[English] 日本語
Yorodumi
- PDB-2f8b: NMR structure of the C-terminal domain (dimer) of HPV45 oncoprotein E7 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2f8b
TitleNMR structure of the C-terminal domain (dimer) of HPV45 oncoprotein E7
ComponentsProtein E7
KeywordsONCOPROTEIN / VIRUS/VIRAL PROTEIN / E7 / DIMER / HPV / ZINC BINDING / VIRUS-VIRAL PROTEIN COMPLEX
Function / homology
Function and homology information


symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / host cell cytoplasm / DNA-binding transcription factor activity / protein domain specific binding / DNA-templated transcription / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / DNA binding / metal ion binding
Similarity search - Function
Double Stranded RNA Binding Domain - #330 / Papillomavirus E7 / E7 protein, Early protein / Double Stranded RNA Binding Domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHuman papillomavirus type 45
MethodSOLUTION NMR / distance geometry, simulated annealing by CYANA, energy minimisation by OPAL
AuthorsOhlenschlager, O. / Gorlach, M.
CitationJournal: Oncogene / Year: 2006
Title: Solution structure of the partially folded high-risk human papilloma virus 45 oncoprotein E7.
Authors: Ohlenschlager, O. / Seiboth, T. / Zengerling, H. / Briese, L. / Marchanka, A. / Ramachandran, R. / Baum, M. / Korbas, M. / Meyer-Klaucke, W. / Durst, M. / Gorlach, M.
History
DepositionDec 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein E7
B: Protein E7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7414
Polymers12,6112
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100target function
RepresentativeModel #1closest to the average

-
Components

#1: Protein Protein E7


Mass: 6305.291 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, residues 55-106
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus type 45 / Genus: Alphapapillomavirus / Species: Human papillomavirus - 18 / Strain: HPV TYPE 45 / Gene: E7 / Plasmid: pET15B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-RIL / References: UniProt: P21736
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
131HNHA
1423D 13C-F1-filtered,13C-F3-edited NOESY-HSQC
NMR detailsText: The structure was determined using heteronuclear triple resonance NMR spectroscopy.

-
Sample preparation

Details
Solution-IDContentsSolvent system
11mM E7 U-15N, 20mM d-TRIS, 100mM NaCl, 90% H2O, 10%D2O90% H2O/10% D2O
21mM E7 U-15N,13C, 20mM d-TRIS, 100mM NaCl, 90% H2O, 10%D2O90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7.4 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502
Varian INOVAVarianINOVA8003

-
Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1Varian Inc.processing
XEASY1.3.9Bartelsdata analysis
CYANA2.1Guntertstructure solution
OPAL2.6Luginbuhlrefinement
RefinementMethod: distance geometry, simulated annealing by CYANA, energy minimisation by OPAL
Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 15

+
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