[English] 日本語
Yorodumi
- PDB-3jba: The U4 antibody epitope on human papillomavirus 16 identified by ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3jba
TitleThe U4 antibody epitope on human papillomavirus 16 identified by cryo-EM
Components
  • H16.U4 antibody heavy chain
  • H16.U4 antibody light chain
  • Major capsid protein L1
KeywordsVIRUS/IMMUNE SYSTEM / HPV16 / antibody / U4 / neutralization / Fab / VIRUS-IMMUNE SYSTEM complex
Function / homology
Function and homology information


T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / host cell nucleus / virion attachment to host cell / 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 / Major capsid protein L1
Similarity search - Component
Biological speciesHuman papillomavirus type 16
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 12 Å
AuthorsGuan, J. / Bywaters, S.M. / Brendle, S.A. / Lee, H. / Ashley, R.E. / Christensen, N.D. / Hafenstein, S.
CitationJournal: J Virol / Year: 2015
Title: The U4 Antibody Epitope on Human Papillomavirus 16 Identified by Cryo-electron Microscopy.
Authors: Jian Guan / Stephanie M Bywaters / Sarah A Brendle / Hyunwook Lee / Robert E Ashley / Neil D Christensen / Susan Hafenstein /
Abstract: The human papillomavirus (HPV) major structural protein L1 composes capsomers that are linked together through interactions mediated by the L1 C terminus to constitute a T=7 icosahedral capsid. H16. ...The human papillomavirus (HPV) major structural protein L1 composes capsomers that are linked together through interactions mediated by the L1 C terminus to constitute a T=7 icosahedral capsid. H16.U4 is a type-specific monoclonal antibody recognizing a conformation-dependent neutralizing epitope of HPV thought to include the L1 protein C terminus. The structure of human papillomavirus 16 (HPV16) complexed with H16.U4 fragments of antibody (Fab) was solved by cryo-electron microscopy (cryo-EM) image reconstruction. Atomic structures of virus and Fab were fitted into the corresponding cryo-EM densities to identify the antigenic epitope. The antibody footprint mapped predominately to the L1 C-terminal arm with an additional contact point on the side of the capsomer. This footprint describes an epitope that is presented capsid-wide. However, although the H16.U4 epitope suggests the presence of 360 potential binding sites exposed in the capsid valley between each capsomer, H16.U4 Fab bound only to epitopes located around the icosahedral five-fold vertex of the capsid. Thus, the binding characteristics of H16.U4 defined in this study showed a distinctive selectivity for local conformation-dependent interactions with specific L1 invading arms between five-fold related capsomers.
IMPORTANCE: Human papillomavirus 16 (HPV16) is the most prevalent oncogenic genotype in HPV-associated anogenital and oral cancers. Here we use cryo-EM reconstruction techniques to solve the ...IMPORTANCE: Human papillomavirus 16 (HPV16) is the most prevalent oncogenic genotype in HPV-associated anogenital and oral cancers. Here we use cryo-EM reconstruction techniques to solve the structures of the HPV16 capsid complexes using H16.U4 fragment of antibody (Fab). Different from most other antibodies directed against surface loops, H16.U4 monoclonal antibody is unique in targeting the C-terminal arm of the L1 protein. This monoclonal antibody (MAb) is used throughout the HPV research community in HPV serological and vaccine development and to define mechanisms of HPV uptake. The unique binding mode of H16.U4 defined here shows important conformation-dependent interactions within the HPV16 capsid. By targeting an important structural and conformational epitope, H16.U4 may identify subtle conformational changes in different maturation stages of the HPV capsid and provide a key probe to analyze the mechanisms of HPV uptake during the early stages of virus infection. Our analyses precisely define important conformational epitopes on HPV16 capsids that are key targets for successful HPV prophylactic vaccines.
History
DepositionAug 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name

-
Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-6424
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-6424
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: H16.U4 antibody light chain
H: H16.U4 antibody heavy chain
B: Major capsid protein L1
A: Major capsid protein L1
E: Major capsid protein L1
D: Major capsid protein L1
C: Major capsid protein L1
F: Major capsid protein L1


Theoretical massNumber of molelcules
Total (without water)346,0848
Polymers346,0848
Non-polymers00
Water00
1
L: H16.U4 antibody light chain
H: H16.U4 antibody heavy chain
B: Major capsid protein L1
A: Major capsid protein L1
E: Major capsid protein L1
D: Major capsid protein L1
C: Major capsid protein L1
F: Major capsid protein L1
x 60


Theoretical massNumber of molelcules
Total (without water)20,765,039480
Polymers20,765,039480
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
L: H16.U4 antibody light chain
H: H16.U4 antibody heavy chain
B: Major capsid protein L1
A: Major capsid protein L1
E: Major capsid protein L1
D: Major capsid protein L1
C: Major capsid protein L1
F: Major capsid protein L1
x 5


  • icosahedral pentamer
  • 1.73 MDa, 40 polymers
Theoretical massNumber of molelcules
Total (without water)1,730,42040
Polymers1,730,42040
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
L: H16.U4 antibody light chain
H: H16.U4 antibody heavy chain
B: Major capsid protein L1
A: Major capsid protein L1
E: Major capsid protein L1
D: Major capsid protein L1
C: Major capsid protein L1
F: Major capsid protein L1
x 6


  • icosahedral 23 hexamer
  • 2.08 MDa, 48 polymers
Theoretical massNumber of molelcules
Total (without water)2,076,50448
Polymers2,076,50448
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

-
Components

#1: Antibody H16.U4 antibody light chain


Mass: 12699.254 Da / Num. of mol.: 1 / Fragment: Fab variable domain / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody H16.U4 antibody heavy chain


Mass: 12711.025 Da / Num. of mol.: 1 / Fragment: Fab variable domain / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Protein
Major capsid protein L1


Mass: 53445.617 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus type 16 / Gene: L1 / Plasmid: SV40 / Cell line (production host): HEK293TT / Production host: Homo sapiens (human) / References: UniProt: C9E771, UniProt: P03101*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeParent-ID
1Quasi-HPV16 complexed with H16.U4 FabCOMPLEX0
2Human papillomavirusVIRUS1
3H16.U4 antibody1
Molecular weightValue: 32.8 MDa / Experimental value: NO
Details of virusEmpty: NO / Enveloped: NO / Host category: VERTEBRATES / Isolate: SEROTYPE / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Homo sapiens
Buffer solutionName: 1 M NaCl, 200 mM Tris / pH: 7.4 / Details: 1 M NaCl, 200 mM Tris
SpecimenConc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: glow-discharged holey carbon support grid
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temp: 102 K / Humidity: 90 % / Details: Plunged into liquid ethane (GATAN CRYOPLUNGE 3).

-
Electron microscopy imaging

MicroscopyModel: JEOL 2100 / Date: Jul 22, 2014
Electron gunElectron source: LAB6 / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 5430 nm / Nominal defocus min: 1600 nm / Cs: 2 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN / Temperature: 95 K
Image recordingElectron dose: 15 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Image scansNum. digital images: 151
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

EM software
IDNameVersionCategory
1Situsmodel fitting
2UCSF Chimeramodel fitting
3Auto3DEM3D reconstruction
4EMAN23D reconstruction
5RELION3D reconstruction
CTF correctionDetails: each particle
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: Cross-common lines / Resolution: 12 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 5806 / Nominal pixel size: 2.33 Å / Actual pixel size: 2.33 Å
Details: (Single particle details: The particles were selected using semi-automatic program e2boxer.py.) (Single particle--Applied symmetry: I)
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Details: REFINEMENT PROTOCOL--rigid body
Atomic model buildingPDB-ID: 3J6R

3j6r


Pdb chain-ID: F
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms13253 0 0 0 13253

+
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