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- PDB-9mlk: Post-fusion HERV-K Envelope Protein in complex with Kenv-4 Fab -

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Basic information

Entry
Database: PDB / ID: 9mlk
TitlePost-fusion HERV-K Envelope Protein in complex with Kenv-4 Fab
Components
  • Kenv-4 Fab Heavy Chain
  • Kenv-4 Fab Light Chain
  • Transmembrane protein
KeywordsVIRAL PROTEIN / Human endogenous retrovirus K / glycoprotein / HERV-K / envelope / post-fusion
Function / homologyRetro-transcribing virus envelope glycoprotein / : / Retro-transcribing viruses envelope glycoprotein / Rec (regulator of expression encoded by corf) of HERV-K-113 / Retroviral envelope protein / Retroviral envelope protein GP41-like / structural molecule activity / plasma membrane / Endogenous retrovirus group K member 6 Env polyprotein
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsSun, C. / Shek, J. / Hastie, K. / Saphire, E.O.
Funding support United States, 2items
OrganizationGrant numberCountry
Other private13502-01-000-408 United States
Other private18030-01-000-408 United States
CitationJournal: Sci Adv / Year: 2025
Title: Human endogenous retrovirus K (HERV-K) envelope structures in pre- and postfusion by cryo-EM.
Authors: Jeremy Shek / Chen Sun / Elise M Wilson / Fatemeh Moadab / Kathryn M Hastie / Roshan R Rajamanickam / Patrick J Penalosa / Stephanie S Harkins / Diptiben Parekh / Chitra Hariharan / Dawid S ...Authors: Jeremy Shek / Chen Sun / Elise M Wilson / Fatemeh Moadab / Kathryn M Hastie / Roshan R Rajamanickam / Patrick J Penalosa / Stephanie S Harkins / Diptiben Parekh / Chitra Hariharan / Dawid S Zyla / Cassandra Yu / Kelly C L Shaffer / Victoria I Lewis / Ruben Diaz Avalos / Tomas Mustelin / Erica Ollmann Saphire /
Abstract: Human endogenous retroviruses (HERVs) are remnants of ancient infections that comprise ~8% of the human genome. The HERV-K envelope glycoprotein (Env) is aberrantly expressed in cancers, autoimmune ...Human endogenous retroviruses (HERVs) are remnants of ancient infections that comprise ~8% of the human genome. The HERV-K envelope glycoprotein (Env) is aberrantly expressed in cancers, autoimmune disorders, and neurodegenerative diseases, and is targeted by patients' own antibodies. However, a lack of structural information has limited molecular and immunological studies of the roles of HERVs in disease. Here, we present cryo-electron microscopy structures of stabilized HERV-K Env in the prefusion conformation, revealing a distinct fold and architecture compared to HIV and simian immunodeficiency virus. We also generated and characterized a panel of monoclonal antibodies with subunit and conformational specificity, serving as valuable research tools. These antibodies enabled structure determination of the postfusion conformation of HERV-K Env, including its unique "tether" helix, and antibody-bound prefusion Env. Together, these results provide a structural framework that opens the door to mechanistic studies of HERV-K Env and tools for its evaluation as a potential therapeutic target.
History
DepositionDec 19, 2024Deposition 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: 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: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Kenv-4 Fab Heavy Chain
L: Kenv-4 Fab Light Chain
I: Kenv-4 Fab Heavy Chain
M: Kenv-4 Fab Light Chain
J: Kenv-4 Fab Heavy Chain
N: Kenv-4 Fab Light Chain
A: Transmembrane protein
C: Transmembrane protein
B: Transmembrane protein


Theoretical massNumber of molelcules
Total (without water)265,3449
Polymers265,3449
Non-polymers00
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: Antibody Kenv-4 Fab Heavy Chain


Mass: 49469.547 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Kenv-4 Fab Light Chain


Mass: 23270.895 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein Transmembrane protein / TM


Mass: 15707.578 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERVK-6, ERVK6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q69384
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: HERV-K env post-fusion TM in complex with Kenv-4 Fab / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightValue: 15.7 kDa/nm / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenConc.: 0.68 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
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: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 70 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4cryoSPARCCTF correction
7UCSF ChimeraXmodel fitting
8Cootmodel fitting
10cryoSPARC4.6initial Euler assignment
11cryoSPARC4.6final Euler assignment
12cryoSPARC4.6classification
13cryoSPARC4.63D reconstruction
14PHENIX1.21.1_5286model refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 143318 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
RefinementHighest resolution: 2.84 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0037505
ELECTRON MICROSCOPYf_angle_d0.50310179
ELECTRON MICROSCOPYf_dihedral_angle_d4.1931002
ELECTRON MICROSCOPYf_chiral_restr0.0391109
ELECTRON MICROSCOPYf_plane_restr0.0041284

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