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- EMDB-65478: Local refinement region of HPV45 in complex with antibody 10G2 -

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Basic information

Entry
Database: EMDB / ID: EMD-65478
TitleLocal refinement region of HPV45 in complex with antibody 10G2
Map data
Sample
  • Complex: Local refinement region of HPV45 in complex with antibody 10G2
    • Complex: Human papillomavirus type 45
      • Protein or peptide: Major capsid protein L1
    • Complex: The Fab fragment of 10G2
      • Protein or peptide: 10G2 Fab light chain
      • Protein or peptide: 10G2 Fab heavy chain
KeywordsHuman papillomavirus / Cryo-EM / structural protein / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity
Similarity search - Function
Major capsid L1 (late) protein, Papillomavirus / Major capsid L1 (late) superfamily, Papillomavirus / L1 (late) protein / Double-stranded DNA virus, group I, capsid
Similarity search - Domain/homology
Major capsid protein L1
Similarity search - Component
Biological specieshuman papillomavirus 45 / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.81 Å
AuthorsJiang Y / Sun H / Zheng Q / Li S
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2026
Title: Cryo-EM structure of human papillomavirus type 45 in complexed with the Fab fragment of 10G2
Authors: Jiang Y / Sun H / Wang Z / Zheng Q / Li S / Xia N
History
DepositionJul 22, 2025-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateFeb 11, 2026-
Current statusFeb 11, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65478.png

Downloads & links

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Map

FileDownload / File: emd_65478.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 300 pix.
= 300. Å		1 Å/pix.
x 300 pix.
= 300. Å		1 Å/pix.
x 300 pix.
= 300. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-1.2301737 - 1.6825769
Average (Standard dev.)0.0014562515 (±0.029075434)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 300.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65478_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_65478_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 : Local refinement region of HPV45 in complex with antibody 10G2

EntireName: Local refinement region of HPV45 in complex with antibody 10G2
Components
  • Complex: Local refinement region of HPV45 in complex with antibody 10G2
    • Complex: Human papillomavirus type 45
      • Protein or peptide: Major capsid protein L1
    • Complex: The Fab fragment of 10G2
      • Protein or peptide: 10G2 Fab light chain
      • Protein or peptide: 10G2 Fab heavy chain

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Supramolecule #1: Local refinement region of HPV45 in complex with antibody 10G2

SupramoleculeName: Local refinement region of HPV45 in complex with antibody 10G2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Human papillomavirus type 45

SupramoleculeName: Human papillomavirus type 45 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: human papillomavirus 45

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Supramolecule #3: The Fab fragment of 10G2

SupramoleculeName: The Fab fragment of 10G2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Major capsid protein L1

MacromoleculeName: Major capsid protein L1 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: human papillomavirus 45
Molecular weightTheoretical: 57.379891 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MALWRPSDST VYLPPPSVAR VVSTDDYVSR TSIFYHAGSS RLLTVGNPYF RVVPNGAGNK QAVPKVSAYQ YRVFRVALPD PNKFGLPDS TIYNPETQRL VWACVGMEIG RGQPLGIGLS GHPFYNKLDD TESAHAATAV ITQDVRDNVS VDYKQTQLCI L GCVPAIGE ...String:
MALWRPSDST VYLPPPSVAR VVSTDDYVSR TSIFYHAGSS RLLTVGNPYF RVVPNGAGNK QAVPKVSAYQ YRVFRVALPD PNKFGLPDS TIYNPETQRL VWACVGMEIG RGQPLGIGLS GHPFYNKLDD TESAHAATAV ITQDVRDNVS VDYKQTQLCI L GCVPAIGE HWAKGTLCKP AQLQPGDCPP LELKNTIIED GDMVDTGYGA MDFSTLQDTK CEVPLDICQS ICKYPDYLQM SA DPYGDSM FFCLRREQLF ARHFWNRAGV MGDTVPTDLY IKGTSANMRE TPGSCVYSPS PSGSIITSDS QLFNKPYWLH KAQ GHNNGI CWHNQLFVTV VDTTRSTNLT LCASTQNPVP STYDPTKFKQ YSRHVEEYDL QFIFQLCTIT LTAEVMSYIH SMNS SILEN WNFGVPPPPT TSLVDTYRFV QSVAVTCQKD TTPPEKQDPY DKLKFWTVDL KEKFSSDLDQ YPLGRKFLVQ AGLRR RPTI GPRKRPAAST STASTASRPA KRVRIRSKK

UniProtKB: Major capsid protein L1

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Macromolecule #2: 10G2 Fab light chain

MacromoleculeName: 10G2 Fab light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 12.215571 KDa
SequenceString:
DIVLTQSPAS LSVSLGQRAT ISCRASQSVS TSSYSYMHWY QQKPGQPPKL LIKYASNLDS GVPARFSGSG SGTDFTLNIH PVEEEDTAK YYCQHSWEIP WTFGGGTKLE IK

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Macromolecule #3: 10G2 Fab heavy chain

MacromoleculeName: 10G2 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.365791 KDa
SequenceString:
QVQLQQPGAE LVKPGASVKL SCKASGYSFT SYWMHWVKQR PGQGLEWIGE IDPSNSNTNY NQKFKGKATL TVDKSSSTAY MQLSSLTSE DSAVYYCARF YGTNYYAMDY WGQGTSVTSL S

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.4 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.81 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 993420
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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