[English] 日本語
Yorodumi
- PDB-5me7: Crystal Structure of eiF4E from C. melo -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5me7
TitleCrystal Structure of eiF4E from C. melo
ComponentsEukaryotic transcription initiation factor 4E
KeywordsTRANSLATION / eIF4E / C. melo
Function / homology
Function and homology information


translation initiation factor activity / translational initiation / defense response to virus / RNA binding / nucleus / 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
Eukaryotic translation initiation factor 4E-1
Similarity search - Component
Biological speciesCucumis melo (muskmelon)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsQuerol-Audi, J. / Silva, C. / Miras, M. / Aranda-Regules, M. / Verdaguer, N.
Funding support Spain, 1items
OrganizationGrant numberCountry
MINECOAGL2015-65838 Spain
CitationJournal: Plant Physiol. / Year: 2017
Title: Structure of eIF4E in Complex with an eIF4G Peptide Supports a Universal Bipartite Binding Mode for Protein Translation.
Authors: Miras, M. / Truniger, V. / Silva, C. / Verdaguer, N. / Aranda, M.A. / Querol-Audi, J.
History
DepositionNov 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)85,8569
Polymers85,3964
Non-polymers4605
Water2,558142
1
A: Eukaryotic transcription initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4412
Polymers21,3491
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Eukaryotic transcription initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4412
Polymers21,3491
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Eukaryotic transcription initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6254
Polymers21,3491
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Eukaryotic transcription initiation factor 4E


Theoretical massNumber of molelcules
Total (without water)21,3491
Polymers21,3491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.746, 108.957, 122.143
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAMETMETAA53 - 2344 - 185
21ALAALAMETMETBB53 - 2344 - 185
12ASNASNVALVALAA51 - 2352 - 186
22ASNASNVALVALCC51 - 2352 - 186
13ALAALAVALVALAA52 - 2353 - 186
23ALAALAVALVALDD52 - 2353 - 186
14ALAALAVALVALBB53 - 2354 - 186
24ALAALAVALVALCC53 - 2354 - 186
15ALAALAVALVALBB53 - 2354 - 186
25ALAALAVALVALDD53 - 2354 - 186
16ALAALAVALVALCC52 - 2353 - 186
26ALAALAVALVALDD52 - 2353 - 186

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
Eukaryotic transcription initiation factor 4E / Eukaryotic translation initiation factor 4E


Mass: 21348.967 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cucumis melo (muskmelon) / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Rosetta / References: UniProt: Q00LS8
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C3H8O3 / Source: (gene. exp.) Cucumis melo (muskmelon) / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Rosetta
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: sodium potassium tartrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.98 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2014
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→81.31 Å / Num. obs: 39619 / % possible obs: 99.3 % / Redundancy: 3.7 % / Rsym value: 0.103 / Net I/av σ(I): 4 / Net I/σ(I): 7.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.2-2.323.60.3842197.8
2.32-2.463.80.2822.6199.7
2.46-2.633.70.2123.4199.8
2.63-2.843.60.1534.6199.6
2.84-3.113.80.1165.4199.9
3.11-3.483.70.0955.8199.4
3.48-4.023.70.0896.2199.4
4.02-4.923.70.0866.5199.3
4.92-6.963.50.0856.6199.3
6.96-47.083.40.0875.8198.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
SCALA3.3.21data scaling
XDSdata reduction
PDB_EXTRACT3.2data extraction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.941 / SU B: 12.595 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.27 / ESU R Free: 0.19 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21392 1985 5 %RANDOM
Rwork0.18671 ---
obs0.1881 37628 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 50.734 Å2
Baniso -1Baniso -2Baniso -3
1--2.16 Å20 Å20 Å2
2--1.95 Å20 Å2
3---0.21 Å2
Refinement stepCycle: 1 / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5708 0 30 142 5880
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0195920
X-RAY DIFFRACTIONr_bond_other_d0.0120.025337
X-RAY DIFFRACTIONr_angle_refined_deg1.9511.9028024
X-RAY DIFFRACTIONr_angle_other_deg1.917312290
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8025695
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.52524.348299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.37715930
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.8611519
X-RAY DIFFRACTIONr_chiral_restr0.1310.2803
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0216744
X-RAY DIFFRACTIONr_gen_planes_other0.0110.021505
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7962.6972804
X-RAY DIFFRACTIONr_mcbond_other1.7922.6962803
X-RAY DIFFRACTIONr_mcangle_it2.8454.0313491
X-RAY DIFFRACTIONr_mcangle_other2.8464.0313492
X-RAY DIFFRACTIONr_scbond_it2.5823.0423116
X-RAY DIFFRACTIONr_scbond_other2.5823.0423116
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.084.424534
X-RAY DIFFRACTIONr_long_range_B_refined5.89721.9136584
X-RAY DIFFRACTIONr_long_range_B_other5.88621.8196548
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A185640.11
12B185640.11
21A188140.09
22C188140.09
31A184380.1
32D184380.1
41B183700.1
42C183700.1
51B182640.11
52D182640.11
61C179520.1
62D179520.1
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 139 -
Rwork0.26 2619 -
obs--95.56 %
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)
12.342-0.7278-1.25122.070.81273.24260.03990.3044-0.0624-0.1586-0.16670.20820.132-0.35590.12680.0504-0.0012-0.03630.0964-0.05620.1091-14.78242.9772-16.7989
21.90070.1977-0.01573.4873-0.07211.62670.03810.159-0.0683-0.1111-0.0186-0.1550.02750.2064-0.01960.00610.0132-0.00460.13590.00890.1104-41.994123.5281-14.9446
32.63720.11080.03572.3616-0.1132.7617-0.005-0.02160.017-0.0383-0.02650.2771-0.1554-0.18830.03150.04110.0028-0.00970.0620.04090.1352-10.843841.0084-20.4629
42.0617-0.76650.30393.3286-0.26442.004-0.1262-0.33460.35890.4209-0.01170.039-0.4806-0.07320.13790.58360.0005-0.03650.2498-0.07230.2372-18.565116.0251-53.013
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A51 - 235
2X-RAY DIFFRACTION2B53 - 235
3X-RAY DIFFRACTION3C51 - 235
4X-RAY DIFFRACTION4D51 - 235

+
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