[English] 日本語
Yorodumi
- EMDB-41275: CryoEM structure of neutralizing antibodies CBH-7 and HC84.26 in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-41275
TitleCryoEM structure of neutralizing antibodies CBH-7 and HC84.26 in complex with Hepatitis C virus envelope glycoprotein E2
Map data
Sample
  • Complex: Ternary complex of CBH7-E2-HC84.26
    • Protein or peptide: CBH-7 Heavy chain
    • Protein or peptide: CBH-7 Light chain
    • Protein or peptide: envelope glycoprotein E2
    • Protein or peptide: HC84.26 Heavy chain
    • Protein or peptide: HC84.26 Light chain
KeywordsImmune system / vaccine target / E2 glycoprotein / HCV / ternary complex / ANTIVIRAL PROTEIN
Function / homology
Function and homology information


host cell lipid droplet / lipid droplet / clathrin-dependent endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / viral envelope / virion membrane / membrane
Similarity search - Function
Hepatitis C virus, Non-structural protein E2/NS1 / Hepatitis C virus non-structural protein E2/NS1 / Hepatitis C virus, Envelope glycoprotein E1 / Hepatitis C virus envelope glycoprotein E1
Similarity search - Domain/homology
Biological speciesHomo sapiens (human) / Hepacivirus C
Methodsingle particle reconstruction / cryo EM / Resolution: 3.25 Å
AuthorsShahid S / Jiang L / Liu Y / Hasan SS / Mariuzza RA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI168048 United States
CitationJournal: To Be Published
Title: CryoEM structure of neutralizing antibodies CBH-7 and HC84.26 in complex with Hepatitis C virus envelope glycoprotein E2
Authors: Shahid S / Jiang L / Liu Y / Hasan SS / Mariuzza RA
History
DepositionJul 18, 2023-
Header (metadata) releaseJul 24, 2024-
Map releaseJul 24, 2024-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_41275.png

Downloads & links

-
Map

FileDownload / File: emd_41275.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 320 pix.
= 358.4 Å		1.12 Å/pix.
x 320 pix.
= 358.4 Å		1.12 Å/pix.
x 320 pix.
= 358.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.2386196 - 2.0475736
Average (Standard dev.)-0.0003000488 (±0.029400777)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 358.4 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_41275_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_41275_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Ternary complex of CBH7-E2-HC84.26

EntireName: Ternary complex of CBH7-E2-HC84.26
Components
  • Complex: Ternary complex of CBH7-E2-HC84.26
    • Protein or peptide: CBH-7 Heavy chain
    • Protein or peptide: CBH-7 Light chain
    • Protein or peptide: envelope glycoprotein E2
    • Protein or peptide: HC84.26 Heavy chain
    • Protein or peptide: HC84.26 Light chain

-
Supramolecule #1: Ternary complex of CBH7-E2-HC84.26

SupramoleculeName: Ternary complex of CBH7-E2-HC84.26 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 340 KDa

-
Macromolecule #1: CBH-7 Heavy chain

MacromoleculeName: CBH-7 Heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.417719 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDWTWRFLFV VAAATVQSQV QLVQSGAEVR KPGSSVKISC KASGGTFNNY ALSWVRQAPG QGLDWMGEIT PIFGTEKYAQ KFQGRVTIT ADESTNTLYM DLSSLRSEDS AVYYCARRGY IYGSPFDYWG QGTLVTVSSA STKGPSVFPL APSSKSTSGG T AALGCLVK ...String:
MDWTWRFLFV VAAATVQSQV QLVQSGAEVR KPGSSVKISC KASGGTFNNY ALSWVRQAPG QGLDWMGEIT PIFGTEKYAQ KFQGRVTIT ADESTNTLYM DLSSLRSEDS AVYYCARRGY IYGSPFDYWG QGTLVTVSSA STKGPSVFPL APSSKSTSGG T AALGCLVK DYFPEPVTVS WNSGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKRVEP KS CDKTAGW SHPQFEK

-
Macromolecule #2: CBH-7 Light chain

MacromoleculeName: CBH-7 Light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.477658 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDMRVPAQLL GLLLLWLRAR CDVLMTQSPS SLSASVGDRV TISCRASQSI SSFLNWYQQK PGKAPKLLIS AASSLSSGVP SRFSGSGSG TSFTLTISSL QPEDVATYYC QQSYSFLLTF GGGTNVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN F YPREAKVQ ...String:
MDMRVPAQLL GLLLLWLRAR CDVLMTQSPS SLSASVGDRV TISCRASQSI SSFLNWYQQK PGKAPKLLIS AASSLSSGVP SRFSGSGSG TSFTLTISSL QPEDVATYYC QQSYSFLLTF GGGTNVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN F YPREAKVQ WKVDNALQSG NSQESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

-
Macromolecule #3: envelope glycoprotein E2

MacromoleculeName: envelope glycoprotein E2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Hepacivirus C
Molecular weightTheoretical: 32.28726 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: METDTLLLWV LLLWVPGSTG DSTHVTGGTA SHTTRHFASL FSSGASQRVQ LINTNGSWHI NRTALNCNDS LHTGFLAALF YTHKFNASG CPERMAHCRP IDEFAQGWGP ITYAEGHGSD QRPYCWHYAP RQCGTIPASQ VCGPVYCFTP SPVVVGTTDR F GAPTYTWG ...String:
METDTLLLWV LLLWVPGSTG DSTHVTGGTA SHTTRHFASL FSSGASQRVQ LINTNGSWHI NRTALNCNDS LHTGFLAALF YTHKFNASG CPERMAHCRP IDEFAQGWGP ITYAEGHGSD QRPYCWHYAP RQCGTIPASQ VCGPVYCFTP SPVVVGTTDR F GAPTYTWG ENETDVLILN NTRPPQGNWF GCTWMNSTGF TKTCGGPPCN IGGVGNNTLT CPTDCFRKHP EATYTKCGSG PW LTPRCLV DYPYRLWHYP CTVNFTIFKV RMYVGGVEHR LNAACNIGHH HHHH

UniProtKB: Genome polyprotein

-
Macromolecule #4: HC84.26 Heavy chain

MacromoleculeName: HC84.26 Heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.356758 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: METDTLLLWV LLLWVPGSTG DQVQPVQSGA EVKKPGSSVK VSCEASGGTH SNYVITWVRQ APGQGLEWMG GFIPDFRTAM YAQGFQGRV TITADESTSL AYMELTNLRS EDTAVYYCAR GPLSRGYYDY WGPGTLVTVS SASTKGPSVF PLAPSSKSTS G GTAALGCL ...String:
METDTLLLWV LLLWVPGSTG DQVQPVQSGA EVKKPGSSVK VSCEASGGTH SNYVITWVRQ APGQGLEWMG GFIPDFRTAM YAQGFQGRV TITADESTSL AYMELTNLRS EDTAVYYCAR GPLSRGYYDY WGPGTLVTVS SASTKGPSVF PLAPSSKSTS G GTAALGCL VKDYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKRV EP KSCDKTA GWSHPQFEKT AATGACTCGA G

-
Macromolecule #5: HC84.26 Light chain

MacromoleculeName: HC84.26 Light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.35215 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: METDTLLLWV LLLWVPGSTG DSYVLTQPPS VSVAPGQTAS ITCSGDKLGD KYVSWYQQRP GQSPVLVLYQ DSKRPSGIPE RFSGSNSGN TATLTISGTQ AMDEADYYCQ AWDSSALVFG GGTKLTVLRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF Y PREAKVQW ...String:
METDTLLLWV LLLWVPGSTG DSYVLTQPPS VSVAPGQTAS ITCSGDKLGD KYVSWYQQRP GQSPVLVLYQ DSKRPSGIPE RFSGSNSGN TATLTISGTQ AMDEADYYCQ AWDSSALVFG GGTKLTVLRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF Y PREAKVQW KVDNALQSGN SQESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.5 mg/mL
BufferpH: 8 / Details: 20 mM Tris-HCl pH 8.0 100 mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 7058 / Average exposure time: 3.6 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.25 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 270875
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final 3D classificationNumber classes: 5 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

6x9x

source_name: PDB, initial_model_type: experimental model

6mei

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-Correlation
Output model

PDB-8thz:
CryoEM structure of neutralizing antibodies CBH-7 and HC84.26 in complex with Hepatitis C virus envelope glycoprotein E2

+
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://pdbjlvh1.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