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- EMDB-64523: Structure of MHV68 glycoprotein B in complex with Fab5 -

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Basic information

Entry
Database: EMDB / ID: EMD-64523
TitleStructure of MHV68 glycoprotein B in complex with Fab5
Map data
Sample
  • Complex: glycoprotein B
    • Protein or peptide: Fab 5 H chain
    • Protein or peptide: Fab5 L chain
    • Protein or peptide: MHV 68 glycoprotein B
KeywordsMHV68 / gB / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesMurid herpesvirus 68 / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsCheng BZ / Xie C / Sun C / Zeng MS / Liu Z / Fang XY
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82030046 China
CitationJournal: To Be Published
Title: Structure of MHV68 glycoprotein B in complex with Fab5
Authors: Cheng BZ / Xie C / Sun C / Zeng MS / Liu Z / Fang XY
History
DepositionMay 9, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_64523.png

Downloads & links

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Map

FileDownload / File: emd_64523.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.)
0.92 Å/pix.
x 400 pix.
= 368. Å		0.92 Å/pix.
x 400 pix.
= 368. Å		0.92 Å/pix.
x 400 pix.
= 368. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0596
Minimum - Maximum-0.1537257 - 0.5052977
Average (Standard dev.)0.00015451152 (±0.012958543)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 368.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_64523_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_64523_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_64523_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: Fab 5 H chain
    • Protein or peptide: Fab5 L chain
    • Protein or peptide: MHV 68 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: Murid herpesvirus 68

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Macromolecule #1: Fab 5 H chain

MacromoleculeName: Fab 5 H chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.199873 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQQPGAE LVRPGASVKL SCKASGFTFT SYWINWVKQR PGQGLEWIGN IFPSDSYTNY NQKFKDKATL TVDKSSSTAY MLLSSPTSE DSAVYYCTRG GYRYDSDYWG QGTTLTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV ...String:
QVQLQQPGAE LVRPGASVKL SCKASGFTFT SYWINWVKQR PGQGLEWIGN IFPSDSYTNY NQKFKDKATL TVDKSSSTAY MLLSSPTSE DSAVYYCTRG GYRYDSDYWG QGTTLTVSSA STKGPSVFPL APSSKSTSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKRVGS HHHHHH

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Macromolecule #2: Fab5 L chain

MacromoleculeName: Fab5 L chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.261846 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QIVLTQSPAI MSASPGEKVT MTCSASSSVT YMYWYQQKPG SSPRLLIYDT SNLASGVPVR FSGSGSGTSY SLTISRMEAE DAATYYCQQ WSSYPYTFGG GTKLEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK ...String:
QIVLTQSPAI MSASPGEKVT MTCSASSSVT YMYWYQQKPG SSPRLLIYDT SNLASGVPVR FSGSGSGTSY SLTISRMEAE DAATYYCQQ WSSYPYTFGG GTKLEIKRTV AAPSVFIFPP SDEQLKSGTA SVVCLLNNFY PREAKVQWKV DNALQSGNSQ E SVTEQDSK DSTYSLSSTL TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC

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Macromolecule #3: MHV 68 glycoprotein B

MacromoleculeName: MHV 68 glycoprotein B / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Murid herpesvirus 68
Molecular weightTheoretical: 74.91975 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MYPTVKSMRV AHLTNLLTLL CLLCHTHLYV CQPTTLRQPS DMTPAQDAPT ETPPPLSTNT NRGFEYFRVC GVAATGETFR FDLDKTCPS TQDKKHVEGI LLVYKINIVP YIFKIRRYRK IITQLTIWRG HRTSSVTGKF EMATQAHEWE VGDFDSIYQC Y NSATMVVN ...String:
MYPTVKSMRV AHLTNLLTLL CLLCHTHLYV CQPTTLRQPS DMTPAQDAPT ETPPPLSTNT NRGFEYFRVC GVAATGETFR FDLDKTCPS TQDKKHVEGI LLVYKINIVP YIFKIRRYRK IITQLTIWRG HRTSSVTGKF EMATQAHEWE VGDFDSIYQC Y NSATMVVN NVRQVYVDRD GVNKTVNIRP VDGLTGNIQR YFSQPTLYSE PGRVEATYRV RTTVNCEIVD MVARSMDPYN YI ATALGDS LELSPFQTFD NTSQSTAPKR ADMRVREVKN YKFVDYNNRG TAPAGQSRTF LETPSATYSW KTATRQTATC DLV HWKTFP RAIQTAHEHS YHFVANEVTA TFNTPLTEVE NFTSTYSCVS DQINKTISEY IQKLNNSYVA SGKTQYFKTD GNLY LIWQP LEHPEIEDID EDSDPEPTPA PPKSTGGSGE AADNGNSTSE VSKGSENPLI TAQIQFAYDK LTTSVNNVLE ELSRA WCRE QVRDTLMWYE LSKVNPTSVM SAIYGKPVAA RYVGDAISVT DCIYVDQSSV NIHQSLRLQH DKTTCYSRPR VTFKFI NST DPLTGQLGPR KEIILSNTNI ETCKDESEHY FIVGEYIYYY KNYIFEEKLN LSSIATLDTF IALNISFIEN IDFKTVE LY SSTERKLASS HHHHHH

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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: 7.3
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: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 116763
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-9uv4:
Structure of MHV68 glycoprotein B in complex with Fab5

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