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- PDB-3eij: Crystal structure of Pdcd4 -

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Basic information

Entry
Database: PDB / ID: 3eij
TitleCrystal structure of Pdcd4
ComponentsProgrammed cell death protein 4
KeywordsANTITUMOR PROTEIN / protein / heat motif / Anti-oncogene / Apoptosis / Cell cycle / Nucleus / Phosphoprotein / RNA-binding / TRANSLATION
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 / 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 ...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 / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsLoh, P.G.
CitationJournal: Embo J. / Year: 2009
Title: Structural basis for translational inhibition by the tumour suppressor Pdcd4
Authors: Loh, P.G. / Yang, H.-S. / Walsh, M.A. / Wang, Q. / Wang, X. / Cheng, Z. / Liu, D. / Song, H.
History
DepositionSep 16, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)71,5182
Polymers71,5182
Non-polymers00
Water1,00956
1
A: Programmed cell death protein 4


Theoretical massNumber of molelcules
Total (without water)35,7591
Polymers35,7591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Programmed cell death protein 4


Theoretical massNumber of molelcules
Total (without water)35,7591
Polymers35,7591
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)170.325, 170.325, 66.919
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 35758.891 Da / Num. of mol.: 2 / Fragment: UNP residues 157-469
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21star / References: UniProt: Q53EL6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.92 Å3/Da / Density % sol: 68.61 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG MME 2000, 0.1M Tris-HCl pH8.5, 0.2M trimethylamine N-oxide (TMAO), 10mM DTT, 10mM sarcosine, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 27711 / % possible obs: 100 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
SnBphasing
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.917 / SU B: 21.915 / SU ML: 0.197 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.438 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27666 1394 5 %RANDOM
Rwork0.23531 ---
obs0.23531 27686 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.577 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20.31 Å2-0 Å2
2--0.62 Å2-0 Å2
3----0.93 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4362 0 0 56 4418
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0224430
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8061.9935980
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.295546
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.36725192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.59715842
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4271522
X-RAY DIFFRACTIONr_chiral_restr0.0530.2704
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213216
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.22213
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2960.23141
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2132
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3210.230
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3560.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2211.52750
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.41924452
X-RAY DIFFRACTIONr_scbond_it0.46531680
X-RAY DIFFRACTIONr_scangle_it0.8264.51528
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.298 1976 -
Rfree-0 -
obs--100 %
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)
12.19920.35340.56981.81140.50663.99730.04040.01480.20150.0002-0.09410.09960.0199-0.31560.05370.0572-0.0507-0.04320.1556-0.04170.1744-66.597183.2157-26.9134
22.35490.10221.16721.8009-0.02154.6867-0.17650.31120.19510.0117-0.065-0.1114-0.460.13210.24160.2228-0.1166-0.04930.3080.0350.1358-64.853664.1974-57.3137
32.6684-0.1373-1.00713.5071-1.07384.4025-0.19180.2623-0.1896-0.088-0.0894-0.83750.2370.29410.28120.045-0.09280.04720.2168-0.00130.4231-43.736842.2252-52.8415
43.11940.6848-1.01862.13390.08453.5138-0.0792-0.0768-0.11570.25510.0693-0.05060.14920.06480.00990.2386-0.0326-0.05780.1661-0.00130.085-65.828352.5404-27.2198
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A157 - 306
2X-RAY DIFFRACTION2A324 - 450
3X-RAY DIFFRACTION3B157 - 306
4X-RAY DIFFRACTION4B324 - 450

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