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- EMDB-64607: Macacine gammaherpesvirus 4 glycoprotein B in complex with Fab5 -

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Basic information

Entry
Database: EMDB / ID: EMD-64607
TitleMacacine gammaherpesvirus 4 glycoprotein B in complex with Fab5
Map data
Sample
  • Complex: Structure of rhLCV glycoprotein B in complex with Fab5
    • Protein or peptide: Fab5 H chain
    • Protein or peptide: Fab5 L chain
    • Protein or peptide: Macacine gammaherpesvirus 4 glycoprotein B
KeywordsrhLCV / gB / VIRAL PROTEIN/IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesMacacine gammaherpesvirus 4 (Rhesus lymphocryptovirus) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsCheng BZ / Liu Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82030046 China
CitationJournal: To Be Published
Title: Macacine gammaherpesvirus 4 glycoprotein B in complex with Fab5
Authors: Cheng BZ / Fang XY / Sun C / Xie C / Liu Z / Zeng MS
History
DepositionMay 15, 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_64607.png

Downloads & links

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Map

FileDownload / File: emd_64607.map.gz / Format: CCP4 / Size: 1000 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 640 pix.
= 424.96 Å		0.66 Å/pix.
x 640 pix.
= 424.96 Å		0.66 Å/pix.
x 640 pix.
= 424.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.664 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0232
Minimum - Maximum-0.06411875 - 0.1560824
Average (Standard dev.)-0.00004985379 (±0.0031893244)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 424.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64607_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_64607_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 : Structure of rhLCV glycoprotein B in complex with Fab5

EntireName: Structure of rhLCV glycoprotein B in complex with Fab5
Components
  • Complex: Structure of rhLCV glycoprotein B in complex with Fab5
    • Protein or peptide: Fab5 H chain
    • Protein or peptide: Fab5 L chain
    • Protein or peptide: Macacine gammaherpesvirus 4 glycoprotein B

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Supramolecule #1: Structure of rhLCV glycoprotein B in complex with Fab5

SupramoleculeName: Structure of rhLCV glycoprotein B in complex with Fab5
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#3, #1
Source (natural)Organism: Macacine gammaherpesvirus 4 (Rhesus lymphocryptovirus)

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Macromolecule #1: Macacine gammaherpesvirus 4 glycoprotein B

MacromoleculeName: Macacine gammaherpesvirus 4 glycoprotein B / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macacine gammaherpesvirus 4 (Rhesus lymphocryptovirus)
Molecular weightTheoretical: 78.05275 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MTPRRKPSVV LLLAALVGCI WAQTTQQPAP PATTVQPAAA RQKTNFPFRV CELSSHGDLF RFSSDIQCPS SGTQEKHTEG LLMVFKDNI IPYSFKVRSY TKIVTNTLVY NGHRADAVTN RHEEMFSVES HETDQMDSIY QCHNAVRMTK DGVERVYVDN D GTNITVNL ...String:
MTPRRKPSVV LLLAALVGCI WAQTTQQPAP PATTVQPAAA RQKTNFPFRV CELSSHGDLF RFSSDIQCPS SGTQEKHTEG LLMVFKDNI IPYSFKVRSY TKIVTNTLVY NGHRADAVTN RHEEMFSVES HETDQMDSIY QCHNAVRMTK DGVERVYVDN D GTNITVNL RPTSGLANGV RRYASQTQVH DAPGRVEATY RTRTTVNCVV TDMMAKSNSP FNFFVTTVGQ TAEMSPFYDG TN KETFNER AGSFHVRENY KIVDYDNRGT VPNGERRAFL DKGTYTLSWK LENRTAYCPL QHWKTFESTI ATETVRSTHF VTQ EGTSSF VTNMTVGMAL PGAFKCIEDQ VNKTMHEKYE ALQDRYVKDQ ENITYFLTSG GLLLAWLPLT PRSLASVKNL TELT TAAPP FPSSPTPPTP STASRSTAAA IVRRRRRQAE GNNTTPAPPK PATPAPGNSL GTLNNPATIQ IQFAYDSLRR QINRM LGDL ARAWCLEQKR QNMVLRELTK INPTTVMSGI YGRPVAAKRL GDVISVSQCV PVNQATVTLR KSMRVPGSES MCYSRP LVS FSFINDTKTY EGQLGTDNEI FLTKKMTEMC LASSQYYFQS GNEIHVYHDY QHFKTIELDG IATLQTFIAL NTSLIEN ID FASLELYSRD EQRASNVFDL EGIFREYNFQ AQNIAGLRKD LDNAVSHHHH HH

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Macromolecule #2: Fab5 H chain

MacromoleculeName: Fab5 H chain / type: protein_or_peptide / ID: 2 / 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 #3: Fab5 L chain

MacromoleculeName: Fab5 L chain / type: protein_or_peptide / ID: 3 / 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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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: FEI FALCON IV (4k x 4k) / Number real images: 5533 / 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 / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 292826
CTF correctionSoftware - Name: cryoSPARC (ver. v4.3.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 32 / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 91810
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. v4.3.0)
Final angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. v4.3.0)
Final 3D classificationNumber classes: 32 / Avg.num./class: 2869 / Software - Name: cryoSPARC (ver. v4.3.0)
FSC plot (resolution estimation)

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