[English] 日本語
Yorodumi
- EMDB-5990: Electron cryo-microscopy of quasi-human papillomavirus 16 complex... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-5990
TitleElectron cryo-microscopy of quasi-human papillomavirus 16 complexed with Fab H16.1A
Map dataReconstruction of quasi-HPV16-Fab1A complex
Sample
  • Sample: Quasi-HPV16 complex with Fab H16.1A
  • Virus: Human papillomavirus 16
  • Protein or peptide: H16.1A Fab
Keywordsneutralization / quasi-human papillomavirus 16 / H16.1A
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 speciesunidentified (others) / Human papillomavirus 16
Methodsingle particle reconstruction / cryo EM / Resolution: 14.0 Å
AuthorsGuan J / Brendle S / Bywaters S / Lee H / Ashley RE / Conway JF / Makhov AM / Christensen N / Hafenstein S
CitationJournal: Virology / Year: 2015
Title: Structural comparison of four different antibodies interacting with human papillomavirus 16 and mechanisms of neutralization.
Authors: Jian Guan / Stephanie M Bywaters / Sarah A Brendle / Hyunwook Lee / Robert E Ashley / Alexander M Makhov / James F Conway / Neil D Christensen / Susan Hafenstein /
Abstract: Cryo-electron microscopy (cryo-EM) was used to solve the structures of human papillomavirus type 16 (HPV16) complexed with fragments of antibody (Fab) from three different neutralizing monoclonals ...Cryo-electron microscopy (cryo-EM) was used to solve the structures of human papillomavirus type 16 (HPV16) complexed with fragments of antibody (Fab) from three different neutralizing monoclonals (mAbs): H16.1A, H16.14J, and H263.A2. The structure-function analysis revealed predominantly monovalent binding of each Fab with capsid interactions that involved multiple loops from symmetry related copies of the major capsid protein. The residues identified in each Fab-virus interface map to a conformational groove on the surface of the capsomer. In addition to the known involvement of the FG and HI loops, the DE loop was also found to constitute the core of each epitope. Surprisingly, the epitope mapping also identified minor contributions by EF and BC loops. Complementary immunological assays included mAb and Fab neutralization. The specific binding characteristics of mAbs correlated with different neutralizing behaviors in pre- and post-attachment neutralization assays.
History
DepositionJun 20, 2014-
Header (metadata) releaseJul 30, 2014-
Map releaseMay 6, 2015-
UpdateJun 3, 2015-
Current statusJun 3, 2015Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3j8z
  • Surface level: 1.2
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j8z
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5990.jpg

Downloads & links

-
Map

FileDownload / File: emd_5990.map.gz / Format: CCP4 / Size: 808.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of quasi-HPV16-Fab1A complex
Voxel sizeX=Y=Z: 1.3 Å
Density
Contour LevelBy AUTHOR: 1.0 / Movie #1: 0.6
Minimum - Maximum-1.82998371 - 4.16103792
Average (Standard dev.)0.00000001 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-300-300-300
Dimensions601601601
Spacing601601601
CellA=B=C: 781.3 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z601601601
origin x/y/z0.0000.0000.000
length x/y/z781.300781.300781.300
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-300-300-300
NC/NR/NS601601601
D min/max/mean-1.8304.1610.000

-
Supplemental data

-
Sample components

-
Entire : Quasi-HPV16 complex with Fab H16.1A

EntireName: Quasi-HPV16 complex with Fab H16.1A
Components
  • Sample: Quasi-HPV16 complex with Fab H16.1A
  • Virus: Human papillomavirus 16
  • Protein or peptide: H16.1A Fab

-
Supramolecule #1000: Quasi-HPV16 complex with Fab H16.1A

SupramoleculeName: Quasi-HPV16 complex with Fab H16.1A / type: sample / ID: 1000
Oligomeric state: Three hundred H16.1A Fabs bind to one HPV16 capsid
Number unique components: 2

-
Supramolecule #1: Human papillomavirus 16

SupramoleculeName: Human papillomavirus 16 / type: virus / ID: 1 / Details: Isolated by gradient centrifugation. / NCBI-ID: 337041 / Sci species name: Human papillomavirus 16 / Database: NCBI / Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Molecular weightTheoretical: 27.8 MDa
Virus shellShell ID: 1 / Name: L1 L2 / Diameter: 720 Å / T number (triangulation number): 7

-
Macromolecule #1: H16.1A Fab

MacromoleculeName: H16.1A Fab / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes / Database: NCBI
Source (natural)Organism: unidentified (others)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1.2 mg/mL
VitrificationCryogen name: ETHANE-PROPANE MIXTURE / Instrument: FEI VITROBOT MARK III

-
Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
DateJan 9, 2013
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Number real images: 50
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: auto3dem
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 14.0 Å / Resolution method: OTHER / Software - Name: auto3dem / Number images used: 2300

-
Atomic model buiding 1

Initial modelPDB ID:

3oae
PDB Unreleased entry

SoftwareName: Chimera, Situs
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-3j8z:
Cryo-EM reconstruction of quasi-HPV16 complex with H16.1A Fab

+
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