[English] 日本語
Yorodumi
- PDB-6sai: NMR solution structure of Hml-2 C-terminal dimer domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6sai
TitleNMR solution structure of Hml-2 C-terminal dimer domain
ComponentsGag proteinHIV-1 protease
KeywordsVIRAL PROTEIN / Human-endogenous-retroviruses / Retroviridae / Ortervirales.
Function / homology
Function and homology information


viral process / nucleic acid binding / zinc ion binding
Similarity search - Function
Retroviral nucleocapsid Gag protein p24, N-terminal / gag protein p24 N-terminal domain / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Biological speciesHuman endogenous retrovirus K
MethodSOLUTION NMR / simulated annealing
AuthorsNicastro, G. / Taylor, I.A. / Ball, N.J. / Ramos, A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
The Francis Crick InstituteFC001178 United Kingdom
Citation
Journal: Nat Commun / Year: 2019
Title: Structural basis for Fullerene geometry in a human endogenous retrovirus capsid.
Authors: Oliver Acton / Tim Grant / Giuseppe Nicastro / Neil J Ball / David C Goldstone / Laura E Robertson / Kasim Sader / Andrea Nans / Andres Ramos / Jonathan P Stoye / Ian A Taylor / Peter B Rosenthal /
Abstract: The HML2 (HERV-K) group constitutes the most recently acquired family of human endogenous retroviruses, with many proviruses less than one million years old. Many maintain intact open reading frames ...The HML2 (HERV-K) group constitutes the most recently acquired family of human endogenous retroviruses, with many proviruses less than one million years old. Many maintain intact open reading frames and provirus expression together with HML2 particle formation are observed in early stage human embryo development and are associated with pluripotency as well as inflammatory disease, cancers and HIV-1 infection. Here, we reconstruct the core structural protein (CA) of an HML2 retrovirus, assemble particles in vitro and employ single particle cryogenic electron microscopy (cryo-EM) to determine structures of four classes of CA Fullerene shell assemblies. These icosahedral and capsular assemblies reveal at high-resolution the molecular interactions that allow CA to form both pentamers and hexamers and show how invariant pentamers and structurally plastic hexamers associate to form the unique polyhedral structures found in retroviral cores.
#1: Journal: Proc Natl Acad Sci U S A. / Year: 2004
Title: Long-term reinfection of the human genome by endogenous retroviruses.
Authors: Belshaw, R.
History
DepositionJul 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Gag protein
B: Gag protein


Theoretical massNumber of molelcules
Total (without water)20,1872
Polymers20,1872
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1320 Å2
ΔGint-7 kcal/mol
Surface area8920 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Gag protein / HIV-1 protease


Mass: 10093.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human endogenous retrovirus K / Gene: gag / Production host: Escherichia coli (E. coli) / References: UniProt: P87891

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D HNCA
121isotropic23D CBCA(CO)NH
131isotropic23D HNCO
141isotropic13D 1H-13C NOESY aliphatic
161isotropic13D 1H-13C NOESY aromatic
151isotropic13D 1H-15N NOESY

-
Sample preparation

DetailsType: solution / Contents: 2.3 mM [U-13C; U-15N] Hml-2 Ctd, 90% H2O/10% D2O / Details: 20mM Tris pH 7, 50mM NaCl 0.5mM TCEP / Label: 13C15N_sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 2.3 mM / Component: Hml-2 Ctd / Isotopic labeling: [U-13C; U-15N]
Sample conditionsDetails: 20mM Tris pH 7, 50mM NaCl 0.5mM TCEP / Ionic strength: 50 mM / Ionic strength err: 0.2 / Label: conditions_1 / pH: 7.0 / PH err: 0.1 / Pressure: 1 mmHg / Pressure err: 0.01 / Temperature: 298 K / Temperature err: 0.2

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE8001
Bruker AVANCEBrukerAVANCE7002

-
Processing

NMR software
NameDeveloperClassification
ARIALinge, O'Donoghue and Nilgesrefinement
ARIALinge, O'Donoghue and Nilgesstructure calculation
XEASYBartels et al.chemical shift assignment
XEASYBartels et al.peak picking
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

+
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