain specific binding / response to antibiotic / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / nucleolus / apoptotic process / negative regulation of transcription by RNA polymerase II / enzyme binding / protein-containing complex / zinc ion binding / nucleoplasm
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
PHOSPHATE ION / E3 ubiquitin-protein ligase Mdm2
Similarity search - Component
Biological speciesAequorea victoria (jellyfish)
Camelus dromedarius (Arabian camel)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.004 Å
AuthorsWongsantichon, J. / Robinson, R.C. / Ghadessy, F.J.
CitationJournal: To Be Published
Title: Green fluorescent protein linked peptide inhibitor PMI in complex with mdm2
Authors: Chee, S.M.Q. / Wongsantichon, J. / Sana, B. / Robinson, R.C. / Ghadessy, F.J.
History
DepositionDec 14, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Nov 6, 2019Group: Data collection / Structure summary / Category: entity / struct / struct_keywords
Item: _entity.pdbx_description / _struct.title / _struct_keywords.text
Revision 1.3Nov 18, 2020Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.4Nov 25, 2020Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_struct_mod_residue / struct_keywords / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_ec / _struct_keywords.pdbx_keywords ..._entity.pdbx_ec / _struct_keywords.pdbx_keywords / _struct_keywords.text / _struct_ref_seq_dif.align_id
Revision 1.5Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Green fluorescent protein linked MTide-02
B: E3 ubiquitin-protein ligase Mdm2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6426
Polymers54,1662
Non-polymers4764
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-26 kcal/mol
Surface area22280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.766, 98.422, 218.988
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

-
Antibody / Protein , 2 types, 2 molecules AB

#1: Antibody Green fluorescent protein linked MTide-02


Mass: 40416.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aequorea victoria (jellyfish), (gene. exp.) Camelus dromedarius (Arabian camel)
Gene: GFP / Production host: Escherichia coli (E. coli)
#2: Protein E3 ubiquitin-protein ligase Mdm2 / Double minute 2 protein / Hdm2 / Oncoprotein 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 (E. coli)
References: UniProt: Q00987, RING-type E3 ubiquitin transferase

-
Non-polymers , 4 types, 11 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. THIS IS AN ENGINEERED CONSTRUCT OF VSFGFP (PDB:4PFE) WITH 12-MER PMI INHIBITOR INSERTION, BASICALLY REPLACING RESIDUES 230-231 (AQ) WITH (TTSFAEYWALLS).

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.23 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.2M sodium chloride, 0.1M Bis-Tris, 25% PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→20.007 Å / Num. obs: 11255 / % possible obs: 97.3 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.088 / Rsym value: 0.065 / Net I/σ(I): 14.25
Reflection shellResolution: 3→3.05 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 2.21 / CC1/2: 0.887 / % possible all: 92.6

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.004→20.007 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2442 527 4.99 %
Rwork0.204 --
obs0.2061 10564 91.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.004→20.007 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3558 0 29 7 3594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023673
X-RAY DIFFRACTIONf_angle_d0.4734964
X-RAY DIFFRACTIONf_dihedral_angle_d15.3422176
X-RAY DIFFRACTIONf_chiral_restr0.041538
X-RAY DIFFRACTIONf_plane_restr0.002635
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0038-3.30490.28551100.25611943X-RAY DIFFRACTION73
3.3049-3.78030.26681300.23472661X-RAY DIFFRACTION98
3.7803-4.75220.21291370.18172709X-RAY DIFFRACTION98
4.7522-20.00770.24651500.19042724X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.20580.61220.64051.95170.01541.20870.1531-0.1570.10860.70670.0909-0.4875-0.2410.5694-0.21360.5738-0.1839-0.07050.48230.00420.5525.2039-18.257-28.7604
21.2751-0.68-0.39380.77450.74692.06380.0564-0.14020.45190.85730.0992-0.1181-0.4790.1966-0.10810.8296-0.19690.08180.3645-0.020.534917.6894-13.0967-27.6812
31.7078-0.1445-0.87741.2581-0.01520.61440.0497-0.11540.2210.7624-0.1106-0.0632-0.43450.4150.12950.6477-0.1108-0.01330.35550.01320.420616.0958-21.7996-29.6887
40.0716-0.2209-0.27011.03620.38181.5009-0.022-0.2809-0.02891.0384-0.23220.32110.0865-0.26780.10860.6453-0.08750.11760.5721-0.05130.36691.0905-40.6002-19.3061
51.7116-0.1168-0.29791.83640.01762.2502-0.24930.12840.07080.0401-0.06030.08190.0735-0.34330.24811.1728-0.04340.10310.5197-0.02540.30352.0096-33.1769-11.8575
60.0064-0.0070.004-0.0004-0.00280.0057-0.04140.2536-0.04010.2441-0.0425-0.17270.0114-0.00440.07470.82890.08130.01390.91530.13540.5442-12.3238-53.6658-19.8962
70.4220.01690.54130.03750.05350.7154-0.02940.1274-0.2654-0.09640.14340.02390.1216-0.0936-0.00840.0398-0.1328-0.14250.58240.27870.7503-17.0697-51.1207-45.1024
81.05940.0174-0.04490.64050.04881.5105-0.00020.03530.5002-0.17250.31330.1711-0.6095-0.06690.0611-0.26640.0617-0.00620.35070.07770.4895-5.1539-40.9042-47.258
92.66541.7993-1.39182.999-0.95310.85890.0919-0.53170.14590.2097-0.0117-0.0988-0.16860.0365-0.01950.29080.22840.07580.651-0.0190.6764-15.1032-38.882-37.8653
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 81 )
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 147 )
3X-RAY DIFFRACTION3chain 'A' and (resid 148 through 232 )
4X-RAY DIFFRACTION4chain 'A' and (resid 233 through 273 )
5X-RAY DIFFRACTION5chain 'A' and (resid 274 through 354 )
6X-RAY DIFFRACTION6chain 'B' and (resid 12 through 24 )
7X-RAY DIFFRACTION7chain 'B' and (resid 25 through 46 )
8X-RAY DIFFRACTION8chain 'B' and (resid 47 through 92 )
9X-RAY DIFFRACTION9chain 'B' and (resid 93 through 107 )

+
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