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- EMDB-10296: Human endogenous retrovirus (HML2) mature capsid assembly, D5 capsule -

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Basic information

Entry
Database: EMDB / ID: EMD-10296
TitleHuman endogenous retrovirus (HML2) mature capsid assembly, D5 capsule
Map dataSharpened map
Sample
  • Complex: Human endogenous retrovirus (HML2) mature capsid assembly, D5 capsule
    • Protein or peptide: Endogenous retrovirus group K member 24 Gag polyprotein
KeywordsMature retrovirus capsid assembly / VIRAL PROTEIN
Function / homology
Function and homology information


nucleic acid binding / viral translational frameshifting / structural molecule activity / zinc ion binding / plasma membrane
Similarity search - Function
Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / 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 / Retroviral matrix protein ...Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / 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 / 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: 3.18 Å
AuthorsActon OJH / Taylor IA
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
The Francis Crick InstituteFC001143 United Kingdom
The Francis Crick InstituteFC001178 United Kingdom
Wellcome Trust108014/Z/15/Z 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 23, 2019-
Map releaseJan 1, 2020-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5.7
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 5.7
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ssk
  • Surface level: 5.7
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6ssk
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10296.png

Downloads & links

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Map

FileDownload / File: emd_10296.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 576 pix.
= 627.84 Å		1.09 Å/pix.
x 576 pix.
= 627.84 Å		1.09 Å/pix.
x 576 pix.
= 627.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.7 / Movie #1: 5.7
Minimum - Maximum-34.261012999999998 - 60.440820000000002
Average (Standard dev.)-0.015153172 (±1.8994232)
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-34.26160.441-0.015

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Supplemental data

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Additional map: Unsharpened map

Fileemd_10296_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, D5 capsule

EntireName: Human endogenous retrovirus (HML2) mature capsid assembly, D5 capsule
Components
  • Complex: Human endogenous retrovirus (HML2) mature capsid assembly, D5 capsule
    • Protein or peptide: Endogenous retrovirus group K member 24 Gag polyprotein

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Supramolecule #1: Human endogenous retrovirus (HML2) mature capsid assembly, D5 capsule

SupramoleculeName: Human endogenous retrovirus (HML2) mature capsid assembly, D5 capsule
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 2.5 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: 9 / 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

UniProtKB: Endogenous retrovirus group K member 24 Gag polyprotein

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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 / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: D5 (2x5 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM / Number images used: 93221
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)

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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-6ssk:
Human endogenous retrovirus (HML2) mature capsid assembly, D5 capsule

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