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- PDB-32zb: Cryo-EM structure of native, mature HERV-K hexameric capsomer -

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Basic information

Entry
Database: PDB / ID: 32zb
TitleCryo-EM structure of native, mature HERV-K hexameric capsomer
ComponentsEndogenous retrovirus group K member 8 Gag polyprotein
KeywordsVIRAL PROTEIN / Viral Capsid / Human Endogenous Retrovirus
Function / homology
Function and homology information


viral process / nucleic acid binding / 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
INOSITOL HEXAKISPHOSPHATE / Endogenous retrovirus group K member 8 Gag polyprotein
Similarity search - Component
Biological speciesHuman endogenous retrovirus K
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.24 Å
AuthorsLyu, C. / Shen, Y. / Zhang, P.
Funding support United Kingdom, China, 2items
OrganizationGrant numberCountry
Wellcome Trust311427/Z/24/Z United Kingdom
Chinese Scholarship CouncilCNR00051 China
CitationJournal: To Be Published
Title: Structural Insights into Native, Mature Human Endogenous Retrovirus K (HERV-K) Capsids
Authors: Lyu, C. / Peeples, C.A. / Zhang, Z. / Shen, Y. / Hou, Z. / Harding, E.F. / Hope, J. / Perilla, J.R. / Katzourakis, A. / Zhang, P.
History
DepositionAug 2, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 19, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endogenous retrovirus group K member 8 Gag polyprotein
B: Endogenous retrovirus group K member 8 Gag polyprotein
C: Endogenous retrovirus group K member 8 Gag polyprotein
D: Endogenous retrovirus group K member 8 Gag polyprotein
E: Endogenous retrovirus group K member 8 Gag polyprotein
F: Endogenous retrovirus group K member 8 Gag polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,7757
Polymers157,1156
Non-polymers6601
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Endogenous retrovirus group K member 8 Gag polyprotein / HERV-K115 Gag protein / HERV-K_8p23.1 provirus ancestral Gag polyprotein / Gag polyprotein


Mass: 26185.752 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human endogenous retrovirus K / Gene: ERVK-8 / Production host: Homo sapiens (human) / References: UniProt: P62685
#2: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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 K / Type: VIRUS / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Human endogenous retrovirus K
Source (recombinant)Organism: Homo sapiens (human)
Details of virusEmpty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
12cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1827160
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 201280 / Symmetry type: POINT
Atomic model buildingB value: 193.1 / Space: REAL

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