[English] 日本語
Yorodumi
- PDB-4axg: Structure of eIF4E-Cup complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4axg
TitleStructure of eIF4E-Cup complex
Components
  • EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
  • PROTEIN CUP
KeywordsTRANSLATION / 4E-BP / MRNA LOCALIZATION
Function / homology
Function and homology information


oocyte growth in germarium-derived egg chamber / negative regulation of eukaryotic translation initiation factor 4F complex assembly / follicle cell of egg chamber migration / negative regulation of oskar mRNA translation / TOR signaling pathway / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / ISG15 antiviral mechanism / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript ...oocyte growth in germarium-derived egg chamber / negative regulation of eukaryotic translation initiation factor 4F complex assembly / follicle cell of egg chamber migration / negative regulation of oskar mRNA translation / TOR signaling pathway / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / ISG15 antiviral mechanism / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / L13a-mediated translational silencing of Ceruloplasmin expression / mTORC1-mediated signalling / Translation initiation complex formation / Ribosomal scanning and start codon recognition / muscle cell postsynaptic specialization / regulation of pole plasm oskar mRNA localization / regulation of synaptic assembly at neuromuscular junction / RNA metabolic process / neuronal ribonucleoprotein granule / meiotic chromosome segregation / eukaryotic initiation factor 4G binding / eukaryotic initiation factor 4E binding / intracellular mRNA localization / RNA cap binding / female meiotic nuclear division / eukaryotic translation initiation factor 4F complex / RNA 7-methylguanosine cap binding / dorsal/ventral pattern formation / oogenesis / translation regulator activity / negative regulation of translational initiation / translation initiation factor activity / translational initiation / P-body / terminal bouton / neuromuscular junction / negative regulation of translation / nuclear body / translation / mRNA binding / RNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Eukaryotic translation initiation factor 4E binding protein / Nucleocytoplasmic shuttling protein for mRNA cap-binding EIF4E / 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
Eukaryotic translation initiation factor 4E1 / Protein cup
Similarity search - Component
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKinkelin, K. / Veith, K. / Gruenwald, M. / Bono, F.
CitationJournal: RNA / Year: 2012
Title: Crystal Structure of a Minimal Eif4E-Cup Complex Revelas a General Mechanism of Eif4E Regulation in Translational Repression
Authors: Kinkelin, K. / Veith, K. / Gruenwald, M. / Bono, F.
History
DepositionJun 12, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
B: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
C: PROTEIN CUP
D: PROTEIN CUP


Theoretical massNumber of molelcules
Total (without water)85,3344
Polymers85,3344
Non-polymers00
Water25214
1
A: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
C: PROTEIN CUP


Theoretical massNumber of molelcules
Total (without water)42,6672
Polymers42,6672
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-14.3 kcal/mol
Surface area11620 Å2
MethodPISA
2
B: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
D: PROTEIN CUP


Theoretical massNumber of molelcules
Total (without water)42,6672
Polymers42,6672
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-8 kcal/mol
Surface area8650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.580, 142.580, 108.050
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A
211CHAIN B

NCS oper: (Code: given
Matrix: (-0.4093, -0.90467, 0.11854), (0.63893, -0.19144, 0.74506), (-0.65134, 0.38069, 0.65638)
Vector: 14.13856, -67.63185, 12.28072)

-
Components

#1: Protein EUKARYOTIC TRANSLATION INITIATION FACTOR 4E / EIF-4E / EIF4E / EIF-4F 25 KDA SUBUNIT / MRNA CAP-BINDING PROTEIN


Mass: 27861.111 Da / Num. of mol.: 2 / Fragment: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PETMCN HIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P48598
#2: Protein PROTEIN CUP / OSKAR RIBONUCLEOPROTEIN COMPLEX 147 KDA SUBUNIT


Mass: 14805.982 Da / Num. of mol.: 2 / Fragment: RESIDUE 296-425
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: Q9VMA3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3.17 Å3/Da / Density % sol: 61.2 % / Description: NONE
Crystal growDetails: 20% PEG3350, 200 MM CALCIUM ACETATE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.0718
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0718 Å / Relative weight: 1
ReflectionResolution: 2.8→81.31 Å / Num. obs: 16494 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 13.4 % / Biso Wilson estimate: 67.1 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 14.23
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 13.62 % / Rmerge(I) obs: 1.14 / Mean I/σ(I) obs: 2.79 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3U7X

3u7x


Resolution: 2.8→81.314 Å / SU ML: 0.46 / σ(F): 2 / Phase error: 24.92 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2442 825 5 %
Rwork0.2282 --
obs0.2291 16464 99.95 %
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.731 Å2 / ksol: 0.316 e/Å3
Displacement parametersBiso mean: 85.45 Å2
Baniso -1Baniso -2Baniso -3
1-6.1776 Å20 Å20 Å2
2--6.1776 Å20 Å2
3----12.3553 Å2
Refinement stepCycle: LAST / Resolution: 2.8→81.314 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3033 0 0 14 3047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033094
X-RAY DIFFRACTIONf_angle_d0.6534213
X-RAY DIFFRACTIONf_dihedral_angle_d13.3141047
X-RAY DIFFRACTIONf_chiral_restr0.047477
X-RAY DIFFRACTIONf_plane_restr0.002538
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1440X-RAY DIFFRACTIONPOSITIONAL
12B1440X-RAY DIFFRACTIONPOSITIONAL0.472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.97560.36111340.31442551X-RAY DIFFRACTION100
2.9756-3.20530.25691340.26282537X-RAY DIFFRACTION100
3.2053-3.52790.27241350.22982554X-RAY DIFFRACTION100
3.5279-4.03840.26171360.21082596X-RAY DIFFRACTION100
4.0384-5.08780.2351390.18972622X-RAY DIFFRACTION100
5.0878-81.34790.21181470.24482779X-RAY DIFFRACTION100
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)
11.82341.16290.69412.25330.35643.8905-0.04260.32010.1848-0.1307-0.00680.089-0.52570.17430.07630.5282-0.1337-0.08870.30750.04250.383547.0754-34.3053-3.3237
21.81120.650.54171.0427-0.50633.7444-0.30260.3635-0.0497-0.14070.2679-0.2616-0.1177-0.38970.02190.6726-0.3448-0.21150.87430.07970.593135.6095-48.0844-23.4612
31.72730.60870.85691.69060.1513.5505-0.3864-0.0740.1361-0.32030.09040.1275-0.3565-0.1264-0.0490.363-0.0107-0.05960.37860.03760.472939.9452-40.5345-5.0435
45.7524-3.53291.4543.8329-2.0093.05350.54131.8426-0.0834-1.8768-0.6343-0.1083-0.5190.2886-0.13020.8466-0.1935-0.08760.7268-0.0190.41652.4546-44.1928-18.5359
52.5069-1.8127-0.28331.50080.56475.03320.22330.5408-0.6317-0.1990.15880.46431.4394-0.11090.26870.4979-0.1062-0.07530.36890.01670.509345.8535-58.2774-5.3899
61.9064-0.3693-0.15623.0913-0.45043.66060.00260.2361-0.309-0.22630.0347-0.00680.01970.4624-0.01670.2021-0.0994-0.05680.2667-0.01310.322351.4735-50.5023-3.8908
73.12040.0372-2.5822.7093-0.49376.20390.06941.3759-0.7789-0.82550.166-0.06331.4377-0.88790.08190.5576-0.0606-0.11030.4316-0.17250.510751.8512-59.2908-7.4025
85.00190.76851.48330.642-0.76632.3342-0.50321.143-1.4479-0.26070.42140.68211.5079-0.1547-0.84450.9564-0.0169-0.0840.5765-0.36870.994753.9483-62.6161-12.8067
90.13040.25-0.3230.9743-1.08852.06730.3461-0.1254-0.0406-0.5471-0.6404-0.4643-0.28411.02920.15620.5491-0.05880.10910.6880.08280.433461.0998-35.22541.2133
101.4585-0.83380.24593.4441-0.5934.582-0.7839-1.1017-0.02190.65810.61720.5947-0.0684-0.30190.0070.3728-0.03410.0240.43480.0040.415145.2761-38.540810.532
113.35821.66071.09872.1346-0.89061.9260.09340.28290.5427-0.0853-1.04040.1903-1.071-0.4318-0.1940.92120.4842-0.3230.90240.05980.946631.0659-32.7354-8.6174
124.0535-3.63423.30053.5833-3.07653.00040.2979-0.01751.03150.227-0.72360.0266-0.0778-0.6083-0.24081.0110.0362-0.21140.6775-0.17990.87730.0853-38.9254-4.6485
132.36941.29650.55822.1062-0.66635.37280.28260.30380.6642-0.17810.63181.2547-0.1119-2.06370.81530.2789-0.5939-0.62991.1344-0.00260.197832.6069-37.7694-33.8076
141.7485-0.74311.0851.60720.21672.51060.01211.46510.3141-1.37390.12280.17650.2909-0.61140.12190.7173-0.3669-0.14061.02720.2520.361539.2266-32.8357-41.7325
152.049-1.72780.91145.692-4.54986.1631-0.24831.36330.8834-0.95630.480.8566-0.4318-1.7928-0.54070.9715-0.2684-0.31711.34950.26950.717833.7934-28.8371-43.8618
162.96510.31271.07663.8192-0.78434.98930.01341.0370.3744-0.7610.17190.3947-0.6814-0.86520.05150.8522-0.2614-0.17031.11690.33240.846539.8681-28.027-47.034
174.2425-2.41711.34184.51430.77681.17050.45830.93580.5045-1.17890.4278-0.50860.5294-0.46410.55921.369-0.59340.00621.40630.25570.753146.0724-28.7737-49.0696
182.79030.15670.53632.11130.65161.70390.05691.46710.9372-1.45520.79240.29310.38570.31210.08491.8551-0.24110.23811.35240.2990.785946.2153-28.8172-55.416
199.74350.8013-0.39947.3328-0.04941.8124-0.74470.21750.9642-0.55420.18511.4482-1.71810.07450.00830.88950.1096-0.06630.8461-0.11381.073429.8954-22.8824-27.2943
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 66:81)
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 82:92)
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 93:128)
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 129:143)
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 144:154)
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 155:217)
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 218:235)
8X-RAY DIFFRACTION8CHAIN A AND (RESSEQ 236:248)
9X-RAY DIFFRACTION9CHAIN C AND (RESSEQ 318:328)
10X-RAY DIFFRACTION10CHAIN C AND (RESSEQ 329:339)
11X-RAY DIFFRACTION11CHAIN C AND (RESSEQ 362:370)
12X-RAY DIFFRACTION12CHAIN C AND (RESSEQ 371:376)
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 69:128)
14X-RAY DIFFRACTION14CHAIN B AND (RESSEQ 129:170)
15X-RAY DIFFRACTION15CHAIN B AND (RESSEQ 171:187)
16X-RAY DIFFRACTION16CHAIN B AND (RESSEQ 188:218)
17X-RAY DIFFRACTION17CHAIN B AND (RESSEQ 219:234)
18X-RAY DIFFRACTION18CHAIN B AND (RESSEQ 235:248)
19X-RAY DIFFRACTION19CHAIN D AND (RESSEQ 325:339)

+
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