[English] 日本語
Yorodumi
- EMDB-39194: HPV11 L1 pentamer in complex with Fab F5-187 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-39194
TitleHPV11 L1 pentamer in complex with Fab F5-187
Map data
Sample
  • Complex: HPV11 L1 pentamer in complex with Fab F5-187
    • Complex: Fab F5-187
      • Protein or peptide: heavy chain of F5-187
      • Protein or peptide: light chain of F5-187
    • Complex: HPV11 L1 pentamer
      • Protein or peptide: Major capsid protein L1
KeywordsHPV / L1 / antibody / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 speciesHomo sapiens (human) / human papillomavirus 11
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsWang X / Fu W
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: HPV11 L1 pentamer in complex with Fab F5-187
Authors: Wang X / Fu W
History
DepositionFeb 22, 2024-
Header (metadata) releaseFeb 26, 2025-
Map releaseFeb 26, 2025-
UpdateFeb 26, 2025-
Current statusFeb 26, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_39194.png

Downloads & links

-
Map

FileDownload / File: emd_39194.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 200 pix.
= 214. Å		1.07 Å/pix.
x 200 pix.
= 214. Å		1.07 Å/pix.
x 200 pix.
= 214. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.097022876 - 0.15367119
Average (Standard dev.)-0.00049807574 (±0.007119039)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 214.00002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #1

Fileemd_39194_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_39194_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : HPV11 L1 pentamer in complex with Fab F5-187

EntireName: HPV11 L1 pentamer in complex with Fab F5-187
Components
  • Complex: HPV11 L1 pentamer in complex with Fab F5-187
    • Complex: Fab F5-187
      • Protein or peptide: heavy chain of F5-187
      • Protein or peptide: light chain of F5-187
    • Complex: HPV11 L1 pentamer
      • Protein or peptide: Major capsid protein L1

-
Supramolecule #1: HPV11 L1 pentamer in complex with Fab F5-187

SupramoleculeName: HPV11 L1 pentamer in complex with Fab F5-187 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

-
Supramolecule #2: Fab F5-187

SupramoleculeName: Fab F5-187 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #3
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #3: HPV11 L1 pentamer

SupramoleculeName: HPV11 L1 pentamer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: human papillomavirus 11

-
Macromolecule #1: heavy chain of F5-187

MacromoleculeName: heavy chain of F5-187 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.179688 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLLESGGG LVQPGGSLRL SCAASGLTFS SYAMSWVRQA PGKGLEWVSS ISASGGSTYY ADSVRGRFTI SRDNSRTTLY LQMNILRAE DTAVYYCAKD RMGVRGSGWF DYWGQGTLVT VSS

-
Macromolecule #2: Major capsid protein L1

MacromoleculeName: Major capsid protein L1 / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: human papillomavirus 11
Molecular weightTheoretical: 50.384586 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AVVATDAYVK RTNIFYHASS SRLLAVGHPY YSIKKVNKTV VPKVSGYQYR VFKVVLPDPN KFALPDSSLF DPTTQRLVWA CTGLEVGRG QPLGVGVSGH PLLNKYDDVE NSGGYGGNPG QDNRVNVGMD YKQTQLCMVG CAPPLGEHWG KGTQCSNTSV Q NGDCPPLE ...String:
AVVATDAYVK RTNIFYHASS SRLLAVGHPY YSIKKVNKTV VPKVSGYQYR VFKVVLPDPN KFALPDSSLF DPTTQRLVWA CTGLEVGRG QPLGVGVSGH PLLNKYDDVE NSGGYGGNPG QDNRVNVGMD YKQTQLCMVG CAPPLGEHWG KGTQCSNTSV Q NGDCPPLE LITSVIQDGD MVDTGFGAMN FADLQTNKSD VPLDICGTVC KYPDYLQMAA DPYGDRLFFY LRKEQMFARH FF NRAGTVG EPVPDDLLVK GGNNRSSVAS SIYVHTPSGS LVSSEAQLFN KPYWLQKAQG HNNGICWGNH LFVTVVDTTR STN MTLCAS VSKSATYTNS DYKEYMRHVE EFDLQFIFQL CSITLSAEVM AYIHTMNPSV LEDWNFGLSP PPNGTLEDTY RYVQ SQAIT CQKPTPEKEK QDPYKDMSFW EVNLKEKFSS ELDQFPLGRK FLLQSGY

UniProtKB: Major capsid protein L1

-
Macromolecule #3: light chain of F5-187

MacromoleculeName: light chain of F5-187 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.51592 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIVMTQSPDS LAVSLGERAT INCKSSQSIL YSSSNKNYLA WYQQKPGQPP KLLIYWASTR ESGVPDRFSG SGSGTDFTLT ISSLLPEDV AVYYCQQYHS TPWTFGQGTK VEIK

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 216722
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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