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- PDB-2kzt: Structure of the Tandem MA-3 Region of Pdcd4 -

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Basic information

Entry
Database: PDB / ID: 2kzt
TitleStructure of the Tandem MA-3 Region of Pdcd4
Components(Programmed cell death protein 4) x 2
KeywordsAPOPTOSIS / Pdcd4 / MA-3 / eIF4A / HEAT
Function / homology
Function and homology information


epithelial to mesenchymal transition involved in cardiac fibroblast development / negative regulation of myofibroblast differentiation / negative regulation of vascular associated smooth muscle cell differentiation / positive regulation of smooth muscle cell apoptotic process / negative regulation of JUN kinase activity / regulation of protein metabolic process / response to alkaloid / positive regulation of endothelial cell apoptotic process / positive regulation of vascular associated smooth muscle cell apoptotic process / negative regulation of vascular associated smooth muscle cell proliferation ...epithelial to mesenchymal transition involved in cardiac fibroblast development / negative regulation of myofibroblast differentiation / negative regulation of vascular associated smooth muscle cell differentiation / positive regulation of smooth muscle cell apoptotic process / negative regulation of JUN kinase activity / regulation of protein metabolic process / response to alkaloid / positive regulation of endothelial cell apoptotic process / positive regulation of vascular associated smooth muscle cell apoptotic process / negative regulation of vascular associated smooth muscle cell proliferation / negative regulation of cytokine production involved in inflammatory response / BMP signaling pathway / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / response to hormone / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to lipopolysaccharide / negative regulation of DNA-templated transcription / apoptotic process / negative regulation of apoptotic process / RNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Programmed cell death protein 4 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / Initiation factor eIF-4 gamma, MA3 / MA3 domain / MI domain profile. / Domain in DAP-5, eIF4G, MA-3 and other proteins. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Programmed cell death protein 4 / Programmed cell death protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodSOLUTION NMR / HADDOCK
Model detailslowest HADDOCK score, model 1
AuthorsWaters, L.C. / Strong, S.L. / Oka, O. / Muskett, F.W. / Veverka, V. / Banerjee, S. / Schmedt, T. / Henry, A.J. / Klempnauer, K.H. / Carr, M.D.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structure of the tandem MA-3 region of Pdcd4 protein and characterization of its interactions with eIF4A and eIF4G: molecular mechanisms of a tumor suppressor
Authors: Waters, L.C. / Strong, S.L. / Ferlemann, E. / Oka, O. / Muskett, F.W. / Veverka, V. / Banerjee, S. / Schmedt, T. / Henry, A.J. / Klempnauer, K.H. / Carr, M.D.
History
DepositionJun 24, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 23, 2011Group: Advisory / Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Programmed cell death protein 4
B: Programmed cell death protein 4


Theoretical massNumber of molelcules
Total (without water)32,7472
Polymers32,7472
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)73 / 200acceptable RMSD to lowest HADDOCK score structure
RepresentativeModel #1lowest haddock score

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Components

#1: Protein Programmed cell death protein 4 / / Pdcd4 / Nuclear antigen H731-like / Neoplastic transformation inhibitor protein / Protein 197/15a


Mass: 17653.211 Da / Num. of mol.: 1 / Fragment: MA-3 Region, residues 157-318
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q53EL6
#2: Protein Programmed cell death protein 4 / / Pdcd4 / Topoisomerase-inhibitor suppressed protein / Protein MA-3


Mass: 15093.329 Da / Num. of mol.: 1 / Fragment: MA-3 Region, residues 319-449
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q61823

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Structure of the tandem MA-3 region of Pdcd4, obtained by docking the structures of the individual domains (PDB 2RG8 and 2HM8) using HADDOCK
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D CBCA(CO)NH
1213D HNCO
1322D 1H-15N HSQC
1423D 1H-15N NOESY-HSQC
1513D TROSY HN(CO)CA
1613D HNCA
1713D IPAP TROSY HNCO
1833D IPAP TROSY HNCO

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Sample preparation

Details
Solution-IDContentsSolvent system
10.15-0.5mM [U-99% 13C; U-99% 15N] Pdcd4 MA-3 M-C; 25mM sodium phosphate; 100mM sodium chloride; 2.5mM DTT; 2.5mM TCEP; 0.05mM EDTA; 0.2mM AEBSF Protease Inhibitor; 0.02% sodium azide; 95% H2O/5% D2O95% H2O/5% D2O
20.5mM [U-99% 13C; U-99% 15N] Pdcd4 MA-3 M-C; 25mM sodium phosphate; 100mM sodium chloride; 2.5mM DTT; 2.5mM TCEP; 0.05mM EDTA; 0.2mM AEBSF Protease Inhibitor; 0.02% sodium azide; 95% H2O/5% D2O95% H2O/5% D2O
30.25mM [U-99% 13C; U-99% 15N] Pdcd4 MA-3 M-C; 25mM sodium phosphate; 100mM sodium chloride; 2.5mM DTT; 2.5mM TCEP; 0.05mM EDTA; 0.2mM AEBSF Protease Inhibitor; 0.02% sodium azide; 10mg/ml Pf1 phage; 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMPdcd4 MA-3 M-C-1[U-99% 13C; U-99% 15N]0.15-0.51
25 mMsodium phosphate-21
100 mMsodium chloride-31
2.5 mMDTT-41
2.5 mMTCEP-51
0.05 mMEDTA-61
0.2 mMAEBSF Protease Inhibitor-71
0.02 %sodium azide-81
0.5 mMPdcd4 MA-3 M-C-9[U-99% 13C; U-99% 15N]2
25 mMsodium phosphate-102
100 mMsodium chloride-112
2.5 mMDTT-122
2.5 mMTCEP-132
0.05 mMEDTA-142
0.2 mMAEBSF Protease Inhibitor-152
0.02 %sodium azide-162
0.25 mMPdcd4 MA-3 M-C-17[U-99% 13C; U-99% 15N]3
25 mMsodium phosphate-183
100 mMsodium chloride-193
2.5 mMDTT-203
2.5 mMTCEP-213
0.05 mMEDTA-223
0.2 mMAEBSF Protease Inhibitor-233
0.02 %sodium azide-243
10 mg/mLPf1 phage-253
Sample conditionsIonic strength: 150 / pH: 6.5 / Pressure: ambient / Temperature: 308 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker DRXBrukerDRX6002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
Sparky3.11Goddardchemical shift assignment
Sparky3.11Goddarddata analysis
HADDOCK2Cyril Dominguez, Rolf Boelens and Alexandre M.J.J. Bonvindocking
HADDOCK2Cyril Dominguez, Rolf Boelens and Alexandre M.J.J. Bonvinrefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: HADDOCK / Software ordinal: 1 / Details: REFINED AS PART OF THE HADDOCK DOCKING PROTOCOL
NMR representativeSelection criteria: lowest haddock score
NMR ensembleConformer selection criteria: acceptable RMSD to lowest HADDOCK score structure
Conformers calculated total number: 200 / Conformers submitted total number: 73 / Representative conformer: 1

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