[English] 日本語
Yorodumi
- PDB-5m80: Translation initiation factor 4E in complex with (RP)-iPr-m7GppSp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5m80
TitleTranslation initiation factor 4E in complex with (RP)-iPr-m7GppSpG mRNA 5' cap analog
ComponentsEukaryotic translation initiation factor 4EEIF4E
KeywordsRNA BINDING PROTEIN / Protein-ligand complex / translation initiation factor / eIF4E / iPr-m7GppSpG / phosphorothioate / mRNA 5' cap analog / translation
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 / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit ...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 / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / mTORC1-mediated signalling / eukaryotic initiation factor 4G binding / regulation of translation at postsynapse, modulating synaptic transmission / chromatoid body / eukaryotic translation initiation factor 4F complex / mRNA cap binding / : / RNA 7-methylguanosine cap binding / nuclear export / RISC complex / postsynaptic cytosol / stem cell population maintenance / negative regulation of neuron differentiation / behavioral fear response / mRNA export from nucleus / translational initiation / translation initiation factor activity / cellular response to dexamethasone stimulus / positive regulation of mitotic cell cycle / P-body / G1/S transition of mitotic cell cycle / cytoplasmic ribonucleoprotein granule / neuron differentiation / cytoplasmic stress granule / regulation of translation / postsynapse / DNA-binding transcription factor binding / negative regulation of translation / nuclear body / nuclear speck / translation / glutamatergic synapse / perinuclear region of cytoplasm / enzyme binding / protein-containing complex / 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
Chem-7L2 / Eukaryotic translation initiation factor 4E
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsWarminski, M. / Nowak, E. / Kowalska, J. / Jemielity, J. / Nowotny, M.
Funding support Poland, 1items
OrganizationGrant numberCountry
Ministry of Science and Higher EducationDI2012 024842 Poland
CitationJournal: To Be Published
Title: Translation initiation factor 4E in complex with (RP)-iPr-m7GppSpG mRNA 5' cap analog
Authors: Warminski, M. / Nowak, E. / Kubacka, D. / Kowalska, J. / Nowotny, M. / Jemielity, J.
History
DepositionOct 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)90,4848
Polymers88,5804
Non-polymers1,9034
Water5,783321
1
A: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0973
Polymers22,1451
Non-polymers9522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Eukaryotic translation initiation factor 4E


Theoretical massNumber of molelcules
Total (without water)22,1451
Polymers22,1451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0973
Polymers22,1451
Non-polymers9522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Eukaryotic translation initiation factor 4E


Theoretical massNumber of molelcules
Total (without water)22,1451
Polymers22,1451
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.237, 38.271, 146.818
Angle α, β, γ (deg.)87.53, 95.37, 102.94
Int Tables number1
Space group name H-MP1

-
Components

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


Mass: 22145.113 Da / Num. of mol.: 4
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-7L2 / [[[(3~{a}~{R},4~{R},6~{R},6~{a}~{R})-4-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-7-ium-9-yl)-2,2-dimethyl-3~{a},4,6,6~{a}-tetrahydrofuro[3,4-d][1,3]dioxol-6-yl]methoxy-oxidanyl-phosphoryl]oxy-sulfanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate


Mass: 859.570 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H34N10O17P3S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.72 % / Description: Thin plates
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 19% PEG 10000, 0.2M CH3COONa, 0.1M TRIS pH 8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.12→50 Å / Num. obs: 43091 / % possible obs: 93.9 % / Redundancy: 1.979 % / CC1/2: 0.996 / Rmerge(I) obs: 0.068 / Net I/σ(I): 10.47
Reflection shellResolution: 2.12→2.25 Å / Redundancy: 1.829 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 2 / CC1/2: 0.68 / % possible all: 89.5

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1L8B

1l8b


Resolution: 2.12→37.29 Å / SU ML: 0.29 / Cross valid method: NONE / σ(F): 1.97 / Phase error: 26.68
RfactorNum. reflection% reflection
Rfree0.2583 2100 4.87 %
Rwork0.204 --
obs0.2066 43088 93.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.12→37.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5168 0 122 321 5611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085516
X-RAY DIFFRACTIONf_angle_d1.0817569
X-RAY DIFFRACTIONf_dihedral_angle_d17.0393173
X-RAY DIFFRACTIONf_chiral_restr0.067828
X-RAY DIFFRACTIONf_plane_restr0.007944
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1182-2.16750.30631270.27162480X-RAY DIFFRACTION86
2.1675-2.22170.31311360.25432660X-RAY DIFFRACTION91
2.2217-2.28170.27561400.23882730X-RAY DIFFRACTION94
2.2817-2.34890.28441410.2342757X-RAY DIFFRACTION95
2.3489-2.42470.27781410.22212749X-RAY DIFFRACTION94
2.4247-2.51130.28041440.23552823X-RAY DIFFRACTION95
2.5113-2.61180.3061380.22572678X-RAY DIFFRACTION94
2.6118-2.73070.28221440.21972813X-RAY DIFFRACTION94
2.7307-2.87460.28871350.20912647X-RAY DIFFRACTION93
2.8746-3.05460.27251420.20522767X-RAY DIFFRACTION96
3.0546-3.29030.25861440.19082803X-RAY DIFFRACTION96
3.2903-3.62120.25611430.18152789X-RAY DIFFRACTION95
3.6212-4.14460.2211390.17862717X-RAY DIFFRACTION93
4.1446-5.21950.23671430.17382796X-RAY DIFFRACTION96
5.2195-37.29570.22621430.21182779X-RAY DIFFRACTION95
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)
13.9301-1.6984-3.11914.68741.91247.4287-0.0021-0.0983-0.1662-0.56510.3342-0.9197-0.07670.7242-0.30740.2481-0.0280.04640.1559-0.10890.517849.774549.1041-60.181
24.53850.24730.35750.1283-0.11990.4521-0.12660.08910.0353-0.02920.0540.272-0.1448-0.090.06420.19850.0037-0.030.1222-0.04720.416622.072957.7038-53.9716
36.9589-3.7952-0.65862.6291.00110.7981-0.0179-0.1195-0.828-0.044-0.06790.21920.2202-0.13180.11770.2018-0.0381-0.060.1484-0.0270.399526.959153.2099-56.4876
43.2032-1.7659-2.1995.00070.35823.13090.14060.2975-0.1248-0.3789-0.17070.1705-0.0796-0.21770.03390.1637-0.0102-0.05820.1133-0.08320.233634.405961.3491-58.8376
50.7775-0.01480.45825.8057-3.1622.3116-0.074-0.1390.16410.32890.07780.0101-0.2615-0.1429-0.02020.15530.0317-0.00050.1564-0.0610.291330.450562.3402-45.0426
61.5780.8343-1.0591.32760.9783.3903-0.0611-0.1647-0.08020.1137-0.0373-0.22090.12760.24970.08120.12250.0071-0.05840.1065-0.04920.35539.888160.6217-47.714
72.14880.67970.25740.4010.73992.36560.0527-0.1572-0.22020.2504-0.09640.0066-0.1035-0.13670.01840.19510.0021-0.03610.1339-0.050.302531.244161.4009-41.8877
81.9017-0.564-2.66446.5532-1.7456.13910.0861-0.40930.19590.7776-0.1503-0.646-0.0060.89510.03430.29150.0008-0.17950.2312-0.0670.375843.755762.5642-37.7662
94.15644.7364-1.09595.3915-1.24195.03840.3706-0.49920.38980.7179-0.36130.5143-0.22040.07580.01750.36460.0503-0.03010.1778-0.02060.316133.908765.456-35.0421
103.62371.1682-1.08426.8378-1.65867.88340.05550.1126-0.0194-0.19250.034-0.38870.779-0.4809-0.07330.63780.0294-0.01660.1262-0.03390.292330.606264.4341-70.8485
112.6317-1.0329-0.25250.7772-0.8412.86370.29710.05610.4242-0.55010.1673-1.1461-0.91960.6381-0.47940.9296-0.03640.45310.3939-0.09880.79850.322882.9878-77.1963
120.2967-0.5078-0.12830.9776-0.00050.58420.36390.17120.3948-0.67620.0062-1.0516-0.25450.1766-0.26680.68730.07010.25270.2449-0.06030.600143.22679.7835-75.6035
130.4512-0.7382-0.81051.20551.31521.43940.23970.22760.0091-0.6034-0.3416-0.0435-0.2298-0.0358-0.02771.25610.26150.35030.38660.03250.528438.512788.8106-86.8942
143.73610.8723-0.68893.95241.51392.41530.14090.2613-0.0259-0.5411-0.11860.03070.1236-0.12050.08070.94830.19780.12920.2814-0.02760.276934.341679.2321-83.4398
153.18220.4227-0.02293.27110.15040.02410.30850.37830.0832-0.6602-0.1374-0.1014-0.08390.0485-0.16551.18640.14250.3980.34640.04990.453241.294983.3788-90.2529
163.82480.98213.54330.72530.67973.39350.04110.1544-0.0071-0.21740.00850.002-0.0592-0.2745-0.05251.43630.3084-0.07070.50470.00370.358929.898979.6446-92.1846
173.7202-0.919-3.64550.37850.98873.62230.4852-0.50950.7515-0.3527-0.1245-0.2102-0.31670.1449-0.36591.19660.44430.23020.8245-0.02340.498740.14484.5926-95.2657
187.38-2.81473.29992.8437-1.65134.54970.4173-0.5238-0.83770.05710.0496-0.07570.5630.0032-0.51090.186-0.0028-0.15770.30020.00390.530464.127365.1678-1.6206
191.8247-2.66810.14975.0315-0.56950.1992-0.0272-0.10130.41150.3237-0.0741-0.3178-0.11660.0620.10380.1578-0.0315-0.06430.2193-0.07010.387951.791988.608-6.5096
201.51760.6352-0.4821.3633-0.74832.7599-0.04320.0493-0.0553-0.0351-0.03580.0292-0.0172-0.08650.06550.11430.0165-0.07330.1652-0.06140.320948.569276.9387-10.9792
214.8621.9856-0.02653.1206-0.30353.083-0.43220.65610.1156-0.65070.29650.02810.0046-0.13110.1170.2643-0.0299-0.06550.2685-0.04760.191848.233874.9119-24.5429
224.9178-0.1931-2.99563.0275-3.48417.71850.2551-0.56720.06490.4345-0.0568-0.1962-0.7835-0.0668-0.17370.2497-0.0928-0.0650.607-0.13580.297445.227880.17789.1164
235.2056-0.30470.33360.0237-0.14592.68980.2393-0.6686-1.5037-0.0085-0.00860.17290.6036-0.6938-0.28960.3521-0.119-0.13440.9430.42410.894331.701256.137315.7571
242.1924-1.91190.58541.708-0.92024.5740.0942-0.9312-1.05890.07550.15780.25720.07710.0162-0.21770.20010.0304-0.08890.53540.08130.479635.567167.74210.2119
255.74680.498-1.14690.1647-0.46661.33730.1818-0.7609-1.21970.17080.21160.25270.4343-0.6792-0.42540.298-0.0856-0.13780.79420.37120.722721.693662.858311.3721
262.6462-0.60081.29920.5145-0.460.9776-0.0082-1.1617-0.34450.26340.0418-0.00880.0365-0.3498-0.05310.23870.03-0.10391.27530.25610.42730.48167.752322.787
270.92530.2922-0.96251.7925-1.261.5377-0.0207-0.3181-0.02960.09250.15760.144-0.0218-0.1154-0.16740.4729-0.1051-0.00461.58360.33430.477828.990764.836528.3072
280.7567-0.0283-2.33173.51-0.87637.4489-0.2156-0.2516-0.00480.3036-0.0032-0.0507-0.27750.18690.17780.56290.29-0.03081.767-0.2260.488330.063376.547831.3797
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 42 )
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 56 )
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 66 )
4X-RAY DIFFRACTION4chain 'A' and (resid 67 through 95 )
5X-RAY DIFFRACTION5chain 'A' and (resid 96 through 125 )
6X-RAY DIFFRACTION6chain 'A' and (resid 126 through 156 )
7X-RAY DIFFRACTION7chain 'A' and (resid 157 through 172 )
8X-RAY DIFFRACTION8chain 'A' and (resid 173 through 186 )
9X-RAY DIFFRACTION9chain 'A' and (resid 187 through 217 )
10X-RAY DIFFRACTION10chain 'C' and (resid 31 through 42 )
11X-RAY DIFFRACTION11chain 'C' and (resid 43 through 55 )
12X-RAY DIFFRACTION12chain 'C' and (resid 56 through 104 )
13X-RAY DIFFRACTION13chain 'C' and (resid 105 through 125 )
14X-RAY DIFFRACTION14chain 'C' and (resid 126 through 155 )
15X-RAY DIFFRACTION15chain 'C' and (resid 156 through 174 )
16X-RAY DIFFRACTION16chain 'C' and (resid 175 through 187 )
17X-RAY DIFFRACTION17chain 'C' and (resid 188 through 201 )
18X-RAY DIFFRACTION18chain 'B' and (resid 31 through 42 )
19X-RAY DIFFRACTION19chain 'B' and (resid 43 through 66 )
20X-RAY DIFFRACTION20chain 'B' and (resid 67 through 161 )
21X-RAY DIFFRACTION21chain 'B' and (resid 162 through 217 )
22X-RAY DIFFRACTION22chain 'D' and (resid 31 through 42 )
23X-RAY DIFFRACTION23chain 'D' and (resid 43 through 56 )
24X-RAY DIFFRACTION24chain 'D' and (resid 57 through 78 )
25X-RAY DIFFRACTION25chain 'D' and (resid 79 through 88 )
26X-RAY DIFFRACTION26chain 'D' and (resid 89 through 156 )
27X-RAY DIFFRACTION27chain 'D' and (resid 157 through 172 )
28X-RAY DIFFRACTION28chain 'D' and (resid 173 through 188 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more