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- PDB-3eiq: Crystal structure of Pdcd4-eIF4A -

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Basic information

Entry
Database: PDB / ID: 3eiq
TitleCrystal structure of Pdcd4-eIF4A
Components
  • Eukaryotic initiation factor 4A-I
  • Programmed cell death protein 4
KeywordsHYDROLASE/ANTITUMOR PROTEIN / Pdcd4 / Anti-oncogene / Apoptosis / Cell cycle / Nucleus / Phosphoprotein / RNA-binding / ATP-binding / Helicase / Hydrolase / Initiation factor / Nucleotide-binding / Protein biosynthesis / ANTITUMOR PROTEIN / translation / HYDROLASE-ANTITUMOR PROTEIN COMPLEX
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 / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / nuclear stress granule / RNA cap binding / eukaryotic translation initiation factor 4F complex / cytoplasmic translational initiation / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / translation factor activity, RNA binding ...epithelial to mesenchymal transition involved in cardiac fibroblast development / negative regulation of myofibroblast differentiation / negative regulation of vascular associated smooth muscle cell differentiation / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / nuclear stress granule / RNA cap binding / eukaryotic translation initiation factor 4F complex / cytoplasmic translational initiation / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / translation factor activity, RNA binding / negative regulation of JUN kinase activity / Deadenylation of mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / response to alkaloid / positive regulation of vascular associated smooth muscle cell apoptotic process / Ribosomal scanning and start codon recognition / Translation initiation complex formation / negative regulation of vascular associated smooth muscle cell proliferation / positive regulation of endothelial cell apoptotic process / negative regulation of cytokine production involved in inflammatory response / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / BMP signaling pathway / response to hormone / translation initiation factor activity / helicase activity / translational initiation / positive regulation of non-canonical NF-kappaB signal transduction / ISG15 antiviral mechanism / positive regulation of inflammatory response / cytoplasmic stress granule / double-stranded RNA binding / cellular response to lipopolysaccharide / RNA helicase activity / RNA helicase / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / DNA clamp loader activity / negative regulation of DNA-templated transcription / mRNA binding / apoptotic process / negative regulation of apoptotic process / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / RNA binding / extracellular exosome / ATP binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Programmed cell death protein 4 / ATP-dependent RNA helicase eIF4A, DEAD-box helicase domain / 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. / DEAD-box subfamily ATP-dependent helicases signature. / RNA helicase, DEAD-box type, Q motif / ATP-dependent RNA helicase DEAD-box, conserved site ...Programmed cell death protein 4 / ATP-dependent RNA helicase eIF4A, DEAD-box helicase domain / 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. / DEAD-box subfamily ATP-dependent helicases signature. / RNA helicase, DEAD-box type, Q motif / ATP-dependent RNA helicase DEAD-box, conserved site / DEAD-box RNA helicase Q motif profile. / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Armadillo-type fold / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Eukaryotic initiation factor 4A-I / Programmed cell death protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsLoh, P.G. / Cheng, Z. / Song, H.
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 17, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 16, 2013Group: Derived calculations
Revision 1.3Nov 1, 2023Group: 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: Eukaryotic initiation factor 4A-I
C: Programmed cell death protein 4
D: Eukaryotic initiation factor 4A-I


Theoretical massNumber of molelcules
Total (without water)133,8283
Polymers133,8283
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)198.362, 198.362, 198.362
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12A
22D

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALASPASPAA22 - 23030 - 238
21VALVALASPASPDC22 - 23030 - 238
12GLYGLYLEULEUAA245 - 400253 - 408
22GLYGLYLEULEUDC245 - 400253 - 408

NCS ensembles :
ID
1
2

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Components

#1: Protein Eukaryotic initiation factor 4A-I / eIF-4A-I / eIF4A-I / ATP-dependent RNA helicase eIF4A-1


Mass: 46992.676 Da / Num. of mol.: 2
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: P60842, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Protein Programmed cell death protein 4 / Topoisomerase-inhibitor suppressed protein / Protein MA-3


Mass: 39842.172 Da / Num. of mol.: 1 / Fragment: UNP residues 120-469
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21star / References: UniProt: Q61823

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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: 4.86 Å3/Da / Density % sol: 74.69 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20% PEG 3350, 0.1M Bis-Tris Propane pH6.5, 0.2M sodium citrate, 0.1M taurine, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9725 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9725 Å / Relative weight: 1
ReflectionResolution: 3.5→30 Å / Num. obs: 32991 / % possible obs: 99.8 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 5.8

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Processing

Software
NameVersionClassification
REFMAC5.4.0077refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3EIJ, 1QDE and 1FUK

3eij

1qde

1fuk


Resolution: 3.5→29.91 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.886 / SU B: 49.259 / SU ML: 0.356 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.488 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26935 1670 5.1 %RANDOM
Rwork0.2199 ---
obs0.2223 31302 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.839 Å2
Refinement stepCycle: LAST / Resolution: 3.5→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8080 0 0 0 8080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0228198
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0421.97311064
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.05351002
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.18624.553380
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.798151549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3431558
X-RAY DIFFRACTIONr_chiral_restr0.1110.21288
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216019
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5571.55033
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.11128164
X-RAY DIFFRACTIONr_scbond_it1.59733165
X-RAY DIFFRACTIONr_scangle_it2.8244.52900
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDNumberTypeRms dev position (Å)Weight position
111633tight positional0.080.05
221152tight positional0.080.05
111633tight thermal0.110.5
221152tight thermal0.10.5
LS refinement shellResolution: 3.5→3.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 141 -
Rwork0.26 2263 -
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)
16.52020.3086-0.19015.1206-0.83676.2697-0.07430.0720.10220.4069-0.0705-0.0118-0.22750.07970.14480.0403-0.01490.00050.0214-0.01720.0269-63.236913.936359.2511
27.1998-0.014-2.15192.9035-1.07964.695-0.0965-0.2749-1.23850.2079-0.18570.19430.736-0.16120.28220.9509-0.00670.3650.3458-0.0550.5471-55.8911-19.759351.2225
32.6512-0.5474-0.83524.4895-0.92323.67420.01410.5448-0.2866-0.586-0.1780.55570.4912-0.92160.16390.3618-0.10960.05690.7821-0.36240.2563-69.00511.518830.187
45.3428-0.8028-1.20154.07611.20183.6179-0.2158-0.17620.08490.70470.1692-0.06650.04060.47780.04660.5150.04950.07550.346-0.08940.0663-31.6759-0.572439.3984
55.58491.59091.1415.6823-0.05868.4962-0.01-0.4272-0.14040.36150.1799-0.04050.1218-0.2426-0.16990.02820.0193-0.00240.05220.0130.006-19.1399-14.624512.9734
69.43481.2168-2.16494.3592-0.94884.84810.09920.11810.2718-0.1202-0.115-0.3358-0.3808-0.24780.01590.51010.17130.12670.2890.01490.2217-36.92517.550715.1194
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 234
2X-RAY DIFFRACTION2A242 - 400
3X-RAY DIFFRACTION3C161 - 304
4X-RAY DIFFRACTION4C314 - 450
5X-RAY DIFFRACTION5D22 - 234
6X-RAY DIFFRACTION6D242 - 400

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