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- PDB-2zu6: crystal structure of the eIF4A-PDCD4 complex -

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Basic information

Entry
Database: PDB / ID: 2zu6
Titlecrystal structure of the eIF4A-PDCD4 complex
Components
  • Eukaryotic initiation factor 4A-I
  • Programmed cell death protein 4
KeywordsHYDROLASE / protein-protein complex / ATP-binding / Helicase / Initiation factor / Nucleotide-binding / Protein biosynthesis / RNA-binding / Anti-oncogene / Apoptosis / Cell cycle / Cytoplasm / Nucleus / Phosphoprotein / Polymorphism
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 / negative regulation of JUN kinase activity / cytoplasmic translational initiation / Z-decay: degradation of maternal mRNAs by zygotically expressed factors ...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 / negative regulation of JUN kinase activity / cytoplasmic translational initiation / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / translation factor activity, RNA binding / 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 / 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 / negative regulation of cytokine production involved in inflammatory response / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / 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 / 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. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif ...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. / ATP-dependent RNA helicase DEAD-box, conserved site / RNA helicase, DEAD-box type, Q motif / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Eukaryotic initiation factor 4A-I / Programmed cell death protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsCho, Y. / Chang, J.H. / Sohn, S.Y.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2009
Title: Crystal structure of the eIF4A-PDCD4 complex
Authors: Chang, J.H. / Cho, Y.H. / Sohn, S.Y. / Choi, J.M. / Kim, A. / Kim, Y.C. / Jang, S.K. / Cho, Y.
History
DepositionOct 13, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
B: Programmed cell death protein 4
C: Eukaryotic initiation factor 4A-I
D: Eukaryotic initiation factor 4A-I
E: Programmed cell death protein 4
F: Eukaryotic initiation factor 4A-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,92111
Polymers246,6146
Non-polymers3065
Water59433
1
A: Eukaryotic initiation factor 4A-I
B: Programmed cell death protein 4
C: Eukaryotic initiation factor 4A-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,4916
Polymers123,3073
Non-polymers1843
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Eukaryotic initiation factor 4A-I
E: Programmed cell death protein 4
F: Eukaryotic initiation factor 4A-I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,4295
Polymers123,3073
Non-polymers1222
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.893, 165.384, 100.424
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E
13C
23F

NCS domain segments:

Component-ID: 1 / Refine code: 3

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETASNASNchain A 19-401AA19 - 4011 - 383
21METMETASNASNchain D 19-401DD19 - 4011 - 383
12ALAALAARGARGchain B 163-450BB163 - 4501 - 288
22ALAALAARGARGchain E 163-450EE163 - 4501 - 288
13SERSERMETMETchain C 25-398CC25 - 3987 - 380
23ALAALAMETMETchain F 87-398FF87 - 39869 - 380

NCS ensembles :
ID
1
2
3

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Components

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


Mass: 44317.922 Da / Num. of mol.: 4 / Fragment: UNP residues 20-406
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4A1, DDX2A, EIF4A / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P60842, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides
#2: Protein Programmed cell death protein 4 / Nuclear antigen H731-like / Neoplastic transformation inhibitor protein / Protein 197/15a


Mass: 34671.262 Da / Num. of mol.: 2 / Fragment: UNP residues 163-469
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD4, H731 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q53EL6
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.64 Å3/Da / Density % sol: 53.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 14% MPD, 0.1M Sodium Citrate, pH6.0, 100mM Ammonium acetate, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 20, 2008
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 64680 / Num. obs: 64611 / % possible obs: 99.9 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.094 / Rsym value: 0.061 / Net I/σ(I): 26.8

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Processing

Software
NameClassification
PHENIXrefinement
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→50 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.891 / SU B: 14.814 / SU ML: 0.305 / Cross valid method: THROUGHOUT / σ(F): 0.19 / σ(I): 0 / ESU R: 2.566 / ESU R Free: 0.416 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29363 3253 5.1 %RANDOM
Rwork0.24768 ---
obs0.25003 61093 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK / Bsol: 50.683 Å2 / ksol: 0.275 e/Å3
Displacement parametersBiso mean: 88.554 Å2
Baniso -1Baniso -2Baniso -3
1-1.31 Å20 Å20 Å2
2--3.55 Å20 Å2
3----4.86 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14933 0 12 41 14986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONf_bond_refined_d0.0130.02215151
X-RAY DIFFRACTIONf_bond_other_d
X-RAY DIFFRACTIONf_angle_refined_deg1.4461.97120413
X-RAY DIFFRACTIONf_angle_other_deg
X-RAY DIFFRACTIONf_dihedral_angle_1_deg7.97951844
X-RAY DIFFRACTIONf_dihedral_angle_2_deg39.08924.38694
X-RAY DIFFRACTIONf_dihedral_angle_3_deg23.197152876
X-RAY DIFFRACTIONf_dihedral_angle_4_deg21.50715112
X-RAY DIFFRACTIONf_chiral_restr0.1060.22388
X-RAY DIFFRACTIONf_gen_planes_refined0.0070.0211049
X-RAY DIFFRACTIONf_gen_planes_other
X-RAY DIFFRACTIONf_nbd_refined0.2780.27770
X-RAY DIFFRACTIONf_nbd_other
X-RAY DIFFRACTIONf_nbtor_refined0.330.210313
X-RAY DIFFRACTIONf_nbtor_other
X-RAY DIFFRACTIONf_xyhbond_nbd_refined0.1930.2543
X-RAY DIFFRACTIONf_xyhbond_nbd_other
X-RAY DIFFRACTIONf_metal_ion_refined
X-RAY DIFFRACTIONf_metal_ion_other
X-RAY DIFFRACTIONf_symmetry_vdw_refined0.3670.2122
X-RAY DIFFRACTIONf_symmetry_vdw_other
X-RAY DIFFRACTIONf_symmetry_hbond_refined0.2360.214
X-RAY DIFFRACTIONf_symmetry_hbond_other
X-RAY DIFFRACTIONf_symmetry_metal_ion_refined
X-RAY DIFFRACTIONf_symmetry_metal_ion_other
X-RAY DIFFRACTIONf_mcbond_it1.1691.59497
X-RAY DIFFRACTIONf_mcbond_other
X-RAY DIFFRACTIONf_mcangle_it1.938215086
X-RAY DIFFRACTIONf_scbond_it2.64536201
X-RAY DIFFRACTIONf_scangle_it4.194.55327
X-RAY DIFFRACTIONf_rigid_bond_restr
X-RAY DIFFRACTIONf_sphericity_free
X-RAY DIFFRACTIONf_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1356tight positional0.320.05
2B1128tight positional0.230.05
3C1068tight positional0.320.05
1A1354loose positional0.795
2B1073loose positional0.545
3C1103loose positional0.85
1A1356tight thermal1.150.5
2B1128tight thermal1.660.5
3C1068tight thermal1.140.5
1A1354loose thermal2.7610
2B1073loose thermal3.3610
3C1103loose thermal2.6310
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 241 -
Rwork0.296 4351 -
obs--97.35 %

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