[English] 日本語
Yorodumi
- PDB-4fql: Influenza B HA Antibody (Fab) CR8033 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fql
TitleInfluenza B HA Antibody (Fab) CR8033
Components
  • monoclonal antibody CR8033 heavy chain
  • monoclonal antibody CR8033 light chain
KeywordsIMMUNE SYSTEM / Fab fragment / monoclonal / viral / immunoglobulin / Influenza B virus
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.898 Å
AuthorsDreyfus, C. / Laursen, N.S. / Wilson, I.A.
CitationJournal: Science / Year: 2012
Title: Highly conserved protective epitopes on influenza B viruses.
Authors: Cyrille Dreyfus / Nick S Laursen / Ted Kwaks / David Zuijdgeest / Reza Khayat / Damian C Ekiert / Jeong Hyun Lee / Zoltan Metlagel / Miriam V Bujny / Mandy Jongeneelen / Remko van der Vlugt ...Authors: Cyrille Dreyfus / Nick S Laursen / Ted Kwaks / David Zuijdgeest / Reza Khayat / Damian C Ekiert / Jeong Hyun Lee / Zoltan Metlagel / Miriam V Bujny / Mandy Jongeneelen / Remko van der Vlugt / Mohammed Lamrani / Hans J W M Korse / Eric Geelen / Özcan Sahin / Martijn Sieuwerts / Just P J Brakenhoff / Ronald Vogels / Olive T W Li / Leo L M Poon / Malik Peiris / Wouter Koudstaal / Andrew B Ward / Ian A Wilson / Jaap Goudsmit / Robert H E Friesen /
Abstract: Identification of broadly neutralizing antibodies against influenza A viruses has raised hopes for the development of monoclonal antibody-based immunotherapy and "universal" vaccines for influenza. ...Identification of broadly neutralizing antibodies against influenza A viruses has raised hopes for the development of monoclonal antibody-based immunotherapy and "universal" vaccines for influenza. However, a substantial part of the annual flu burden is caused by two cocirculating, antigenically distinct lineages of influenza B viruses. Here, we report human monoclonal antibodies, CR8033, CR8071, and CR9114, that protect mice against lethal challenge from both lineages. Antibodies CR8033 and CR8071 recognize distinct conserved epitopes in the head region of the influenza B hemagglutinin (HA), whereas CR9114 binds a conserved epitope in the HA stem and protects against lethal challenge with influenza A and B viruses. These antibodies may inform on development of monoclonal antibody-based treatments and a universal flu vaccine for all influenza A and B viruses.
History
DepositionJun 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: monoclonal antibody CR8033 heavy chain
L: monoclonal antibody CR8033 light chain


Theoretical massNumber of molelcules
Total (without water)48,7642
Polymers48,7642
Non-polymers00
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-27 kcal/mol
Surface area20070 Å2
MethodPISA
2
H: monoclonal antibody CR8033 heavy chain
L: monoclonal antibody CR8033 light chain

H: monoclonal antibody CR8033 heavy chain
L: monoclonal antibody CR8033 light chain


Theoretical massNumber of molelcules
Total (without water)97,5294
Polymers97,5294
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8130 Å2
ΔGint-63 kcal/mol
Surface area38590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.200, 55.000, 80.800
Angle α, β, γ (deg.)90.00, 121.20, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-310-

HOH

-
Components

#1: Antibody monoclonal antibody CR8033 heavy chain


Mass: 25381.422 Da / Num. of mol.: 1 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#2: Antibody monoclonal antibody CR8033 light chain


Mass: 23382.951 Da / Num. of mol.: 1 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.66 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 200 mM zinc acetate, 10% PEG8000, 100 mM MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.898→69.113 Å / Num. all: 40203 / Num. obs: 40203 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rsym value: 0.13 / Net I/σ(I): 6.9
Reflection shellResolution: 1.898→2 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.63 / % possible all: 98.2

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3N9G

3n9g


Resolution: 1.898→40.245 Å / SU ML: 0.51 / σ(F): 1.99 / Phase error: 23.1 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2311 1999 4.98 %
Rwork0.1944 --
obs0.1962 40102 98.61 %
all-42101 -
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.348 Å2 / ksol: 0.331 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.792 Å20 Å27.0118 Å2
2--7.3507 Å2-0 Å2
3----1.5587 Å2
Refinement stepCycle: LAST / Resolution: 1.898→40.245 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3334 0 0 305 3639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073413
X-RAY DIFFRACTIONf_angle_d1.1774629
X-RAY DIFFRACTIONf_dihedral_angle_d14.3271224
X-RAY DIFFRACTIONf_chiral_restr0.077517
X-RAY DIFFRACTIONf_plane_restr0.005596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8984-1.94580.30461380.24192611X-RAY DIFFRACTION94
1.9458-1.99840.26511390.21342667X-RAY DIFFRACTION99
1.9984-2.05720.21661420.20122717X-RAY DIFFRACTION99
2.0572-2.12360.2291420.20242708X-RAY DIFFRACTION99
2.1236-2.19950.25171420.19132705X-RAY DIFFRACTION99
2.1995-2.28760.24451440.19342725X-RAY DIFFRACTION99
2.2876-2.39170.2141420.19612732X-RAY DIFFRACTION99
2.3917-2.51780.26811430.20092723X-RAY DIFFRACTION99
2.5178-2.67550.24211420.20362707X-RAY DIFFRACTION99
2.6755-2.8820.26391450.20812750X-RAY DIFFRACTION99
2.882-3.17190.21661430.19712734X-RAY DIFFRACTION99
3.1719-3.63070.21891430.18772735X-RAY DIFFRACTION99
3.6307-4.57320.20641460.16692767X-RAY DIFFRACTION99
4.5732-40.25370.22611480.20032822X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3901-0.43660.27180.93510.00270.7047-0.02150.08790.1240.01610.0357-0.1075-0.0121-0.0619-00.1818-0.0034-0.01370.16780.01240.2211-5.642-13.179925.1769
20.81220.19070.05330.5237-0.07490.6942-0.056-0.2624-0.0905-0.01340.0337-0.01170.03470.1289-0.00040.23350.07380.03420.27950.06170.24130.4152-35.651352.9828
30.5398-0.2216-0.62970.4573-0.04531.1614-0.06050.1112-0.01460.0845-0.01040.03570.0659-0.0927-00.1913-0.0039-0.02220.2255-0.00830.1616-6.2311-31.811411.618
40.4825-0.16660.43410.6740.48360.6564-0.1265-0.1851-0.22520.0644-0.03080.20350.1564-0.015200.27320.0430.06480.20670.04380.3386-10.4769-43.85844.6486
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain L and resid 1:108
2X-RAY DIFFRACTION2chain L and resid 109:213
3X-RAY DIFFRACTION3chain H and resid 1:118
4X-RAY DIFFRACTION4chain H and resid 119:216

+
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