[English] 日本語
Yorodumi
- EMDB-49960: Atomic resolution cryoEM structure of HPV16 bound to heparin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-49960
TitleAtomic resolution cryoEM structure of HPV16 bound to heparin
Map dataComposite map generated from two subparticles, one copy of the pentavalent subparticle and six copies of the hexavalent subparticle.
Sample
  • Virus: Human papillomavirus 16
    • Protein or peptide: Major capsid protein L1
  • Ligand: MAGNESIUM ION
  • Ligand: water
KeywordsHPV / heparin / VIRUS
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 16
Methodsingle particle reconstruction / cryo EM / Resolution: 1.9 Å
AuthorsLangley CH / Hafenstein SL
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)7R01AI134910-04 United States
CitationJournal: Nat Commun / Year: 2026
Title: Atomic resolution structure of human papillomavirus bound to heparin.
Authors: Caroline H Langley / Daniel J Goetschius / Santiago Antolínez / Ebere Precious Orji / Carol M Bator / Sarah A Brendle / Neil D Christensen / Jodi A Hadden-Perilla / Susan L Hafenstein /
Abstract: Human papillomavirus (HPV) is a significant health burden and leading cause of virus-induced cancers. The mechanisms of HPV receptor binding and host entry are not completely understood, although it ...Human papillomavirus (HPV) is a significant health burden and leading cause of virus-induced cancers. The mechanisms of HPV receptor binding and host entry are not completely understood, although it is known that heparan sulfate proteoglycans (HSPGs) mediate entry. HPV16 quasivirus, composed of L1 and L2 capsid proteins with a packaged cottontail rabbit papillomavirus genome was incubated with heparin. The complex was vitrified, and data were collected for cryoEM single particle analysis. Subparticles were extracted and hexavalent and pentavalent capsomers were refined separately. Here we present the resulting 1.9 Å resolution structure, with heparin visualized around the capsomer at the icosahedral fivefold vertex. A model of the asymmetric unit was built unambiguously into the atomic resolution cryoEM map. Hydrogen bonds are predicted between L1 N-terminal regions, which are supported by molecular dynamics. The heparin binding site was identified, along with local L1 conformational changes and global flexibility changes. These changes induced by heparin binding likely reflect the structure of HPV during early stages of entry and provide a framework for future HPV biochemical, genetic, and biophysical studies.
History
DepositionApr 1, 2025-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_49960.png

Downloads & links

-
Map

FileDownload / File: emd_49960.map.gz / Format: CCP4 / Size: 1.6 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map generated from two subparticles, one copy of the pentavalent subparticle and six copies of the hexavalent subparticle.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.52 Å/pix.
x 760 pix.
= 392.92 Å		0.52 Å/pix.
x 760 pix.
= 392.92 Å		0.52 Å/pix.
x 760 pix.
= 392.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.517 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.9
Minimum - Maximum-0.2735523 - 7.9058557
Average (Standard dev.)0.12660898 (±0.21094131)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions760760760
Spacing760760760
CellA=B=C: 392.92 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Human papillomavirus 16

EntireName: Human papillomavirus 16
Components
  • Virus: Human papillomavirus 16
    • Protein or peptide: Major capsid protein L1
  • Ligand: MAGNESIUM ION
  • Ligand: water

-
Supramolecule #1: Human papillomavirus 16

SupramoleculeName: Human papillomavirus 16 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / NCBI-ID: 333760 / Sci species name: Human papillomavirus 16 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Major capsid protein L1

MacromoleculeName: Major capsid protein L1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Human papillomavirus 16
Molecular weightTheoretical: 54.160387 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSLWLPSEAT VYLPPVPVSK VVSTDEYVAR TNIYYHAGTS RLLAVGHPYF PIKKPNNNKI LVPKVSGLQY RVFRIHLPDP NKFGFPDTS FYNPDTQRLV WACVGVEVGR GQPLGVGISG HPLLNKLDDT ENASAYAANA GVDNRECISM DYKQTQLCLI G CKPPIGEH ...String:
MSLWLPSEAT VYLPPVPVSK VVSTDEYVAR TNIYYHAGTS RLLAVGHPYF PIKKPNNNKI LVPKVSGLQY RVFRIHLPDP NKFGFPDTS FYNPDTQRLV WACVGVEVGR GQPLGVGISG HPLLNKLDDT ENASAYAANA GVDNRECISM DYKQTQLCLI G CKPPIGEH WGKGSPCTNV AVNPGDCPPL ELINTVIQDG DMVDTGFGAM DFTTLQANKS EVPLDICTSI CKYPDYIKMV SE PYGDSLF FYLRREQMFV RHLFNRAGAV GENVPDDLYI KGSGSTANLA SSNYFPTPSG SMVTSDAQIF NKPYWLQRAQ GHN NGICWG NQLFVTVVDT TRSTNMSLCA AISTSETTYK NTNFKEYLRH GEEYDLQFIF QLCKITLTAD VMTYIHSMNS TILE DWNFG LQPPPGGTLE DTYRFVTSQA IACQKHTPPA PKEDPLKKYT FWEVNLKEKF SADLDQFPLG RKFLLQAGLK AKPKF TLGK R

UniProtKB: Major capsid protein L1

-
Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 189 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 1369 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 39.75 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: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 44159
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more