[English] 日本語
Yorodumi
- EMDB-48351: Pre-fusion HERV-K Envelope Protein Trimer Ectodomain in complex w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-48351
TitlePre-fusion HERV-K Envelope Protein Trimer Ectodomain in complex with Kenv-6 Fab
Map data
Sample
  • Complex: Pre-fusion HERV-K Envelope glycoprotein in complex with Kenv-6 Fabs
    • Complex: Pre-fusion Stabilized HERV-K Envelope Trimer
      • Protein or peptide: Surface protein
      • Protein or peptide: Transmembrane protein,Fibritin
    • Complex: Kenv-6 Antibody Fab
      • Protein or peptide: Kenv-6 Fab heavy chain
      • Protein or peptide: Kenv-6 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHuman endogenous retrovirus K / glycoprotein / HERV-K / envelope / pre-fusion / Fab complex / VIRAL PROTEIN
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 25 Env polyprotein
Similarity search - Component
Biological speciesHomo sapiens (human) / Enterobacteria phage T4 (virus) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.24 Å
AuthorsShek J / Sun C / Hastie K / Saphire EO
Funding support United States, 2 items
OrganizationGrant numberCountry
Other private18030-01-000-408 United States
Other private13502-01-000-408 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 18, 2024-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_48351.png

Downloads & links

-
Map

FileDownload / File: emd_48351.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 448 pix.
= 422.401 Å		0.94 Å/pix.
x 448 pix.
= 422.401 Å		0.94 Å/pix.
x 448 pix.
= 422.401 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94286 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.16
Minimum - Maximum-0.3505268 - 0.8903439
Average (Standard dev.)-0.000019405625 (±0.014573656)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 422.40128 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Sharpened Map

Fileemd_48351_additional_1.map
AnnotationSharpened Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_48351_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_48351_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Pre-fusion HERV-K Envelope glycoprotein in complex with Kenv-6 Fabs

EntireName: Pre-fusion HERV-K Envelope glycoprotein in complex with Kenv-6 Fabs
Components
  • Complex: Pre-fusion HERV-K Envelope glycoprotein in complex with Kenv-6 Fabs
    • Complex: Pre-fusion Stabilized HERV-K Envelope Trimer
      • Protein or peptide: Surface protein
      • Protein or peptide: Transmembrane protein,Fibritin
    • Complex: Kenv-6 Antibody Fab
      • Protein or peptide: Kenv-6 Fab heavy chain
      • Protein or peptide: Kenv-6 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: Pre-fusion HERV-K Envelope glycoprotein in complex with Kenv-6 Fabs

SupramoleculeName: Pre-fusion HERV-K Envelope glycoprotein in complex with Kenv-6 Fabs
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 500 KDa

-
Supramolecule #2: Pre-fusion Stabilized HERV-K Envelope Trimer

SupramoleculeName: Pre-fusion Stabilized HERV-K Envelope Trimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #3: Kenv-6 Antibody Fab

SupramoleculeName: Kenv-6 Antibody Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Details: Fab fragment generated by proteolytic cleave of Kenv-6 IgG antibody
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Surface protein

MacromoleculeName: Surface protein / type: protein_or_peptide / ID: 1
Details: Phoenix consensus sequence (Dewannieux, Marie, et al. 2006). Engineered V437C mutation
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.193434 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: AAANYTYWAY VPFPPLIRAV TWMDNPIEVY VNDSVWVPGP IDDRCPAKPE EEGMMINISI GYRYPPICLG RAPGCLMPAV QNWLVEVPT VSPISRFTYH MVSGMSLRPR VNYLQDFSYQ RSLKFRPKGK PCPKEIPKES KNTEVLVWEE CVANSAVILQ N NEFGTIID ...String:
AAANYTYWAY VPFPPLIRAV TWMDNPIEVY VNDSVWVPGP IDDRCPAKPE EEGMMINISI GYRYPPICLG RAPGCLMPAV QNWLVEVPT VSPISRFTYH MVSGMSLRPR VNYLQDFSYQ RSLKFRPKGK PCPKEIPKES KNTEVLVWEE CVANSAVILQ N NEFGTIID WAPRGQFYHN CSGQTQSCPS AQVSPAVDSD LTESLDKHKH KKLQSFYPWE WGEKGISTPR PKIISPVSGP EH PELWRLT VASHHIRIWS GNQTLETRDR KPFYTVDLNS SLTVPLQSCV KPPYMLVVGN IVIKPDSQTI TCENCRLLTC IDS TFNWQH RILLVRAREG VWIPCSMDRP WEASPSIHIL TEVLKGVLNR RRR

UniProtKB: Endogenous retrovirus group K member 25 Env polyprotein

-
Macromolecule #2: Transmembrane protein,Fibritin

MacromoleculeName: Transmembrane protein,Fibritin / type: protein_or_peptide / ID: 2
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.
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Enterobacteria phage T4 (virus)
Molecular weightTheoretical: 27.4555 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: FIFTLIAVIM GLIAVTATAA VAGVALHSSV QSCNFVNDWQ KNSTRLWNSQ SSIDQKLANQ INDLRQTVIW MGDRLMSLEH RFQLQCDWN TSDFCITPQI YNESEHHWDM VRRHLQGRED NLTLDISKLK EQIFEASKAH LNLVPGTEAI AGVADGLANL N PVTWVKTD ...String:
FIFTLIAVIM GLIAVTATAA VAGVALHSSV QSCNFVNDWQ KNSTRLWNSQ SSIDQKLANQ INDLRQTVIW MGDRLMSLEH RFQLQCDWN TSDFCITPQI YNESEHHWDM VRRHLQGRED NLTLDISKLK EQIFEASKAH LNLVPGTEAI AGVADGLANL N PVTWVKTD DDDKAGGSGG SGGSGGGYIP EAPRDGQAYV RKDGEWVLLS TFLASGLEVL FQGPGAGWSH PQFEKGGGSG GG SGGGSWS HPQFEK

UniProtKB: Endogenous retrovirus group K member 25 Env polyprotein, Fibritin

-
Macromolecule #3: Kenv-6 Fab heavy chain

MacromoleculeName: Kenv-6 Fab heavy chain / type: protein_or_peptide / ID: 3 / Details: Cleaved Fabs / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.437055 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
QIQLVQSGPE LKKPGETVKI SCKASGYTFT IYGMNWLKQA PGKGLKWMGW INTYTGEPTY ADDFKGRFAF SLETSASTAY LQVNNLKNE DTATYFCAKY YDGYYGWYFD VWGAGTTLTV

-
Macromolecule #4: Kenv-6 Fab light chain

MacromoleculeName: Kenv-6 Fab light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.671895 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
IVLTQSPASL AVTLGQRATI SCRGSESVDS YGNSFMHWYQ QKPGQPPKLL IYRASNLESG IPARFSGSGS RTDFTLTINP VEADDVATY YCQQSYEDPY TFGGGTKL

-
Macromolecule #9: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 9 / Number of copies: 6 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.179 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
25.0 mMC4H11NO3Tris
150.0 mMNaClSodium Chloride

Details: Filtered and degassed
GridModel: C-flat-2/1 / Material: GRAPHENE OXIDE / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 15947 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.24 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 479625
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 10
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-9mla:
Pre-fusion HERV-K Envelope Protein Trimer Ectodomain in complex with Kenv-6 Fab

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more