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- PDB-6wos: Structure of broadly neutralizing antibody AR3B -

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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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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

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Experimental details

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Experiment

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

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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

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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

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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

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