[English] 日本語
Yorodumi
- PDB-5aby: Complex of C. elegans eIF4E-3 with the 4E-binding protein Mextli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5aby
TitleComplex of C. elegans eIF4E-3 with the 4E-binding protein Mextli
Components
  • 4E-BINDING PROTEIN MEXTLI
  • EUKARYOTIC TRANSLATION INITIATION FACTOR 4E-3
KeywordsTRANSLATION / GENE REGULATION / CAP BINDING PROTEIN / 4E BINDING PROTEIN
Function / homology
Function and homology information


translation initiation complex / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / regulation of formation of translation initiation ternary complex / ISG15 antiviral mechanism / L13a-mediated translational silencing of Ceruloplasmin expression / Translation initiation complex formation / Ribosomal scanning and start codon recognition / 21U-RNA metabolic process / RNA cap binding complex / piRNA processing ...translation initiation complex / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / regulation of formation of translation initiation ternary complex / ISG15 antiviral mechanism / L13a-mediated translational silencing of Ceruloplasmin expression / Translation initiation complex formation / Ribosomal scanning and start codon recognition / 21U-RNA metabolic process / RNA cap binding complex / piRNA processing / eukaryotic initiation factor 4E binding / eukaryotic translation initiation factor 4F complex / RNA 7-methylguanosine cap binding / embryo development ending in birth or egg hatching / translation initiation factor activity / positive regulation of translation / translational initiation / regulation of translation / perinuclear region of cytoplasm / RNA binding / cytoplasm
Similarity search - Function
Eukaryotic translation initiation factor 4E-binding protein Mextli / 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 / KH domain / K Homology domain, type 1 ...Eukaryotic translation initiation factor 4E-binding protein Mextli / 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 / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Eukaryotic translation initiation factor 4E-3 / Eukaryotic translation initiation factor 4E-binding protein Mextli homolog
Similarity search - Component
Biological speciesCAENORHABDITIS ELEGANS (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPeter, D. / Weichenrieder, O.
CitationJournal: Genes Dev. / Year: 2015
Title: Mextli Proteins Use Both Canonical Bipartite and Novel Tripartite Binding Modes to Form Eif4E Complexes that Display Differential Sensitivity to 4E-BP Regulation
Authors: Peter, D. / Weber, R. / Koene, C. / Chung, M.-Y. / Ebertsch, L. / Truffault, V. / Weichenrieder, O. / Igreja, C. / Izaurralde, E.
History
DepositionAug 9, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E-3
B: 4E-BINDING PROTEIN MEXTLI
C: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E-3
D: 4E-BINDING PROTEIN MEXTLI
E: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E-3
F: 4E-BINDING PROTEIN MEXTLI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,67911
Polymers81,3546
Non-polymers3255
Water7,819434
1
A: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E-3
B: 4E-BINDING PROTEIN MEXTLI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2103
Polymers27,1182
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-17.9 kcal/mol
Surface area11330 Å2
MethodPISA
2
C: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E-3
D: 4E-BINDING PROTEIN MEXTLI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2595
Polymers27,1182
Non-polymers1413
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-29.1 kcal/mol
Surface area11460 Å2
MethodPISA
3
E: EUKARYOTIC TRANSLATION INITIATION FACTOR 4E-3
F: 4E-BINDING PROTEIN MEXTLI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2103
Polymers27,1182
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-18.3 kcal/mol
Surface area11400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.240, 157.580, 55.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11C-2051-

HOH

-
Components

#1: Protein EUKARYOTIC TRANSLATION INITIATION FACTOR 4E-3 / EIF-4E-3 / EIF4E-3 / EIF-4F 25 KDA SUBUNIT / MRNA CAP-BINDING PROTEIN


Mass: 22377.488 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 30-215
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAENORHABDITIS ELEGANS (invertebrata) / Plasmid: PETMCN (PNYC) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: O61955
#2: Protein/peptide 4E-BINDING PROTEIN MEXTLI


Mass: 4740.511 Da / Num. of mol.: 3 / Fragment: UNP RESIDUES 471-507
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAENORHABDITIS ELEGANS (invertebrata) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: Q9XW13
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST FOUR RESIDUES OF CHAINS A, C, E REMAIN FROM THE EXPRESSION TAG. THE FIRST FOUR RESIDUES ...THE FIRST FOUR RESIDUES OF CHAINS A, C, E REMAIN FROM THE EXPRESSION TAG. THE FIRST FOUR RESIDUES OF CHAINS B, D, F REMAIN FROM THE EXPRESSION TAG.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growpH: 8 / Details: 0.1M TRIS, PH=8.0, 0.2M MGCL2, 17% PEG6000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00001
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2015 / Details: DYNAMICALLY BENDABLE MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 1.95→47.2 Å / Num. obs: 58918 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Biso Wilson estimate: 29.49 Å2 / Rsym value: 0.12 / Net I/σ(I): 11.8
Reflection shellResolution: 1.95→2 Å / Redundancy: 8.6 % / Mean I/σ(I) obs: 2 / Rsym value: 1.17 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5ABX

5abx


Resolution: 1.95→45.522 Å / SU ML: 0.2 / σ(F): 1.36 / Phase error: 20.91 / Stereochemistry target values: ML
Details: HYDROGENS WERE REFINED IN THE RIDING POSITIONS. THE FOLLOWING RESIDUES ARE DISORDERED. CHAIN A, RESIDUES 203 TO 209. CHAIN C, RESIDUES 203 TO 208. CHAIN E, RESIDUES 202 TO 209. CHAIN F, RESIDUE 507.
RfactorNum. reflection% reflection
Rfree0.2071 2937 5 %
Rwork0.1719 --
obs0.1737 58873 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.1 Å2
Refinement stepCycle: LAST / Resolution: 1.95→45.522 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5464 0 20 434 5918
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085604
X-RAY DIFFRACTIONf_angle_d1.0457574
X-RAY DIFFRACTIONf_dihedral_angle_d13.3352109
X-RAY DIFFRACTIONf_chiral_restr0.042809
X-RAY DIFFRACTIONf_plane_restr0.004963
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.9820.27471410.23832635X-RAY DIFFRACTION100
1.982-2.01610.29131270.2272618X-RAY DIFFRACTION100
2.0161-2.05280.28291350.22062643X-RAY DIFFRACTION100
2.0528-2.09230.26251600.21642600X-RAY DIFFRACTION100
2.0923-2.1350.27331400.21012651X-RAY DIFFRACTION100
2.135-2.18140.24651430.19252577X-RAY DIFFRACTION100
2.1814-2.23220.23931390.19112657X-RAY DIFFRACTION100
2.2322-2.2880.22921330.17822645X-RAY DIFFRACTION100
2.288-2.34980.23591510.18222607X-RAY DIFFRACTION100
2.3498-2.4190.25191420.17842650X-RAY DIFFRACTION100
2.419-2.49710.18711500.1742630X-RAY DIFFRACTION100
2.4971-2.58630.21241110.16562657X-RAY DIFFRACTION100
2.5863-2.68980.21451210.17142673X-RAY DIFFRACTION100
2.6898-2.81220.25541220.17872677X-RAY DIFFRACTION100
2.8122-2.96050.23041440.17872663X-RAY DIFFRACTION100
2.9605-3.14590.21751230.18162692X-RAY DIFFRACTION100
3.1459-3.38870.22311490.18032657X-RAY DIFFRACTION100
3.3887-3.72960.18541310.1592716X-RAY DIFFRACTION100
3.7296-4.2690.1791530.1422706X-RAY DIFFRACTION100
4.269-5.37710.16231510.13542725X-RAY DIFFRACTION100
5.3771-45.53440.17981710.18412857X-RAY DIFFRACTION100

+
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