[English] 日本語
Yorodumi
- PDB-6bt3: High-Resolution Structure Analysis of Antibody V5 Conformational ... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6bt3
TitleHigh-Resolution Structure Analysis of Antibody V5 Conformational Epitope on Human Papillomavirus 16
Components
  • Major capsid protein L1
  • V5 Fab Heavy-chain
  • V5 Fab Light-chain
KeywordsVIRUS / HPV16 / H16.V5 / Fab / VIRUS LIKE PARTICLE-IMMUNE SYSTEM complex
Function / homologyDouble-stranded DNA virus, group I, capsid / Major capsid L1 (late) protein, Papillomavirus / Major capsid L1 (late) superfamily, Papillomavirus / L1 (late) protein / T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / host cell nucleus / virion attachment to host cell / structural molecule activity / Major capsid protein L1
Function and homology information
Specimen sourceMus musculus (house mouse)
Human papillomavirus type 16
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.7 Å resolution
AuthorsGuan, J. / Bywaters, S.M. / Brendle, S.A. / Ashley, R.E. / Makhov, A.M. / Conway, J.F. / Christensen, N.D. / Hafenstein, S.
CitationJournal: Viruses / Year: 2017
Title: High-Resolution Structure Analysis of Antibody V5 and U4 Conformational Epitopes on Human Papillomavirus 16.
Authors: Jian Guan / Stephanie M Bywaters / Sarah A Brendle / Robert E Ashley / Alexander M Makhov / James F Conway / Neil D Christensen / Susan Hafenstein
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 5, 2017 / Release: Jan 17, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jan 17, 2018Structure modelrepositoryInitial release
1.1Jan 24, 2018Structure modelSource and taxonomyentity_src_nat_entity_src_nat.common_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-8243
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-8243
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: V5 Fab Light-chain
B: V5 Fab Heavy-chain
C: V5 Fab Light-chain
D: V5 Fab Heavy-chain
E: V5 Fab Light-chain
F: V5 Fab Heavy-chain
G: V5 Fab Light-chain
H: V5 Fab Heavy-chain
I: Major capsid protein L1
J: Major capsid protein L1
K: Major capsid protein L1
L: Major capsid protein L1
M: Major capsid protein L1
N: Major capsid protein L1


Theoretical massNumber of molelcules
Total (without water)526,88014
Polyers526,88014
Non-polymers00
Water0
1
A: V5 Fab Light-chain
B: V5 Fab Heavy-chain
C: V5 Fab Light-chain
D: V5 Fab Heavy-chain
E: V5 Fab Light-chain
F: V5 Fab Heavy-chain
G: V5 Fab Light-chain
H: V5 Fab Heavy-chain
I: Major capsid protein L1
J: Major capsid protein L1
K: Major capsid protein L1
L: Major capsid protein L1
M: Major capsid protein L1
N: Major capsid protein L1
x 60


Theoretical massNumber of molelcules
Total (without water)31,612,780840
Polyers31,612,780840
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
A: V5 Fab Light-chain
B: V5 Fab Heavy-chain
C: V5 Fab Light-chain
D: V5 Fab Heavy-chain
E: V5 Fab Light-chain
F: V5 Fab Heavy-chain
G: V5 Fab Light-chain
H: V5 Fab Heavy-chain
I: Major capsid protein L1
J: Major capsid protein L1
K: Major capsid protein L1
L: Major capsid protein L1
M: Major capsid protein L1
N: Major capsid protein L1
x 5


  • icosahedral pentamer
  • 2.63 MDa, 70 polymers
Theoretical massNumber of molelcules
Total (without water)2,634,39870
Polyers2,634,39870
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: V5 Fab Light-chain
B: V5 Fab Heavy-chain
C: V5 Fab Light-chain
D: V5 Fab Heavy-chain
E: V5 Fab Light-chain
F: V5 Fab Heavy-chain
G: V5 Fab Light-chain
H: V5 Fab Heavy-chain
I: Major capsid protein L1
J: Major capsid protein L1
K: Major capsid protein L1
L: Major capsid protein L1
M: Major capsid protein L1
N: Major capsid protein L1
x 6


  • icosahedral 23 hexamer
  • 3.16 MDa, 84 polymers
Theoretical massNumber of molelcules
Total (without water)3,161,27884
Polyers3,161,27884
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

-
Components

#1: Protein/peptide
V5 Fab Light-chain


Mass: 23832.492 Da / Num. of mol.: 4 / Source: (natural) Mus musculus (house mouse)
#2: Protein/peptide
V5 Fab Heavy-chain


Mass: 23739.500 Da / Num. of mol.: 4 / Source: (natural) Mus musculus (house mouse)
#3: Protein/peptide
Major capsid protein L1


Mass: 56098.617 Da / Num. of mol.: 6 / Source: (natural) Human papillomavirus type 16 / References: UniProt: P03101

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: HPV16 complexed with V5 Fab / Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5, 6, 7 / Source: MULTIPLE SOURCES
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 7 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 17612 / Symmetry type: POINT

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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