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- PDB-6ylr: Translation initiation factor 4E in complex with bn7GpppG mRNA 5'... -

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Basic information

Entry
Database: PDB / ID: 6ylr
TitleTranslation initiation factor 4E in complex with bn7GpppG mRNA 5' cap analog
ComponentsEukaryotic translation initiation factor 4E
KeywordsTRANSLATION / cap analog / translation initiation / N7-benzyl dinucleotide
Function / homology
Function and homology information


Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Deadenylation of mRNA / Translation initiation complex formation / Ribosomal scanning and start codon recognition / ISG15 antiviral mechanism / mTORC1-mediated signalling / L13a-mediated translational silencing of Ceruloplasmin expression ...Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Deadenylation of mRNA / Translation initiation complex formation / Ribosomal scanning and start codon recognition / ISG15 antiviral mechanism / mTORC1-mediated signalling / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / eukaryotic initiation factor 4G binding / regulation of translation at postsynapse, modulating synaptic transmission / eukaryotic translation initiation factor 4F complex / chromatoid body / mRNA cap binding / RNA 7-methylguanosine cap binding / RISC complex / nuclear export / stem cell population maintenance / negative regulation of neuron differentiation / behavioral fear response / mRNA export from nucleus / translation initiation factor activity / positive regulation of mitotic cell cycle / cellular response to dexamethasone stimulus / translational initiation / P-body / neuron differentiation / G1/S transition of mitotic cell cycle / cytoplasmic stress granule / regulation of translation / DNA-binding transcription factor binding / postsynapse / nuclear body / negative regulation of translation / nuclear speck / translation / perinuclear region of cytoplasm / glutamatergic synapse / enzyme binding / nucleus / cytosol / cytoplasm
Similarity search - Function
RNA Cap, Translation Initiation Factor Eif4e / RNA Cap, Translation Initiation Factor Eif4e / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
bn7GpppG mRNA 5' cap analog / Eukaryotic translation initiation factor 4E
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1954544917 Å
AuthorsKubacka, D. / Wojcik, R. / Baranowski, M.R. / Warminski, M. / Kowalska, J. / Jemielity, J.
Funding support Poland, 2items
OrganizationGrant numberCountry
Foundation for Polish ScienceTEAM/2016_2/13 Poland
Polish National Science CentreUMO- 2017/24/C/NZ1/00169 Poland
CitationJournal: Pharmaceutics / Year: 2021
Title: Novel N7-Arylmethyl Substituted Dinucleotide mRNA 5' cap Analogs: Synthesis and Evaluation as Modulators of Translation.
Authors: Wojcik, R. / Baranowski, M.R. / Markiewicz, L. / Kubacka, D. / Bednarczyk, M. / Baran, N. / Wojtczak, A. / Sikorski, P.J. / Zuberek, J. / Kowalska, J. / Jemielity, J.
History
DepositionApr 7, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 29, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _citation.country / _struct_ncs_dom_lim.beg_auth_comp_id ..._citation.country / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3064
Polymers44,5532
Non-polymers1,7532
Water3,459192
1
A: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1532
Polymers22,2761
Non-polymers8771
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1532
Polymers22,2761
Non-polymers8771
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.047, 94.047, 42.446
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43
Space group name HallP4cw
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: -x,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUPHEPHE(chain 'A' and (resid 32 through 34 or (resid 35...AA32 - 486 - 22
12LYSLYSCYSCYS(chain 'A' and (resid 32 through 34 or (resid 35...AA54 - 17028 - 144
13ARGARGALAALA(chain 'A' and (resid 32 through 34 or (resid 35...AA173 - 201147 - 175
24GLUGLUPHEPHE(chain 'B' and ((resid 32 through 33 and (name N...BB32 - 486 - 22
25LYSLYSCYSCYS(chain 'B' and ((resid 32 through 33 and (name N...BB54 - 17028 - 144
26ARGARGALAALA(chain 'B' and ((resid 32 through 33 and (name N...BB173 - 201147 - 175

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Components

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


Mass: 22276.309 Da / Num. of mol.: 2 / Mutation: 0
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Eif4e / Production host: Escherichia coli (E. coli) / References: UniProt: P63073
#2: Chemical ChemComp-OYE / bn7GpppG mRNA 5' cap analog / [[(2~{R},3~{S},4~{R},5~{R})-5-[2-azanyl-6-oxidanylidene-7-(phenylmethyl)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate


Mass: 876.513 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H31N10O18P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.11 Å3/Da / Density % sol: 41.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 9
Details: 0.1 M Bis-Tris propane pH 9.0, 0.1 M NaCl, 25 % w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 26, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.195→42.06 Å / Num. obs: 19244 / % possible obs: 99.42 % / Redundancy: 7 % / Biso Wilson estimate: 37.5 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.1473 / Rpim(I) all: 0.06037 / Rrim(I) all: 0.1596 / Net I/σ(I): 11.01
Reflection shellResolution: 2.195→2.274 Å / Redundancy: 7 % / Rmerge(I) obs: 0.8653 / Mean I/σ(I) obs: 1.99 / Num. unique obs: 1869 / CC1/2: 0.805 / CC star: 0.944 / Rpim(I) all: 0.3486 / Rrim(I) all: 0.9346 / % possible all: 96.92

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L8B

1l8b


Resolution: 2.1954544917→42.06 Å / SU ML: 0.348259496425 / Cross valid method: NONE / σ(F): 1.37750892456 / Phase error: 32.7141503198
RfactorNum. reflection% reflection
Rfree0.269553771557 961 5.00964395559 %
Rwork0.224039294544 --
obs0.226350871249 19183 99.4401534394 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 58.3221400192 Å2
Refinement stepCycle: LAST / Resolution: 2.1954544917→42.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2756 0 93 192 3041
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003151353336312938
X-RAY DIFFRACTIONf_angle_d0.7607196415534026
X-RAY DIFFRACTIONf_chiral_restr0.0485318648276436
X-RAY DIFFRACTIONf_plane_restr0.00279147244875500
X-RAY DIFFRACTIONf_dihedral_angle_d9.627054727162014
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1955-2.31120.3688826376851330.3430866770812520X-RAY DIFFRACTION97.7884260966
2.3112-2.4560.4107538663661370.3290314941792590X-RAY DIFFRACTION99.6346364633
2.456-2.64560.39629211181370.3064850499752600X-RAY DIFFRACTION99.6722505462
2.6456-2.91180.2971454674731360.2584329472832580X-RAY DIFFRACTION99.8162440279
2.9118-3.33310.2825092858211380.2246387119412620X-RAY DIFFRACTION99.8190372783
3.3331-4.19890.2096105713331370.1791072564472610X-RAY DIFFRACTION99.6011602611
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)
15.859539756942.472379237391.256833111997.917794299032.251573273886.26507736431-0.0136167938503-0.731764680320.7422604714680.723459646849-0.3037777488990.953932771148-0.3747954203860.1039419913570.2208311999750.4284037777310.01483408144320.04134423685980.525271924759-0.08419136296230.320772246557117.215057323-37.035807007720.0480069261
21.54737667033-0.255312387553-0.3156897296172.044220225241.21029509981.065544446170.0411688342571-0.01559122774640.0856524423487-0.1445481674540.09561209157070.118257282469-0.0994340276809-0.0937876385183-0.1262021540720.26186782067-0.00188545767581-0.02913496366340.2759321108890.0233568549260.134358274742123.763939554-43.02849632250.659951693323
33.752691394350.915352862516-1.435763029793.186364421811.223829875061.74448891658-0.06543496010770.01930235790010.136153046623-0.120722379825-0.03630306558790.343030316116-0.291875230289-0.3747877052520.02858454581070.2018813773420.00831547324105-0.03503378932570.3309035775860.01518948011490.194103241595112.391113872-45.13711615942.6194849658
42.95903206694-0.860705260153-0.2845870617763.159087956150.4121670689632.04829029766-0.01628794991030.402822287117-0.349432987855-0.309980169177-0.03849355796080.5483116544930.123723515491-0.2793494161310.01539090849830.247146860141-0.0184765184353-0.0638377150240.3193710720750.01319629040130.253949370145112.916866692-55.0977249509-3.55278242264
55.25640040878-5.06444285502-6.859598217755.012968194246.655339586188.97587158493-1.24497011454-0.894151940388-0.9922936059471.5106991741.070826349150.9295920439721.260138429390.06755615752690.2490087716430.7672804623460.1599503953320.07601308089620.8012930364590.1014554975270.746583445137101.461536876-49.297714103516.1390702162
65.43076557289-4.092027733933.540595633418.64564478204-2.54901942692.426726461150.01515979243521.561618480360.591753173189-0.790793576209-0.707366709330.684430573957-0.210799329884-0.5503135255390.4432857452820.4171895760780.2404490825640.01926499233510.8853407235340.09132985443290.70594679998488.4265367937-27.22969717568.15527305054
74.97139842363-3.28274633023-1.734618993195.065251247740.4420144954191.454873174350.2591809746160.516189145571-0.185575039452-0.624260593483-0.3263670557480.7411988279570.119409687617-0.7183997695970.2914234889010.2578423093540.08809315349370.03992873755050.631841540162-0.03544541647010.6328590102194.418975833-34.09767777236.40582548306
87.398972097111.865874289561.672448693875.68306296632-0.8374717971926.06317893024-1.4786121262-1.445138771841.421655079471.549024912391.19553627171-0.0612321549352-1.06796966394-0.2131982815040.2942514498110.7347587908940.2928463570670.005694522387740.955318599755-0.199711340040.94225237163889.8049763279-22.201319703819.1427714359
97.11487987842-1.53762997661-1.026075371815.78776857588-0.7581464493282.31984120779-0.332986372154-0.4265517465831.380293586320.0457981961990.450168065424-1.30495516571-0.500176586201-0.10628945131-0.057320838480.4642635575450.08146939847570.09166497290790.472134850167-0.09678722371561.06310740926103.964186907-25.90912596839.86370146505
108.94997137504-3.656805185140.2275110080087.487445273960.9054220737034.96740510422-0.7290281473650.2072659077042.16106824388-0.268642091259-0.358361078148-1.04697778804-1.189941702370.6959505907240.8901621407920.5285013151150.0460012222915-0.03901079744310.5693722485140.1940250164781.5210766699498.6353509731-19.559976721210.1398049194
111.44467820095-1.75722796594-0.792718165834.238296491520.09341674759271.0652121403-0.901915328264-0.6356673267230.4688241249140.7633955575270.569610238737-1.15746474046-0.02325895499660.182227466961-0.4330647018310.5134324717860.120532777717-0.04343711209760.588922553131-0.4189711752611.39052941797109.701249487-21.668049698817.8492181003
120.6719096550071.001916704171.815789443831.514729309462.581663092935.895621668330.867555997123-0.01592271393271.35156049842-0.679826602167-0.470111331682-0.669541642256-1.67925656887-0.110029435855-0.1213055737141.00014294155-0.0576085619250.09426140688180.5055627322910.03713395871871.85237998155106.214957427-15.996606511511.0041263501
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 42 )
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 119 )
3X-RAY DIFFRACTION3chain 'A' and (resid 120 through 155 )
4X-RAY DIFFRACTION4chain 'A' and (resid 156 through 217 )
5X-RAY DIFFRACTION5chain 'B' and (resid 29 through 42 )
6X-RAY DIFFRACTION6chain 'B' and (resid 43 through 56 )
7X-RAY DIFFRACTION7chain 'B' and (resid 57 through 95 )
8X-RAY DIFFRACTION8chain 'B' and (resid 96 through 110 )
9X-RAY DIFFRACTION9chain 'B' and (resid 111 through 155 )
10X-RAY DIFFRACTION10chain 'B' and (resid 156 through 172 )
11X-RAY DIFFRACTION11chain 'B' and (resid 173 through 186 )
12X-RAY DIFFRACTION12chain 'B' and (resid 187 through 202 )

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