[English] 日本語
Yorodumi
- PDB-7d8b: Engineering Disulphide-Free Autonomous Antibody VH Domains to mod... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7d8b
TitleEngineering Disulphide-Free Autonomous Antibody VH Domains to modulate intracellular pathways
Components
  • Eukaryotic translation initiation factor 4E
  • VH-S4
KeywordsRNA BINDING PROTEIN / Cap dependent translation / Complex / VH domain
Function / homology
Function and homology information


eukaryotic initiation factor 4G binding / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / regulation of translation at postsynapse, modulating synaptic transmission / RNA cap binding / eukaryotic translation initiation factor 4F complex / chromatoid body / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / mRNA cap binding / Deadenylation of mRNA / RNA 7-methylguanosine cap binding ...eukaryotic initiation factor 4G binding / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / regulation of translation at postsynapse, modulating synaptic transmission / RNA cap binding / eukaryotic translation initiation factor 4F complex / chromatoid body / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / mRNA cap binding / Deadenylation of mRNA / RNA 7-methylguanosine cap binding / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / Transport of Mature mRNA Derived from an Intronless Transcript / RISC complex / Ribosomal scanning and start codon recognition / stem cell population maintenance / negative regulation of neuron differentiation / Translation initiation complex formation / mTORC1-mediated signalling / GTP hydrolysis and joining of the 60S ribosomal subunit / cellular response to dexamethasone stimulus / L13a-mediated translational silencing of Ceruloplasmin expression / behavioral fear response / mRNA export from nucleus / translation initiation factor activity / positive regulation of mitotic cell cycle / translational initiation / P-body / G1/S transition of mitotic cell cycle / ISG15 antiviral mechanism / cytoplasmic ribonucleoprotein granule / neuron differentiation / cytoplasmic stress granule / regulation of translation / DNA-binding transcription factor binding / postsynapse / negative regulation of translation / nuclear speck / perinuclear region of cytoplasm / glutamatergic synapse / enzyme binding / RNA binding / extracellular exosome / nucleus / cytoplasm / cytosol
Similarity search - Function
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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Eukaryotic translation initiation factor 4E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsFrosi, Y. / Lin, Y.C. / Jiang, S. / Brown, C.J.
CitationJournal: Nat Commun / Year: 2022
Title: Engineering an autonomous VH domain to modulate intracellular pathways and to interrogate the eIF4F complex.
Authors: Frosi, Y. / Lin, Y.C. / Shimin, J. / Ramlan, S.R. / Hew, K. / Engman, A.H. / Pillai, A. / Yeung, K. / Cheng, Y.X. / Cornvik, T. / Nordlund, P. / Goh, M. / Lama, D. / Gates, Z.P. / Verma, C.S. ...Authors: Frosi, Y. / Lin, Y.C. / Shimin, J. / Ramlan, S.R. / Hew, K. / Engman, A.H. / Pillai, A. / Yeung, K. / Cheng, Y.X. / Cornvik, T. / Nordlund, P. / Goh, M. / Lama, D. / Gates, Z.P. / Verma, C.S. / Thean, D. / Lane, D.P. / Asial, I. / Brown, C.J.
History
DepositionOct 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Derived calculations / Category: atom_type / citation / citation_author
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Eukaryotic translation initiation factor 4E
B: VH-S4
C: Eukaryotic translation initiation factor 4E
D: VH-S4


Theoretical massNumber of molelcules
Total (without water)84,5544
Polymers84,5544
Non-polymers00
Water1,838102
1
A: Eukaryotic translation initiation factor 4E
B: VH-S4


Theoretical massNumber of molelcules
Total (without water)42,2772
Polymers42,2772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-8 kcal/mol
Surface area15080 Å2
MethodPISA
2
C: Eukaryotic translation initiation factor 4E
D: VH-S4


Theoretical massNumber of molelcules
Total (without water)42,2772
Polymers42,2772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-8 kcal/mol
Surface area14770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.595, 140.394, 61.961
Angle α, β, γ (deg.)90.000, 104.037, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Eukaryotic translation initiation factor 4E / eIF4E / eIF-4F 25 kDa subunit / mRNA cap-binding protein


Mass: 25130.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF4E, EIF4EL1, EIF4F / Production host: Escherichia coli (E. coli) / References: UniProt: P06730
#2: Protein VH-S4


Mass: 17146.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.38 Å3/Da / Density % sol: 48.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.01M Tri-sodium citrate, 16% PEG 6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.46→70.197 Å / Num. obs: 28611 / % possible obs: 99.9 % / Redundancy: 7.7 % / Rsym value: 0.177 / Net I/σ(I): 3.6
Reflection shellResolution: 2.46→2.59 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4143 / Rsym value: 0.876

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V8W

2v8w


Resolution: 2.46→46.216 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.86 / SU B: 12.299 / SU ML: 0.275 / Cross valid method: FREE R-VALUE / ESU R: 0.509 / ESU R Free: 0.311
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2918 1450 5.072 %
Rwork0.25 27137 -
all0.252 --
obs-28587 99.871 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 34.813 Å2
Baniso -1Baniso -2Baniso -3
1-0.068 Å20 Å20.896 Å2
2---2.743 Å20 Å2
3---1.98 Å2
Refinement stepCycle: LAST / Resolution: 2.46→46.216 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4817 0 0 102 4919
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0134928
X-RAY DIFFRACTIONr_bond_other_d0.0010.0184595
X-RAY DIFFRACTIONr_angle_refined_deg1.1851.6356675
X-RAY DIFFRACTIONr_angle_other_deg1.0761.58410544
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.665604
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.79721.311267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.83515822
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5691539
X-RAY DIFFRACTIONr_chiral_restr0.0370.2633
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025598
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021220
X-RAY DIFFRACTIONr_nbd_refined0.1620.2765
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1680.24081
X-RAY DIFFRACTIONr_nbtor_refined0.1520.22287
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.22238
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2164
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1340.216
X-RAY DIFFRACTIONr_nbd_other0.1330.254
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2250.213
X-RAY DIFFRACTIONr_mcbond_it1.1753.6782434
X-RAY DIFFRACTIONr_mcbond_other1.1753.6782433
X-RAY DIFFRACTIONr_mcangle_it2.1075.5073029
X-RAY DIFFRACTIONr_mcangle_other2.1075.5073030
X-RAY DIFFRACTIONr_scbond_it0.9333.7652494
X-RAY DIFFRACTIONr_scbond_other0.9333.7652494
X-RAY DIFFRACTIONr_scangle_it1.6655.5913645
X-RAY DIFFRACTIONr_scangle_other1.6655.5913646
X-RAY DIFFRACTIONr_lrange_it3.22740.3595247
X-RAY DIFFRACTIONr_lrange_other3.18640.3165214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.46-2.5240.3671070.3131997X-RAY DIFFRACTION99.8576
2.524-2.5930.334990.2971935X-RAY DIFFRACTION100
2.593-2.6680.416850.31920X-RAY DIFFRACTION99.9501
2.668-2.750.347910.2771844X-RAY DIFFRACTION99.7423
2.75-2.840.2891060.2571789X-RAY DIFFRACTION99.8946
2.84-2.940.295970.281727X-RAY DIFFRACTION100
2.94-3.050.3810.2551655X-RAY DIFFRACTION99.9424
3.05-3.1750.292940.2491615X-RAY DIFFRACTION99.8831
3.175-3.3150.307920.2541522X-RAY DIFFRACTION99.8145
3.315-3.4770.267790.2431475X-RAY DIFFRACTION99.8715
3.477-3.6640.275690.2451423X-RAY DIFFRACTION99.933
3.664-3.8860.284720.2471310X-RAY DIFFRACTION99.6395
3.886-4.1540.258710.2311249X-RAY DIFFRACTION100
4.154-4.4850.246670.2051153X-RAY DIFFRACTION100
4.485-4.9110.221580.2051063X-RAY DIFFRACTION99.9109
4.911-5.4870.336510.227979X-RAY DIFFRACTION99.8062
5.487-6.330.366450.257851X-RAY DIFFRACTION99.7773
6.33-7.7370.347380.277747X-RAY DIFFRACTION99.8728
7.737-10.8760.231290.221559X-RAY DIFFRACTION99.8302
10.876-46.2160.254190.314324X-RAY DIFFRACTION98.5632

+
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