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- PDB-6sai: NMR solution structure of Hml-2 C-terminal dimer domain -

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Basic information

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


viral process / nucleic acid binding / zinc ion binding
Similarity search - Function
GAG-polyprotein viral zinc-finger / : / gag protein p24 N-terminal domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily ...GAG-polyprotein viral zinc-finger / : / gag protein p24 N-terminal domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-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
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gag protein
B: Gag protein


Theoretical massNumber of molelcules
Total (without water)20,1872
Polymers20,1872
Non-polymers00
Water00
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

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Components

#1: Protein Gag protein


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

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Experimental details

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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

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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 / PH err: 0.1 / Pressure: 1 mmHg / Pressure err: 0.01 / Temperature: 298 K / Temperature err: 0.2

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NMR measurement

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

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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

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