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- PDB-7d8b: Engineering Disulphide-Free Autonomous Antibody VH Domains to mod... -

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Basic information

Entry
Database: PDB / ID: 7d8b
TitleEngineering Disulphide-Free Autonomous Antibody VH Domains to modulate intracellular pathways
Components
  • Eukaryotic translation initiation factor 4EEIF4E
  • VH-S4
KeywordsRNA BINDING PROTEIN / Cap dependent translation / Complex / VH domain
Function / homology
Function and homology information


Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / : / eukaryotic initiation factor 4G binding / regulation of translation at postsynapse, modulating synaptic transmission / RNA cap binding / chromatoid body / eukaryotic translation initiation factor 4F complex / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / mRNA cap binding / Deadenylation of mRNA ...Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / : / eukaryotic initiation factor 4G binding / regulation of translation at postsynapse, modulating synaptic transmission / RNA cap binding / chromatoid body / eukaryotic translation initiation factor 4F complex / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / mRNA cap binding / Deadenylation of mRNA / Transport of the SLBP independent Mature mRNA / RNA 7-methylguanosine cap binding / 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 / Translation initiation complex formation / stem cell population maintenance / mTORC1-mediated signalling / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of neuron differentiation / L13a-mediated translational silencing of Ceruloplasmin expression / behavioral fear response / mRNA export from nucleus / translational initiation / translation initiation factor activity / positive regulation of mitotic cell cycle / cellular response to dexamethasone stimulus / P-body / neuron differentiation / G1/S transition of mitotic cell cycle / ISG15 antiviral mechanism / cytoplasmic stress granule / cytoplasmic ribonucleoprotein granule / regulation of translation / postsynapse / DNA-binding transcription factor binding / negative regulation of translation / nuclear speck / glutamatergic synapse / perinuclear region of cytoplasm / enzyme binding / RNA binding / extracellular exosome / nucleus / cytosol / cytoplasm
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
Similarity search - Domain/homology
Eukaryotic translation initiation factor 4E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsFrosi, Y. / Lin, Y.C. / Jiang, S. / Brown, C.J.
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
DepositionOct 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Derived calculations / Category: atom_type / citation / citation_author
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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

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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: VH-S4
C: Eukaryotic translation initiation factor 4E
D: VH-S4


Theoretical massNumber of molelcules
Total (without water)84,5544
Polymers84,5544
Non-polymers00
Water1,838102
1
A: Eukaryotic translation initiation factor 4E
B: VH-S4


Theoretical massNumber of molelcules
Total (without water)42,2772
Polymers42,2772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-8 kcal/mol
Surface area15080 Å2
MethodPISA
2
C: Eukaryotic translation initiation factor 4E
D: VH-S4


Theoretical massNumber of molelcules
Total (without water)42,2772
Polymers42,2772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-8 kcal/mol
Surface area14770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.595, 140.394, 61.961
Angle α, β, γ (deg.)90.000, 104.037, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Eukaryotic translation initiation factor 4E / EIF4E / eIF4E / eIF-4F 25 kDa subunit / mRNA cap-binding protein


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 (E. coli) / References: UniProt: P06730
#2: Protein VH-S4


Mass: 17146.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.38 Å3/Da / Density % sol: 48.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.01M Tri-sodium citrate, 16% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.46→70.197 Å / Num. obs: 28611 / % possible obs: 99.9 % / Redundancy: 7.7 % / Rsym value: 0.177 / Net I/σ(I): 3.6
Reflection shellResolution: 2.46→2.59 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4143 / Rsym value: 0.876

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V8W

2v8w


Resolution: 2.46→46.216 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.86 / SU B: 12.299 / SU ML: 0.275 / Cross valid method: FREE R-VALUE / ESU R: 0.509 / ESU R Free: 0.311
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2918 1450 5.072 %
Rwork0.25 27137 -
all0.252 --
obs-28587 99.871 %
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: 34.813 Å2
Baniso -1Baniso -2Baniso -3
1-0.068 Å20 Å20.896 Å2
2---2.743 Å20 Å2
3---1.98 Å2
Refinement stepCycle: LAST / Resolution: 2.46→46.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4817 0 0 102 4919
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0134928
X-RAY DIFFRACTIONr_bond_other_d0.0010.0184595
X-RAY DIFFRACTIONr_angle_refined_deg1.1851.6356675
X-RAY DIFFRACTIONr_angle_other_deg1.0761.58410544
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.665604
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.79721.311267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.83515822
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5691539
X-RAY DIFFRACTIONr_chiral_restr0.0370.2633
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025598
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021220
X-RAY DIFFRACTIONr_nbd_refined0.1620.2765
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1680.24081
X-RAY DIFFRACTIONr_nbtor_refined0.1520.22287
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.22238
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2164
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1340.216
X-RAY DIFFRACTIONr_nbd_other0.1330.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2250.213
X-RAY DIFFRACTIONr_mcbond_it1.1753.6782434
X-RAY DIFFRACTIONr_mcbond_other1.1753.6782433
X-RAY DIFFRACTIONr_mcangle_it2.1075.5073029
X-RAY DIFFRACTIONr_mcangle_other2.1075.5073030
X-RAY DIFFRACTIONr_scbond_it0.9333.7652494
X-RAY DIFFRACTIONr_scbond_other0.9333.7652494
X-RAY DIFFRACTIONr_scangle_it1.6655.5913645
X-RAY DIFFRACTIONr_scangle_other1.6655.5913646
X-RAY DIFFRACTIONr_lrange_it3.22740.3595247
X-RAY DIFFRACTIONr_lrange_other3.18640.3165214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.5240.3671070.3131997X-RAY DIFFRACTION99.8576
2.524-2.5930.334990.2971935X-RAY DIFFRACTION100
2.593-2.6680.416850.31920X-RAY DIFFRACTION99.9501
2.668-2.750.347910.2771844X-RAY DIFFRACTION99.7423
2.75-2.840.2891060.2571789X-RAY DIFFRACTION99.8946
2.84-2.940.295970.281727X-RAY DIFFRACTION100
2.94-3.050.3810.2551655X-RAY DIFFRACTION99.9424
3.05-3.1750.292940.2491615X-RAY DIFFRACTION99.8831
3.175-3.3150.307920.2541522X-RAY DIFFRACTION99.8145
3.315-3.4770.267790.2431475X-RAY DIFFRACTION99.8715
3.477-3.6640.275690.2451423X-RAY DIFFRACTION99.933
3.664-3.8860.284720.2471310X-RAY DIFFRACTION99.6395
3.886-4.1540.258710.2311249X-RAY DIFFRACTION100
4.154-4.4850.246670.2051153X-RAY DIFFRACTION100
4.485-4.9110.221580.2051063X-RAY DIFFRACTION99.9109
4.911-5.4870.336510.227979X-RAY DIFFRACTION99.8062
5.487-6.330.366450.257851X-RAY DIFFRACTION99.7773
6.33-7.7370.347380.277747X-RAY DIFFRACTION99.8728
7.737-10.8760.231290.221559X-RAY DIFFRACTION99.8302
10.876-46.2160.254190.314324X-RAY DIFFRACTION98.5632

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