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- EMDB-38910: Structure of KSHV glycoprotein B -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-38910
TitleStructure of KSHV glycoprotein B
Map data
Sample
  • Complex: glycoprotein B
    • Protein or peptide: Envelope glycoprotein B
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


host cell Golgi membrane / host cell endosome membrane / symbiont entry into host cell / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B, PH-like domain 1 / Herpesvirus Glycoprotein B, PH-like domain 2 / Herpesvirus Glycoprotein B, PH-like domain 2 superfamily / Herpesvirus Glycoprotein B ectodomain / Herpesvirus Glycoprotein B / Herpesvirus Glycoprotein B PH-like domain
Similarity search - Domain/homology
Envelope glycoprotein B
Similarity search - Component
Biological speciesHuman gammaherpesvirus 8 / Human herpesvirus 8 strain GK18
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsFang XY / Sun C / Xie C / Liu Z / Zeng MS
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82030046 China
CitationJournal: To Be Published
Title: Structure of KSHV glycoprotein B
Authors: Fang XY / Sun C / Liu Z / Zeng MS
History
DepositionJan 30, 2024-
Header (metadata) releaseFeb 19, 2025-
Map releaseFeb 19, 2025-
UpdateFeb 19, 2025-
Current statusFeb 19, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_38910.png

Downloads & links

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Map

FileDownload / File: emd_38910.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 320 pix.
= 273.6 Å		0.86 Å/pix.
x 320 pix.
= 273.6 Å		0.86 Å/pix.
x 320 pix.
= 273.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.086
Minimum - Maximum-0.16679929 - 0.42838722
Average (Standard dev.)0.00007486962 (±0.012767386)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 273.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: local map of protein bottom

Fileemd_38910_additional_1.map
Annotationlocal map of protein bottom
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_38910_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38910_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 : glycoprotein B

EntireName: glycoprotein B
Components
  • Complex: glycoprotein B
    • Protein or peptide: Envelope glycoprotein B

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Supramolecule #1: glycoprotein B

SupramoleculeName: glycoprotein B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human gammaherpesvirus 8

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Macromolecule #1: Envelope glycoprotein B

MacromoleculeName: Envelope glycoprotein B / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human herpesvirus 8 strain GK18 / Strain: GK18
Molecular weightTheoretical: 73.137594 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTPRSRLATL GTVILLVCFC AGAAHSRGDT FQTSSSPTPP GSSSKAPTKP GEEASGPKSV DFYQFRVCSA SITGELFRFN LEQTCPDTK DKYHQEGILL VYKKNIVPHI FKVRRYRKIA TSVTVYRGHR ESAITNKYEL PRPVPLYEIS HMDSTYQCFS S MKVNVNGV ...String:
MTPRSRLATL GTVILLVCFC AGAAHSRGDT FQTSSSPTPP GSSSKAPTKP GEEASGPKSV DFYQFRVCSA SITGELFRFN LEQTCPDTK DKYHQEGILL VYKKNIVPHI FKVRRYRKIA TSVTVYRGHR ESAITNKYEL PRPVPLYEIS HMDSTYQCFS S MKVNVNGV ENTFTDRDDV NTTVFLQPVE GLTDNIQRYF SQPVIYAEPG RVEATYRVRT TVNCEIVDMI ARSAEPYNYF VT SLGDTVE VSPFCYNESS CSTTPSNKNG LSVQVVLNHT VVTYSDRGTS PTPQNRIFVE TGAYTLSWAS ESKTTAVCPL ALW KTFPRS IQTTHEDSFH FVANEITATF TAPLTPVANF TDTYSCLTSD INTTLNASKA KLASTHVPNG TVQYFHTTGG LYLV WQPMS AINLTHAQGD SGNPTSSPPP SASPMTTSAS RGGSGGASTA AAGGGGSTDN LSYTQLQFAY DKLRDGINQV LEELS RAWC REQVRDNLMW YELSKINPTS VMTAIYGRPV SAKFVGDAIS VTECINVDQS SVNIHKSLRT NSKDVCYARP LVTFKF LNS SNLFTGQLGA RNEIILTNNQ VETCKDTCEH YFITRNETLV YKDYAYLRTI NTTDISTLNT FIALNLSFIQ NIDFKAI EL YSSAEKRLAS SGSHHHHHH

UniProtKB: Envelope glycoprotein B

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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: 8.3
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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 120100
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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