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- EMDB-10295: Human endogenous retrovirus (HML2) mature capsid assembly, T=1 ic... -

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Basic information

Entry
Database: EMDB / ID: EMD-10295
TitleHuman endogenous retrovirus (HML2) mature capsid assembly, T=1 icosahedron
Map dataSharpened map
Sample
  • Complex: Human endogenous retrovirus (HML2) mature capsid assembly, T=1 icosahedron
    • Protein or peptide: Endogenous retrovirus group K member 24 Gag polyprotein
Function / homology
Function and homology information


viral process / nucleic acid binding / structural molecule activity / zinc ion binding / plasma membrane
Similarity search - Function
GAG-polyprotein viral zinc-finger / Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / gag protein p24 N-terminal domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal ...GAG-polyprotein viral zinc-finger / Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / gag protein p24 N-terminal domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein / 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
Endogenous retrovirus group K member 24 Gag polyprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsActon OJH / Taylor IA / Rosenthal PB
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
The Francis Crick InstituteFC001143 United Kingdom
Wellcome Trust108014/Z/15/Z United Kingdom
The Francis Crick InstituteFC001178 United Kingdom
CitationJournal: 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.
History
DepositionSep 8, 2019-
Header (metadata) releaseOct 30, 2019-
Map releaseJan 1, 2020-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6.4
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 6.4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ssj
  • Surface level: 6.4
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6ssj
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10295.png

Downloads & links

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Map

FileDownload / File: emd_10295.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Voxel sizeX=Y=Z: 1.09 Å
Density
Contour LevelBy AUTHOR: 6.4 / Movie #1: 6.4
Minimum - Maximum-41.70136 - 70.23241
Average (Standard dev.)-0.01720201 (±1.8068129)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions576576576
Spacing576576576
CellA=B=C: 627.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z576576576
origin x/y/z0.0000.0000.000
length x/y/z627.840627.840627.840
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS576576576
D min/max/mean-41.70170.232-0.017

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Supplemental data

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Additional map: Unsharpened map

Fileemd_10295_additional.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human endogenous retrovirus (HML2) mature capsid assembly, T=1 ic...

EntireName: Human endogenous retrovirus (HML2) mature capsid assembly, T=1 icosahedron
Components
  • Complex: Human endogenous retrovirus (HML2) mature capsid assembly, T=1 icosahedron
    • Protein or peptide: Endogenous retrovirus group K member 24 Gag polyprotein

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Supramolecule #1: Human endogenous retrovirus (HML2) mature capsid assembly, T=1 ic...

SupramoleculeName: Human endogenous retrovirus (HML2) mature capsid assembly, T=1 icosahedron
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
Molecular weightExperimental: 1.7 MDa

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Macromolecule #1: Endogenous retrovirus group K member 24 Gag polyprotein

MacromoleculeName: Endogenous retrovirus group K member 24 Gag polyprotein
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.570488 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: PVTLEPMPPG EGAQEGEPPT VEARYKSFSI KMLKDMKEGV KQYGPNSPYM RTLLDSIAHG HRLIPYDWEI LAKSSLSPSQ FLQFKTWWI DGVQEQVRRN RAANPPVNID ADQLLGIGQN WSTISQQALM QNEAIEQVRA ICLRAWEKIQ DPGSACPSFN T VRQGSKEP ...String:
PVTLEPMPPG EGAQEGEPPT VEARYKSFSI KMLKDMKEGV KQYGPNSPYM RTLLDSIAHG HRLIPYDWEI LAKSSLSPSQ FLQFKTWWI DGVQEQVRRN RAANPPVNID ADQLLGIGQN WSTISQQALM QNEAIEQVRA ICLRAWEKIQ DPGSACPSFN T VRQGSKEP YPDFVARLQD VAQKSIADEK ARKVIVELMA YENANPECQS AIKPLKGKVP AGSDVISEYV KACDGIGGAM HK AMLMAQL E

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration16 mg/mL
BufferpH: 8
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 10935 / Average exposure time: 60.0 sec. / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 64731

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER / Overall B value: 90 / Target criteria: map vs model FSC
Output model

PDB-6ssj:
Human endogenous retrovirus (HML2) mature capsid assembly, T=1 icosahedron

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