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- PDB-7xtp: eIF4E in Complex with a Disulphide-Free Autonomous VH Domain -

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Basic information

Entry
Database: PDB / ID: 7xtp
TitleeIF4E in Complex with a Disulphide-Free Autonomous VH Domain
Components
  • Eukaryotic translation initiation factor 4E
  • VH-S4ss
KeywordsRNA BINDING PROTEIN / Cap-Dependent Translation
Function / homology
Function and homology information


eukaryotic initiation factor 4G binding / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / regulation of translation at postsynapse, modulating synaptic transmission / RNA cap binding / eukaryotic translation initiation factor 4F complex / chromatoid body / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / mRNA cap binding / Deadenylation of mRNA / RNA 7-methylguanosine cap binding ...eukaryotic initiation factor 4G binding / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / regulation of translation at postsynapse, modulating synaptic transmission / RNA cap binding / eukaryotic translation initiation factor 4F complex / chromatoid body / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / mRNA cap binding / Deadenylation of mRNA / RNA 7-methylguanosine cap binding / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / Transport of Mature mRNA Derived from an Intronless Transcript / RISC complex / Ribosomal scanning and start codon recognition / stem cell population maintenance / negative regulation of neuron differentiation / Translation initiation complex formation / mTORC1-mediated signalling / GTP hydrolysis and joining of the 60S ribosomal subunit / cellular response to dexamethasone stimulus / L13a-mediated translational silencing of Ceruloplasmin expression / behavioral fear response / mRNA export from nucleus / translation initiation factor activity / positive regulation of mitotic cell cycle / translational initiation / P-body / G1/S transition of mitotic cell cycle / ISG15 antiviral mechanism / cytoplasmic ribonucleoprotein granule / neuron differentiation / cytoplasmic stress granule / regulation of translation / DNA-binding transcription factor binding / postsynapse / negative regulation of translation / nuclear speck / perinuclear region of cytoplasm / glutamatergic synapse / enzyme binding / RNA binding / extracellular exosome / nucleus / cytoplasm / cytosol
Similarity search - Function
Eukaryotic translation initiation factor 4E (eIF-4E), conserved site / Eukaryotic initiation factor 4E signature. / Translation Initiation factor eIF- 4e / Eukaryotic initiation factor 4E / Translation Initiation factor eIF- 4e-like / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-MGO / Eukaryotic translation initiation factor 4E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.828 Å
AuthorsBrown, C.J. / Frosi, Y. / Jiang, S. / Lin, Y.C.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Other government Singapore
CitationJournal: Nat Commun / Year: 2022
Title: Engineering an autonomous VH domain to modulate intracellular pathways and to interrogate the eIF4F complex.
Authors: Frosi, Y. / Lin, Y.C. / Shimin, J. / Ramlan, S.R. / Hew, K. / Engman, A.H. / Pillai, A. / Yeung, K. / Cheng, Y.X. / Cornvik, T. / Nordlund, P. / Goh, M. / Lama, D. / Gates, Z.P. / Verma, C.S. ...Authors: Frosi, Y. / Lin, Y.C. / Shimin, J. / Ramlan, S.R. / Hew, K. / Engman, A.H. / Pillai, A. / Yeung, K. / Cheng, Y.X. / Cornvik, T. / Nordlund, P. / Goh, M. / Lama, D. / Gates, Z.P. / Verma, C.S. / Thean, D. / Lane, D.P. / Asial, I. / Brown, C.J.
History
DepositionMay 17, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Eukaryotic translation initiation factor 4E
B: Eukaryotic translation initiation factor 4E
C: VH-S4ss
D: VH-S4ss
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,3446
Polymers83,2694
Non-polymers1,0742
Water6,990388
1
A: Eukaryotic translation initiation factor 4E
hetero molecules

C: VH-S4ss


Theoretical massNumber of molelcules
Total (without water)42,1723
Polymers41,6352
Non-polymers5371
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_544-x,y-1/2,-z-11
Buried area2010 Å2
ΔGint-5 kcal/mol
Surface area14620 Å2
MethodPISA
2
B: Eukaryotic translation initiation factor 4E
hetero molecules

D: VH-S4ss


Theoretical massNumber of molelcules
Total (without water)42,1723
Polymers41,6352
Non-polymers5371
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_644-x+1,y-1/2,-z-11
Buried area2040 Å2
ΔGint-5 kcal/mol
Surface area14620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.623, 57.207, 78.963
Angle α, β, γ (deg.)90.000, 93.951, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Eukaryotic translation initiation factor 4E / eIF4E


Mass: 25130.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4E, EIF4EL1, EIF4F / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P06730
#2: Antibody VH-S4ss


Mass: 16504.285 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Engineered Autonomous VH domain with Intra-disulphide Bond.
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
#3: Chemical ChemComp-MGO / [[(2R,3S,4R,5R)-5-(6-AMINO-3-METHYL-4-OXO-5H-IMIDAZO[4,5-C]PYRIDIN-1-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL] PHOSPHONO HYDROGEN PHOSPHATE


Mass: 537.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H20N4O14P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.05 Å3/Da / Density % sol: 39.89 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1M Sodium HEPES pH7.5, 25% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.828→46.332 Å / Num. obs: 59269 / % possible obs: 99.2 % / Redundancy: 7 % / Biso Wilson estimate: 18.7 Å2 / Rrim(I) all: 0.147 / Net I/σ(I): 11.8
Reflection shellResolution: 1.828→1.89 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3593 / Rrim(I) all: 1.691 / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7D6Y

7d6y


Resolution: 1.828→46.332 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.216 / SU ML: 0.123 / Cross valid method: FREE R-VALUE / ESU R: 0.166 / ESU R Free: 0.149
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2593 3060 5.163 %
Rwork0.2263 56209 -
all0.228 --
obs-59269 99.059 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.465 Å2
Baniso -1Baniso -2Baniso -3
1-1.332 Å20 Å2-0.491 Å2
2---0.832 Å2-0 Å2
3----0.428 Å2
Refinement stepCycle: LAST / Resolution: 1.828→46.332 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4849 0 58 388 5295
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0135101
X-RAY DIFFRACTIONr_bond_other_d0.0060.0154709
X-RAY DIFFRACTIONr_angle_refined_deg1.1721.6396949
X-RAY DIFFRACTIONr_angle_other_deg1.1341.58810833
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8535637
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.62221.375269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.49615853
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg10.802158
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4961539
X-RAY DIFFRACTIONr_chiral_restr0.0410.2663
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026107
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021255
X-RAY DIFFRACTIONr_nbd_refined0.1670.2844
X-RAY DIFFRACTIONr_symmetry_nbd_other0.170.24343
X-RAY DIFFRACTIONr_nbtor_refined0.1540.22386
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.070.22253
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2378
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1280.225
X-RAY DIFFRACTIONr_nbd_other0.190.297
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.10.239
X-RAY DIFFRACTIONr_mcbond_it0.7462.3312485
X-RAY DIFFRACTIONr_mcbond_other0.7462.332484
X-RAY DIFFRACTIONr_mcangle_it1.3453.4873110
X-RAY DIFFRACTIONr_mcangle_other1.3453.4873111
X-RAY DIFFRACTIONr_scbond_it0.6552.432616
X-RAY DIFFRACTIONr_scbond_other0.6552.432616
X-RAY DIFFRACTIONr_scangle_it1.1653.6013828
X-RAY DIFFRACTIONr_scangle_other1.1653.6013829
X-RAY DIFFRACTIONr_lrange_it2.94726.7555768
X-RAY DIFFRACTIONr_lrange_other2.79826.4845672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.828-1.8760.3212060.3174095X-RAY DIFFRACTION97.8389
1.876-1.9270.3172080.3124063X-RAY DIFFRACTION99.6965
1.927-1.9830.2892100.2673948X-RAY DIFFRACTION99.7601
1.983-2.0440.3251920.2543852X-RAY DIFFRACTION99.5324
2.044-2.1110.31880.2543717X-RAY DIFFRACTION99.4145
2.111-2.1850.3011850.2343570X-RAY DIFFRACTION99.3124
2.185-2.2670.262240.2283446X-RAY DIFFRACTION99.5659
2.267-2.360.271970.2313302X-RAY DIFFRACTION99.2906
2.36-2.4640.2751830.2213042X-RAY DIFFRACTION95.5839
2.464-2.5850.251830.2123046X-RAY DIFFRACTION99.3844
2.585-2.7240.2451710.2212922X-RAY DIFFRACTION99.5174
2.724-2.8890.2681510.212747X-RAY DIFFRACTION99.759
2.889-3.0890.2451490.2182585X-RAY DIFFRACTION99.6356
3.089-3.3360.2751150.2212452X-RAY DIFFRACTION99.8833
3.336-3.6530.2731140.2162265X-RAY DIFFRACTION99.8321
3.653-4.0830.2381380.2072012X-RAY DIFFRACTION99.768
4.083-4.7130.1981050.1811684X-RAY DIFFRACTION94.606
4.713-5.7670.225780.2051535X-RAY DIFFRACTION99.3839
5.767-8.1340.237350.2171231X-RAY DIFFRACTION100
8.134-46.3320.188280.234695X-RAY DIFFRACTION99.4498

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