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- EMDB-49572: Structure of the HERV-K (HML-2) spike complex -

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Basic information

Entry
Database: EMDB / ID: EMD-49572
TitleStructure of the HERV-K (HML-2) spike complex
Map dataMain map - unfiltered
Sample
  • Complex: The HERV-K spike complex
    • Protein or peptide: Endogenous retrovirus group K member 7 Pol protein
    • Protein or peptide: Surface protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
KeywordsHERV-K Endogenous retrovirus K Spike protein Viral glycoprotein / VIRAL PROTEIN / HML-2
Function / homology
Function and homology information


ribonuclease H / DNA synthesis involved in DNA repair / RNA-directed DNA polymerase activity / DNA integration / RNA-directed DNA polymerase / DNA-templated DNA replication / RNA stem-loop binding / RNA-DNA hybrid ribonuclease activity / DNA recombination / structural molecule activity ...ribonuclease H / DNA synthesis involved in DNA repair / RNA-directed DNA polymerase activity / DNA integration / RNA-directed DNA polymerase / DNA-templated DNA replication / RNA stem-loop binding / RNA-DNA hybrid ribonuclease activity / DNA recombination / structural molecule activity / DNA binding / zinc ion binding / 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 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. ...Retro-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 / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / RNase H type-1 domain profile. / Ribonuclease H domain / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Endogenous retrovirus group K member 25 Env polyprotein / Endogenous retrovirus group K member 7 Pol protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.13 Å
AuthorsShaked R / Katz M / Diskin R
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMar 5, 2025-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49572.png

Downloads & links

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Map

FileDownload / File: emd_49572.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map - unfiltered
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 256 pix.
= 210.944 Å		0.82 Å/pix.
x 256 pix.
= 210.944 Å		0.82 Å/pix.
x 256 pix.
= 210.944 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.075
Minimum - Maximum-0.18736663 - 0.5458597
Average (Standard dev.)0.0012395079 (±0.023156375)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 210.944 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Local resolution-filtered map

Fileemd_49572_additional_1.map
AnnotationLocal resolution-filtered map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_49572_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_49572_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The HERV-K spike complex

EntireName: The HERV-K spike complex
Components
  • Complex: The HERV-K spike complex
    • Protein or peptide: Endogenous retrovirus group K member 7 Pol protein
    • Protein or peptide: Surface protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: The HERV-K spike complex

SupramoleculeName: The HERV-K spike complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Endogenous retrovirus group K member 7 Pol protein

MacromoleculeName: Endogenous retrovirus group K member 7 Pol protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: RNA-directed DNA polymerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.730771 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: FIFTLIAVIM GLIAVTATAA VAGVALHSSV QSVNFVNDWQ KNSTRLWNSQ SSIDQKLANQ INDLRQTVIW MGDRLMSLEH RFQLQCDWN TSDFCITPQI YNESEHHWDM VRRHLQGRED NLTLDISKLK EQIFEASKAH LNLVPGTEAI AGVADGLANL N PVTWVKTI ...String:
FIFTLIAVIM GLIAVTATAA VAGVALHSSV QSVNFVNDWQ KNSTRLWNSQ SSIDQKLANQ INDLRQTVIW MGDRLMSLEH RFQLQCDWN TSDFCITPQI YNESEHHWDM VRRHLQGRED NLTLDISKLK EQIFEASKAH LNLVPGTEAI AGVADGLANL N PVTWVKTI GSTTIINLIL ILVCLFCLLL VCRCTQQLRR DSDHRERAMM TMAVLSKRKG GNVGKSKRDQ IVTVSVGSGG GG DYKDDDD K

UniProtKB: Endogenous retrovirus group K member 7 Pol protein

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Macromolecule #2: Surface protein

MacromoleculeName: Surface protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.729082 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LPMPAGAAAA NYTYWAYVPF PPLIRAVTWM DNPIEVYVND SVWVPGPIDD RCPAKPEEEG MMINISIGYR YPPICLGRAP GCLMPAVQN WLVEVPTVSP ISRFTYHMVS GMSLRPRVNY LQDFSYQRSL KFRPKGKPCP KEIPKESKNT EVLVWEECVA N SAVILQNN ...String:
LPMPAGAAAA NYTYWAYVPF PPLIRAVTWM DNPIEVYVND SVWVPGPIDD RCPAKPEEEG MMINISIGYR YPPICLGRAP GCLMPAVQN WLVEVPTVSP ISRFTYHMVS GMSLRPRVNY LQDFSYQRSL KFRPKGKPCP KEIPKESKNT EVLVWEECVA N SAVILQNN EFGTIIDWAP RGQFYHNCSG QTQSCPSAQV SPAVDSDLTE SLDKHKHKKL QSFYPWEWGE KGISTPRPKI IS PVSGPEH PELWRLTVAS HHIRIWSGNQ TLETRDRKPF YTVDLNSSLT VPLQSCVKPP YMLVVGNIVI KPDSQTITCE NCR LLTCID STFNWQHRIL LVRAREGVWI PVSMDRPWEA SPSIHILTEV LKGVLNRSKR

UniProtKB: Endogenous retrovirus group K member 25 Env polyprotein

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 1626 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 38.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.13 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 501255
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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