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- EMDB-61589: Structure of HHV6B glycoprotein B -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-61589
TitleStructure of HHV6B glycoprotein B
Map data
Sample
  • Complex: glycoprotein B
    • Protein or peptide: Envelope glycoprotein B
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHHV6B / gB / VIRAL 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 6 strain Z29
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsFang XY / Xie C / Sun C / Zeng MS / Liu Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82030046 China
CitationJournal: To Be Published
Title: Structure of HHV6B glycoprotein B
Authors: Fang XY / Xie C / Sun C / Zeng MS / Liu Z
History
DepositionSep 19, 2024-
Header (metadata) releaseJun 25, 2025-
Map releaseJun 25, 2025-
UpdateJun 25, 2025-
Current statusJun 25, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61589.png

Downloads & links

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Map

FileDownload / File: emd_61589.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 400 pix.
= 264. Å		0.66 Å/pix.
x 400 pix.
= 264. Å		0.66 Å/pix.
x 400 pix.
= 264. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.66 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.054
Minimum - Maximum-0.09462209 - 0.2595838
Average (Standard dev.)0.00020126908 (±0.008146149)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61589_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_61589_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
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: glycoprotein B

SupramoleculeName: glycoprotein B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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 6 strain Z29 / Strain: Z29
Molecular weightTheoretical: 72.54232 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSKMRVLFLA VFLMNSVLMI YCDSDDYIRA GYNHKYPFRI CSIAKGTDLM RFDRDISCSP YKSNAKMSEG FFIIYKTNIE TYTFPVRTY KNELTFPTSY RDHRTTYFLD RTVMGLAMPV YEANLVNSRA QCYSAVAIKR PDGTVFSAYH EDNNKNETLE L FPLNFKSV ...String:
MSKMRVLFLA VFLMNSVLMI YCDSDDYIRA GYNHKYPFRI CSIAKGTDLM RFDRDISCSP YKSNAKMSEG FFIIYKTNIE TYTFPVRTY KNELTFPTSY RDHRTTYFLD RTVMGLAMPV YEANLVNSRA QCYSAVAIKR PDGTVFSAYH EDNNKNETLE L FPLNFKSV TNKRFITTKE PYFARGPLAT HSTSTSLNCI VTEATAKAKY PFSYFALTTG EIVEGSPFFD GSNGKHFAEP LE KLTILEN YTMIEDLMNG MNGATTLVRK IAFLEKGDTL FSWEIKEENE SVCMLKHWTT VTHGLRAETD ETYHFISKEL TAA FVASKE SLNLTDPKQT CIKNEFEKII TDVYMSDYND AYSMNGSYQI FKTTGDLILI WQPLVQKSLM VLEQGSVNLR RRRD LVDVK SRHDILYVQL QYLYDTLKDY INDALGNLAE SWCLDQKRTI TMLHELSKIS PSSIVSEVYG RPISAQLHGD VLAIS KCIE VNQSSVQLYK SMRVVDAKGV RSETMCYNRP LVTFSFVNST PEVVLGQLGL DNEILLGDHR TEECEIPSTK IFLSGN HAH VYTDYTHTNS TPIEDIEVLD AFIRLKIDPL ENADFKLLDL YSPDELSRAN VFDLENILRE YNSYKSALYT

UniProtKB: Envelope glycoprotein B

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 2 / 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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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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 272190
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-9jli:
Structure of HHV6B glycoprotein B

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