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

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Basic information

Entry
Database: PDB / ID: 6ssk
TitleHuman endogenous retrovirus (HML2) mature capsid assembly, D5 capsule
ComponentsEndogenous retrovirus group K member 24 Gag polyprotein
KeywordsVIRAL PROTEIN / Mature retrovirus capsid assembly
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.18 Å
AuthorsActon, O.J.H. / Taylor, I.A. / Rosenthal, P.B.
Funding support United Kingdom, 3items
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, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: Endogenous retrovirus group K member 24 Gag polyprotein
B: Endogenous retrovirus group K member 24 Gag polyprotein
C: Endogenous retrovirus group K member 24 Gag polyprotein
D: Endogenous retrovirus group K member 24 Gag polyprotein
E: Endogenous retrovirus group K member 24 Gag polyprotein
F: Endogenous retrovirus group K member 24 Gag polyprotein
G: Endogenous retrovirus group K member 24 Gag polyprotein
H: Endogenous retrovirus group K member 24 Gag polyprotein
I: Endogenous retrovirus group K member 24 Gag polyprotein


Theoretical massNumber of molelcules
Total (without water)248,1349
Polymers248,1349
Non-polymers00
Water0
1
A: Endogenous retrovirus group K member 24 Gag polyprotein
B: Endogenous retrovirus group K member 24 Gag polyprotein
C: Endogenous retrovirus group K member 24 Gag polyprotein
D: Endogenous retrovirus group K member 24 Gag polyprotein
E: Endogenous retrovirus group K member 24 Gag polyprotein
F: Endogenous retrovirus group K member 24 Gag polyprotein
G: Endogenous retrovirus group K member 24 Gag polyprotein
H: Endogenous retrovirus group K member 24 Gag polyprotein
I: Endogenous retrovirus group K member 24 Gag polyprotein
x 10


Theoretical massNumber of molelcules
Total (without water)2,481,34490
Polymers2,481,34490
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation9
MethodUCSF CHIMERA

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Components

#1: Protein
Endogenous retrovirus group K member 24 Gag polyprotein / HERV-K101 Gag protein / HERV-K_22q11.21 provirus ancestral Gag polyprotein / Gag polyprotein


Mass: 27570.488 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERVK-24 / Production host: Escherichia coli (E. coli) / References: UniProt: P63145

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human endogenous retrovirus (HML2) mature capsid assembly, D5 capsule
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 2.5 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 16 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 60 sec. / Electron dose: 30 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10935

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM software
IDNameVersionCategory
1RELION2.1particle selection
2EPUimage acquisition
4CTFFIND4.1CTF correction
7Coot0.9.8model fitting
9RELION2.1initial Euler assignment
10RELION2.1final Euler assignment
11RELION2.1classification
12cisTEM3D reconstruction
19PHENIX1.14model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D5 (2x5 fold dihedral)
3D reconstructionResolution: 3.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 93221 / Symmetry type: POINT
Atomic model buildingB value: 90 / Protocol: OTHER / Space: REAL / Target criteria: map vs model FSC
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00815931
ELECTRON MICROSCOPYf_angle_d0.85521568
ELECTRON MICROSCOPYf_dihedral_angle_d6.75310239
ELECTRON MICROSCOPYf_chiral_restr0.0562334
ELECTRON MICROSCOPYf_plane_restr0.0092811

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