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- EMDB-48374: Post-fusion HERV-K Envelope Protein in complex with Kenv-4 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-48374
TitlePost-fusion HERV-K Envelope Protein in complex with Kenv-4 Fab
Map data
Sample
  • Complex: HERV-K env post-fusion TM in complex with Kenv-4 Fab
    • Protein or peptide: Kenv-4 Fab Heavy Chain
    • Protein or peptide: Kenv-4 Fab Light Chain
    • Protein or peptide: Transmembrane protein
KeywordsHuman endogenous retrovirus K / glycoprotein / HERV-K / envelope / post-fusion / VIRAL PROTEIN
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 speciesHomo sapiens (human) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsSun C / Shek J / Hastie K / Saphire EO
Funding support United States, 2 items
OrganizationGrant numberCountry
Other private13502-01-000-408 United States
Other private18030-01-000-408 United States
CitationJournal: To Be Published
Title: Human endogenous retrovirus HERV-K envelope glycoprotein structures in pre- and post-fusion conformations by cryo-EM
Authors: Shek J / Sun C / Hastie K / Saphire EO
History
DepositionDec 19, 2024-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48374.png

Downloads & links

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Map

FileDownload / File: emd_48374.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 384 pix.
= 337.92 Å		0.88 Å/pix.
x 384 pix.
= 337.92 Å		0.88 Å/pix.
x 384 pix.
= 337.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.155
Minimum - Maximum-0.32115334 - 0.6093473
Average (Standard dev.)0.0003355365 (±0.009649638)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 337.91998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_48374_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_48374_half_map_2.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 : HERV-K env post-fusion TM in complex with Kenv-4 Fab

EntireName: HERV-K env post-fusion TM in complex with Kenv-4 Fab
Components
  • Complex: HERV-K env post-fusion TM in complex with Kenv-4 Fab
    • Protein or peptide: Kenv-4 Fab Heavy Chain
    • Protein or peptide: Kenv-4 Fab Light Chain
    • Protein or peptide: Transmembrane protein

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Supramolecule #1: HERV-K env post-fusion TM in complex with Kenv-4 Fab

SupramoleculeName: HERV-K env post-fusion TM in complex with Kenv-4 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.7 kDa/nm

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Macromolecule #1: Kenv-4 Fab Heavy Chain

MacromoleculeName: Kenv-4 Fab Heavy Chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 49.469547 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: DVQLQESGPG LVKPSQSLSL TCTVTGYSIT SDYAWNWIRQ FPGNELEWMG YISYSGSTSY NPSLKSRISI TRDTSKNQFF LQLNPVTTE DTATYYCARS VILGAWFAYW GQGTLVTVSA ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS W NSGALTSG ...String:
DVQLQESGPG LVKPSQSLSL TCTVTGYSIT SDYAWNWIRQ FPGNELEWMG YISYSGSTSY NPSLKSRISI TRDTSKNQFF LQLNPVTTE DTATYYCARS VILGAWFAYW GQGTLVTVSA ASTKGPSVFP LAPSSKSTSG GTAALGCLVK DYFPEPVTVS W NSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP SNTKVDKRVE PKSCDKTHTC PPCPAPELLG GP SVFLFPP KPKDTLMISR TPEVTCVVVD VSHEDPEVKF NWYVDGVEVH NAKTKPREEQ YNSTYRVVSV LTVLHQDWLN GKE YKCKVS NKALPAPIEK TISKAKGQPR EPQVYTLPPS REEMTKNQVS LTCLVKGFYP SDIAVEWESN GQPENNYKTT PPVL DSDGS FFLYSKLTVD KSRWQQGNVF SCSVMHEALH NHYTQKSLSL SPGK

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Macromolecule #2: Kenv-4 Fab Light Chain

MacromoleculeName: Kenv-4 Fab Light Chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.270895 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: DIKMTQSPSL MSASPGEKVT MTCSASSSIT YMYWYQQKPR SSPKPWIYLT SNLASGVPAR FSGSGSGTSY SLTISSMEAE DAATYYCQQ WSSNPLTFGA GTKLEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK ...String:
DIKMTQSPSL MSASPGEKVT MTCSASSSIT YMYWYQQKPR SSPKPWIYLT SNLASGVPAR FSGSGSGTSY SLTISSMEAE DAATYYCQQ WSSNPLTFGA GTKLEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK DSTYSLSSTL TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC

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Macromolecule #3: Transmembrane protein

MacromoleculeName: Transmembrane protein / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.707578 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
VNFVNDWQKN STRLWNSQSS IDQKLANQIN DLRQTVIWMG DRLMSLEHRF QLQCDWNTSD FCITPQIYNE SEHHWDMVRR HLQGREDNL TLDISKLKEQ IFEASKAHLN LVPGTEAIAG VADGLANLNP VTWVKT

UniProtKB: Endogenous retrovirus group K member 6 Env 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

Concentration0.68 mg/mL
BufferpH: 7.4
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: NONE
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6) / Number images used: 143318
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 4.6)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER
Output model

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

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