[English] 日本語
Yorodumi
- PDB-6vjt: Co-crystals of broadly neutralizing antibody with the linear epit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vjt
TitleCo-crystals of broadly neutralizing antibody with the linear epitope from Hepatitis B surface antigen
Components
  • Heavy Chain Fab Fragment of Monoclonal Ab15
  • Light Chain Fab Fragment of Monoclonal antibody A15
  • antigenic region 139-148 of Hepatitis B surface antigen protein
KeywordsANTIVIRAL PROTEIN/IMMUNE SYSTEM / Hepatitis B / HepB / Fab / Ab / antibody / ANTIVIRAL PROTEIN / ANTIVIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


caveolin-mediated endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / membrane
Similarity search - Function
Large envelope protein S / Major surface antigen from hepadnavirus / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Large envelope protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Hepatitis B virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.782 Å
AuthorsOren, D.A. / Nussenzweig, M.C. / Wang, Q.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)PHS AI129795 United States
CitationJournal: Cell Host Microbe / Year: 2020
Title: A Combination of Human Broadly Neutralizing Antibodies against Hepatitis B Virus HBsAg with Distinct Epitopes Suppresses Escape Mutations.
Authors: Wang, Q. / Michailidis, E. / Yu, Y. / Wang, Z. / Hurley, A.M. / Oren, D.A. / Mayer, C.T. / Gazumyan, A. / Liu, Z. / Zhou, Y. / Schoofs, T. / Yao, K.H. / Nieke, J.P. / Wu, J. / Jiang, Q. / ...Authors: Wang, Q. / Michailidis, E. / Yu, Y. / Wang, Z. / Hurley, A.M. / Oren, D.A. / Mayer, C.T. / Gazumyan, A. / Liu, Z. / Zhou, Y. / Schoofs, T. / Yao, K.H. / Nieke, J.P. / Wu, J. / Jiang, Q. / Zou, C. / Kabbani, M. / Quirk, C. / Oliveira, T. / Chhosphel, K. / Zhang, Q. / Schneider, W.M. / Jahan, C. / Ying, T. / Horowitz, J. / Caskey, M. / Jankovic, M. / Robbiani, D.F. / Wen, Y. / de Jong, Y.P. / Rice, C.M. / Nussenzweig, M.C.
History
DepositionJan 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: Heavy Chain Fab Fragment of Monoclonal Ab15
L: Light Chain Fab Fragment of Monoclonal antibody A15
P: antigenic region 139-148 of Hepatitis B surface antigen protein


Theoretical massNumber of molelcules
Total (without water)48,4173
Polymers48,4173
Non-polymers00
Water6,503361
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-33 kcal/mol
Surface area20650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.848, 71.150, 134.704
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody Heavy Chain Fab Fragment of Monoclonal Ab15


Mass: 24024.889 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: IGgamma1 / Details (production host): von Boehmer et al., 2016 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody Light Chain Fab Fragment of Monoclonal antibody A15


Mass: 23310.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: IGchai / Details (production host): von Boehmer et al., 2016 / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Protein/peptide antigenic region 139-148 of Hepatitis B surface antigen protein


Mass: 1081.071 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Hepatitis B virus / References: UniProt: A0A5A4RHH5*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.36 % / Description: plates
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / Details: Morpheus position E1

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 3, 2019
Details: Cryogenically-cooled single crystal Si(220) side bounce monochromator.
RadiationMonochromator: Cryogenically-cooled single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.78→134.7 Å / Num. obs: 46432 / % possible obs: 99.5 % / Redundancy: 12.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.025 / Rrim(I) all: 0.088 / Net I/σ(I): 17.2 / Num. measured all: 598818
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.78-1.8212.11.2562847623560.7930.3661.311.391
9.09-134.710.70.04546974380.9990.0140.04847.399.9

-
Processing

Software
NameVersionClassification
PHENIX1.16refinement
XDS1.11.7data reduction
XDS0.5.32data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GGU

5ggu


Resolution: 1.782→67.352 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2268 1999 4.31 %random
Rwork0.1816 44329 --
obs0.1835 46328 99.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.32 Å2 / Biso mean: 39.4993 Å2 / Biso min: 20.84 Å2
Refinement stepCycle: final / Resolution: 1.782→67.352 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3377 0 0 361 3738
Biso mean---43.72 -
Num. residues----447
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.782-1.82650.29251290.2762287092
1.8265-1.87590.28141410.23723130100
1.8759-1.93110.27491420.21943149100
1.9311-1.99340.26221420.21163142100
1.9934-2.06470.28961410.20723126100
2.0647-2.14730.23591420.19253148100
2.1473-2.24510.22571430.18653172100
2.2451-2.36340.24211440.20033179100
2.3634-2.51150.24761420.19433155100
2.5115-2.70540.27031430.20933181100
2.7054-2.97770.26461450.20563200100
2.9777-3.40860.21591440.18633211100
3.4086-4.29430.22041470.16143252100
4.2943-67.3520.17611540.15133414100

+
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