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- PDB-9o4f: Pre-fusion Stabilized HERV-K Envelope Trimer Ectodomain -

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Basic information

Entry
Database: PDB / ID: 9o4f
TitlePre-fusion Stabilized HERV-K Envelope Trimer Ectodomain
Components
  • Surface protein
  • Transmembrane protein,Fibritin
KeywordsVIRAL PROTEIN / Human endogenous retrovirus K / glycoprotein / HERV-K / envelope / pre-fusion
Function / homology
Function and homology information


virion component / structural molecule activity / plasma membrane
Similarity search - Function
Retro-transcribing virus envelope glycoprotein / : / Retro-transcribing viruses envelope glycoprotein / Rec (regulator of expression encoded by corf) of HERV-K-113 / Fibritin C-terminal / Fibritin C-terminal region / Retroviral envelope protein / Retroviral envelope protein GP41-like
Similarity search - Domain/homology
Fibritin / Endogenous retrovirus group K member 6 Env polyprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
Enterobacteria phage T4 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.24 Å
AuthorsShek, J. / Sun, C. / Hastie, K. / Saphire, E.O.
Funding support United States, 2items
OrganizationGrant numberCountry
Other private18030-01-000-408 United States
Other private13502-01-000-408 United States
CitationJournal: To Be Published
Title: Human endogenous retrovirus K (HERV-K) envelope structures in pre- and post-fusion by Cryo-EM
Authors: Shek, J. / Sun, C. / Hastie, K. / Saphire, E.O.
History
DepositionApr 8, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jul 30, 2025Data content type: Primary map / Data content type: Primary map / 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: Surface protein
B: Surface protein
C: Surface protein
D: Transmembrane protein,Fibritin
E: Transmembrane protein,Fibritin
F: Transmembrane protein,Fibritin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,30336
Polymers208,9476
Non-polymers15,35630
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

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Protein , 2 types, 6 molecules ABCDEF

#1: Protein Surface protein / SU


Mass: 42193.434 Da / Num. of mol.: 3 / Mutation: V437C, S463R, K464R,
Source method: isolated from a genetically manipulated source
Details: Phoenix consensus sequence (Dewannieux, Marie, et al. 2006). Engineered V437C mutation
Source: (gene. exp.) Homo sapiens (human) / Gene: ERVK-6, ERVK6 / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q69384
#2: Protein Transmembrane protein,Fibritin / TM / Collar protein / Whisker antigen control protein


Mass: 27455.500 Da / Num. of mol.: 3 / Mutation: V498C
Source method: isolated from a genetically manipulated source
Details: Phoenix consensus sequence (Dewannieux, Marie, et al. 2006). Engineered V498C mutation. Fusion protein with enterokinase site, GGS linkers, and T4-fibritin foldon trimerization domain. C- ...Details: Phoenix consensus sequence (Dewannieux, Marie, et al. 2006). Engineered V498C mutation. Fusion protein with enterokinase site, GGS linkers, and T4-fibritin foldon trimerization domain. C-terminal HRV-3C protease site and twin-strep II tag.,Phoenix consensus sequence (Dewannieux, Marie, et al. 2006). Engineered V498C mutation. Fusion protein with enterokinase site, GGS linkers, and T4-fibritin foldon trimerization domain. C-terminal HRV-3C protease site and twin-strep II tag.
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Enterobacteria phage T4 (virus)
Gene: ERVK-6, ERVK6 / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q69384, UniProt: P10104

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Sugars , 5 types, 30 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#6: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#7: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestN
Has protein modificationY

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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: Pre-fusion Stabilized HERV-K Envelope Trimer / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.190 MDaNO
210.190 MDaNO
310.5 MDaNO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Drosophila melanogaster (fruit fly) / Plasmid: pMT-puro
Buffer solutionpH: 8 / Details: Filtered and degassed
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMTrisC4H11NO31
2150 mMSodium ChlorideNaCl1
SpecimenConc.: 0.184 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 4 K

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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: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8603

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6.0particle selection
2EPUimage acquisition
4cryoSPARC4.6.0CTF correction
7UCSF ChimeraX1.7.1model fitting
8Coot0.9.8.93model fitting
10PHENIX1.21.1_5286model refinement
11cryoSPARC4.6.0initial Euler assignment
12cryoSPARC4.6.0final Euler assignment
13cryoSPARC46classification
14cryoSPARC4.6.03D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 1640558
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 81000 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Atomic model buildingDetails: Initial model was built using ModelAngelo / Source name: Other / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 43.14 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002513701
ELECTRON MICROSCOPYf_angle_d0.526518699
ELECTRON MICROSCOPYf_chiral_restr0.04342298
ELECTRON MICROSCOPYf_plane_restr0.00482280
ELECTRON MICROSCOPYf_dihedral_angle_d12.34916123

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