[English] 日本語
Yorodumi
- PDB-6wos: Structure of broadly neutralizing antibody AR3B -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6wos
TitleStructure of broadly neutralizing antibody AR3B
Components
  • Fab AR3B heavy chain
  • Fab AR3B light chain
KeywordsIMMUNE SYSTEM / HCV / broadly neutralizing antibodies / bNAbs / E2 core / IGHV1-69
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.645 Å
AuthorsTzarum, N. / Wilson, I.A. / Law, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)Al123365 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)Al106005 United States
CitationJournal: Sci Adv / Year: 2020
Title: An alternate conformation of HCV E2 neutralizing face as an additional vaccine target.
Authors: Tzarum, N. / Giang, E. / Kadam, R.U. / Chen, F. / Nagy, K. / Augestad, E.H. / Velazquez-Moctezuma, R. / Keck, Z.Y. / Hua, Y. / Stanfield, R.L. / Dreux, M. / Prentoe, J. / Foung, S.K.H. / ...Authors: Tzarum, N. / Giang, E. / Kadam, R.U. / Chen, F. / Nagy, K. / Augestad, E.H. / Velazquez-Moctezuma, R. / Keck, Z.Y. / Hua, Y. / Stanfield, R.L. / Dreux, M. / Prentoe, J. / Foung, S.K.H. / Bukh, J. / Wilson, I.A. / Law, M.
History
DepositionApr 25, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: Fab AR3B heavy chain
L: Fab AR3B light chain


Theoretical massNumber of molelcules
Total (without water)47,4542
Polymers47,4542
Non-polymers00
Water7,350408
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-24 kcal/mol
Surface area19740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.341, 72.167, 135.468
Angle α, β, γ (deg.)90.000, 91.200, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11L-491-

HOH

-
Components

#1: Antibody Fab AR3B heavy chain


Mass: 24035.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Fab AR3B light chain


Mass: 23418.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.39 Å3/Da / Density % sol: 48.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG 3350, 0.2M Na thiocyanate, 10% ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.645→35 Å / Num. obs: 52082 / % possible obs: 96.5 % / Redundancy: 2.6 % / CC1/2: 0.92 / Net I/σ(I): 24.2
Reflection shellResolution: 1.645→1.68 Å / Num. unique obs: 1976 / CC1/2: 0.72

-
Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
Blu-Ice3.25data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BKC

6bkc


Resolution: 1.645→29.768 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.76
RfactorNum. reflection% reflection
Rfree0.2317 2547 4.89 %
Rwork0.1937 --
obs0.1955 52069 96.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.84 Å2 / Biso mean: 23.0917 Å2 / Biso min: 7.39 Å2
Refinement stepCycle: final / Resolution: 1.645→29.768 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3216 0 0 408 3624
Biso mean---32.21 -
Num. residues----427
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063291
X-RAY DIFFRACTIONf_angle_d0.8544480
X-RAY DIFFRACTIONf_chiral_restr0.059510
X-RAY DIFFRACTIONf_plane_restr0.006573
X-RAY DIFFRACTIONf_dihedral_angle_d15.2321981
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.645-1.67630.3655810.3222193268
1.6763-1.71060.3421420.29241884
1.7106-1.74770.33611230.2729258492
1.7477-1.78840.31391400.2543278095
1.7884-1.83310.2711310.2445269696
1.8331-1.88270.28831510.2279280299
1.8827-1.93810.27471400.2301287499
1.9381-2.00060.23381680.22312772100
2.0006-2.07210.24131330.21982861100
2.0721-2.1550.24751790.20912850100
2.155-2.25310.24191520.20892863100
2.2531-2.37180.25151450.2032856100
2.3718-2.52030.25551530.20522849100
2.5203-2.71480.24691840.20512810100
2.7148-2.98780.2211250.19632857100
2.9878-3.41960.22541280.18072893100
3.4196-4.30630.19021190.1493292899
4.3063-29.7680.16431530.1492289799

+
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