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- PDB-2rg8: Crystal Structure of Programmed for Cell Death 4 Middle MA3 domain -

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Basic information

Entry
Database: PDB / ID: 2rg8
TitleCrystal Structure of Programmed for Cell Death 4 Middle MA3 domain
ComponentsProgrammed cell death protein 4
KeywordsAPOPTOSIS / TRANSLATION / MA3 domain / HEAT repeats / Anti-oncogene / Cell cycle / Cytoplasm / Nucleus / Phosphorylation / Polymorphism / RNA-binding
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 / negative regulation of JUN kinase activity / positive regulation of endothelial cell apoptotic process / response to alkaloid / 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 ...epithelial to mesenchymal transition involved in cardiac fibroblast development / negative regulation of myofibroblast differentiation / negative regulation of vascular associated smooth muscle cell differentiation / negative regulation of JUN kinase activity / positive regulation of endothelial cell apoptotic process / response to alkaloid / 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 / negative regulation of apoptotic process / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsGarces, R. / Suzuki, C. / Wagner, G.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: PDCD4 inhibits translation initiation by binding to eIF4A using both its MA3 domains.
Authors: Suzuki, C. / Garces, R.G. / Edmonds, K.A. / Hiller, S. / Hyberts, S.G. / Marintchev, A. / Wagner, G.
History
DepositionOct 3, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1437
Polymers36,0042
Non-polymers1405
Water7,746430
1
A: Programmed cell death protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0603
Polymers18,0021
Non-polymers582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Programmed cell death protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0834
Polymers18,0021
Non-polymers813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.680, 70.060, 110.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 18001.789 Da / Num. of mol.: 2 / Fragment: MA3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD4, H731 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q53EL6
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 200mM sodium acetate, 28%-30% PEG4000, 8% Jeffamine M-600, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C10.9793
SYNCHROTRONAPS 24-ID-C20.8551
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDApr 8, 2007mirrors
ADSC QUANTUM 3152CCDApr 8, 2007mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Cryo-Si MonochromatorSINGLE WAVELENGTHMx-ray1
2Cryo-Si MonochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.85511
ReflectionResolution: 1.8→35.68 Å / Num. all: 34183 / Num. obs: 34012 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 11.7 % / Biso Wilson estimate: 14.8 Å2 / Rsym value: 0.095

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Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→35.68 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 85310.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2675 9.7 %RANDOM
Rwork0.202 ---
all0.202 34012 --
obs0.202 27452 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.1428 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 18.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.06 Å20 Å20 Å2
2---1.29 Å20 Å2
3----0.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.05 Å
Refinement stepCycle: LAST / Resolution: 1.8→35.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2272 0 5 430 2707
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.421.5
X-RAY DIFFRACTIONc_mcangle_it2.172
X-RAY DIFFRACTIONc_scbond_it2.632
X-RAY DIFFRACTIONc_scangle_it3.822.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.237 421 9.7 %
Rwork0.201 3902 -
obs--95 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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