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- EMDB-60272: Structure of Epstein-Barr virus major glycoprotein gp350 in compl... -

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Basic information

Entry
Database: EMDB / ID: EMD-60272
TitleStructure of Epstein-Barr virus major glycoprotein gp350 in complex with the receptor CR2
Map data
Sample
  • Complex: glycoprotein gp350 in complex with the receptor CR2
    • Protein or peptide: Complement receptor type 2
    • Protein or peptide: BLLF1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsVIRAL PROTEIN
Function / homology
Function and homology information


negative regulation of complement activation, classical pathway / complement receptor activity / T cell mediated immunity / complement binding / complement activation, alternative pathway / immunoglobulin receptor binding / type I interferon-mediated signaling pathway / B cell activation / B cell proliferation / complement activation, classical pathway ...negative regulation of complement activation, classical pathway / complement receptor activity / T cell mediated immunity / complement binding / complement activation, alternative pathway / immunoglobulin receptor binding / type I interferon-mediated signaling pathway / B cell activation / B cell proliferation / complement activation, classical pathway / B cell differentiation / Regulation of Complement cascade / transmembrane signaling receptor activity / virus receptor activity / receptor complex / immune response / symbiont entry into host cell / viral envelope / protein homodimerization activity / DNA binding / extracellular space / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Herpesvirus major outer envelope glycoprotein / : / : / : / : / Herpes virus envelope glycoprotein gp350, N-terminal A domain / Herpesvirus envelope glycoprotein gp350, N-terminal B domain / Herpesvirus envelope glycoprotein gp350 N-terminal C domain / Herpesvirus Envelope glycoprotein GP350 C-terminal / : ...Herpesvirus major outer envelope glycoprotein / : / : / : / : / Herpes virus envelope glycoprotein gp350, N-terminal A domain / Herpesvirus envelope glycoprotein gp350, N-terminal B domain / Herpesvirus envelope glycoprotein gp350 N-terminal C domain / Herpesvirus Envelope glycoprotein GP350 C-terminal / : / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily
Similarity search - Domain/homology
BLLF1 / Complement receptor type 2
Similarity search - Component
Biological speciesHuman gammaherpesvirus 4 (Epstein-Barr virus) / Homo sapiens (human) / human gammaherpesvirus 4 (Epstein-Barr virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsFang XY / Sun C / Liu Z / Zeng MS
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82030046 China
CitationJournal: Cell Rep / Year: 2025
Title: Structural basis of Epstein-Barr virus gp350 receptor recognition and neutralization.
Authors: Cong Sun / Xin-Yan Fang / Guo-Long Bu / Lan-Yi Zhong / Chu Xie / Ge-Xin Zhao / Sen-Fang Sui / Zheng Liu / Mu-Sheng Zeng /
Abstract: Epstein-Barr virus (EBV) is an oncogenic virus associated with multiple lymphoid malignancies and autoimmune diseases. During infection in B cells, EBV uses its major glycoprotein gp350 to recognize ...Epstein-Barr virus (EBV) is an oncogenic virus associated with multiple lymphoid malignancies and autoimmune diseases. During infection in B cells, EBV uses its major glycoprotein gp350 to recognize the host receptor CR2, initiating viral attachment, a process that has lacked direct structural evidence for decades. In this study, we resolved the structure of the gp350-CR2 complex, elucidated their key interactions, and determined the site-specific N-glycosylation map of gp350. Our findings reveal that CR2 primarily binds to gp350 through an electrostatically complementary and glycan-free interface and that the diversity of key residues in CR2 across different species influences EBV host selectivity mediated by gp350. With the confirmed binding, we constructed a CR2-Fc antibody analog that targets the vulnerable site of gp350, demonstrating a potent neutralization effect against EBV infection in B cells. Our work provides essential structural insights into the mechanism of EBV infection and host tropism, suggesting a potential antiviral agent.
History
DepositionMay 27, 2024-
Header (metadata) releaseJan 15, 2025-
Map releaseJan 15, 2025-
UpdateJan 22, 2025-
Current statusJan 22, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60272.png

Downloads & links

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Map

FileDownload / File: emd_60272.map.gz / Format: CCP4 / Size: 107.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 304 pix.
= 252.32 Å		0.83 Å/pix.
x 304 pix.
= 252.32 Å		0.83 Å/pix.
x 304 pix.
= 252.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.21052225 - 0.48745054
Average (Standard dev.)0.0002500374 (±0.009217388)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions304304304
Spacing304304304
CellA=B=C: 252.31999 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60272_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_60272_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 gp350 in complex with the receptor CR2

EntireName: glycoprotein gp350 in complex with the receptor CR2
Components
  • Complex: glycoprotein gp350 in complex with the receptor CR2
    • Protein or peptide: Complement receptor type 2
    • Protein or peptide: BLLF1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: glycoprotein gp350 in complex with the receptor CR2

SupramoleculeName: glycoprotein gp350 in complex with the receptor CR2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Human gammaherpesvirus 4 (Epstein-Barr virus)

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Macromolecule #1: Complement receptor type 2

MacromoleculeName: Complement receptor type 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 106.960758 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGAAGLLGVF LALVAPGVLG ISCGSPPPIL NGRISYYSTP IAVGTVIRYS CSGTFRLIGE KSLLCITKDK VDGTWDKPAP KCEYFNKYS SCPEPIVPGG YKIRGSTPYR HGDSVTFACK TNFSMNGNKS VWCQANNMWG PTRLPTCVSV FPLECPALPM I HNGHHTSE ...String:
MGAAGLLGVF LALVAPGVLG ISCGSPPPIL NGRISYYSTP IAVGTVIRYS CSGTFRLIGE KSLLCITKDK VDGTWDKPAP KCEYFNKYS SCPEPIVPGG YKIRGSTPYR HGDSVTFACK TNFSMNGNKS VWCQANNMWG PTRLPTCVSV FPLECPALPM I HNGHHTSE NVGSIAPGLS VTYSCESGYL LVGEKIINCL SSGKWSAVPP TCEEARCKSL GRFPNGKVKE PPILRVGVTA NF FCDEGYR LQGPPSSRCV IAGQGVAWTK MPVCEEIFCP SPPPILNGRH IGNSLANVSY GSIVTYTCDP DPEEGVNFIL IGE STLRCT VDSQKTGTWS GPAPRCELST SAVQCPHPQI LRGRMVSGQK DRYTYNDTVI FACMFGFTLK GSKQIRCNAQ GTWE PSAPV CEKECQAPPN ILNGQKEDRH MVRFDPGTSI KYSCNPGYVL VGEESIQCTS EGVWTPPVPQ CKVAACEATG RQLLT KPQH QFVRPDVNSS CGEGYKLSGS VYQECQGTIP WFMEIRLCKE ITCPPPPVIY NGAHTGSSLE DFPYGTTVTY TCNPGP ERG VEFSLIGEST IRCTSNDQER GTWSGPAPLC KLSLLAVQCS HVHIANGYKI SGKEAPYFYN DTVTFKCYSG FTLKGSS QI RCKADNTWDP EIPVCEKETC QHVRQSLQEL PAGSRVELVN TSCQDGYQLT GHAYQMCQDA ENGIWFKKIP LCKVIHCH P PPVIVNGKHT GMMAENFLYG NEVSYECDQG FYLLGEKKLQ CRSDSKGHGS WSGPSPQCLR SPPVTRCPNP EVKHGYKLN KTHSAYSHND IVYVDCNPGF IMNGSRVIRC HTDNTWVPGV PTCIKKAFIG CPPPPKTPNG NHTGGNIARF SPGMSILYSC DQGYLLVGE ALLLCTHEGT WSQPAPHCKE VNCSSPADMD GIQKGLEPRK MYQYGAVVTL ECEDGYMLEG SPQSQCQSDH Q WNPPLAVC RSRHHHHHH

UniProtKB: Complement receptor type 2

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Macromolecule #2: BLLF1

MacromoleculeName: BLLF1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: human gammaherpesvirus 4 (Epstein-Barr virus)
Molecular weightTheoretical: 90.96225 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARGSHHH HHHHHHHEAA LLVCQYTIQS LIHLTGEDPG FFNVEIPEFP FYPTCNVCT ADVNVTINFD VGGKKHQLDL DFGQLTPHTK AVYQPRGAFG GSENATNLFL LELLGAGELA LTMRSKKLPI N VTTGEEQQ ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARGSHHH HHHHHHHEAA LLVCQYTIQS LIHLTGEDPG FFNVEIPEFP FYPTCNVCT ADVNVTINFD VGGKKHQLDL DFGQLTPHTK AVYQPRGAFG GSENATNLFL LELLGAGELA LTMRSKKLPI N VTTGEEQQ VSLESVDVYF QDVFGTMWCH HAEMQNPVYL IPETVPYIKW DNCNSTNITA VVRAQGLDVT LPLSLPTSAQ DS NFSVKTQ MLGNEIDIEC IMEDGEISQV LPGDNKFNIT CSGYESHVPS GGILTSTSPV ATPIPGTGYA YSLRLTPRPV SRF LGNNSI LYVFYSGNGP KASGGDYCIQ SNIVFSDEIP ASQDMPTNTT DITYVGDNAT YSVPMVTSED ANSPNVTVTA FWAW PNNTE TDFKCKWTLT SGTPSGCENI SGAFASNRTF DITVSGLGTA PKTLIITRTA TNATTTTHKV IFSKAPESTT TSPTL NTTG FADPNTTTGL PSSTHVPTNL TAPASTGPTV STADVTSPTP AGTTSGASPV TPSPSPRDNG TESKAPDMTS PTSAVT TPT PNGTSPTPAM TTPTPNATSP TLGKTSPTSA VTTPTPNATS PTPAVTTPTP NATSPTVGET SPQANATNHT LGGTSPT PV VTSPPKNATS DVTTGQHNRT SSSTSSMSLR PSSIPETTSH MPLLTSAHPT GGENITQVTP ASISTHHVST SSPAPRPG T TSQASGPGNS STSTKPGEVN VTKGTPPKNA TSPQAPSGQK TAVPTVTSTG GKANSTTGGK HTTGHGARTS TEPTTDYGD DSTTPRPRYN ATTYLPPSTS SKLRPRWTFT SPPVTTAQAT VPVPPTSQPR FSNLHHHHHH HHHH

UniProtKB: BLLF1

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Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / 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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 139264
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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