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- PDB-6wor: Structure of the broadly neutralizing antibody HC1AM -

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Basic information

Entry
Database: PDB / ID: 6wor
TitleStructure of the broadly neutralizing antibody HC1AM
Components
  • Fab HC1AM heavy chain
  • Fab HC1AM 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: 2.601 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 9, 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 HC1AM heavy chain
L: Fab HC1AM light chain


Theoretical massNumber of molelcules
Total (without water)47,7772
Polymers47,7772
Non-polymers00
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-26 kcal/mol
Surface area20220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.639, 80.966, 181.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Antibody Fab HC1AM heavy chain


Mass: 24198.385 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 HC1AM light chain


Mass: 23578.311 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.: 21 / 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: 2.52 Å3/Da / Density % sol: 51.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 17% (w/v) PEG 4000, 15% (v/v) glycerol, 8.5% (v/v) isopropanol, 0.085M Na-HEPES pH 7.5
PH range: 7.5

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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: Dec 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 15091 / % possible obs: 99.1 % / Redundancy: 7.4 % / CC1/2: 0.94 / Net I/σ(I): 26.1
Reflection shellResolution: 2.6→2.64 Å / Num. unique obs: 640 / CC1/2: 0.94

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Processing

Software
NameVersionClassification
REFMAC1.12_2829refinement
Blu-Ice3.25data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WOQ

6woq


Resolution: 2.601→29.518 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2529 743 4.93 %
Rwork0.219 --
obs0.2207 15059 99.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.09 Å2 / Biso mean: 59.1386 Å2 / Biso min: 25.67 Å2
Refinement stepCycle: final / Resolution: 2.601→29.518 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3226 0 0 21 3247
Biso mean---46.8 -
Num. residues----426
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023298
X-RAY DIFFRACTIONf_angle_d0.6034483
X-RAY DIFFRACTIONf_dihedral_angle_d16.6831986
X-RAY DIFFRACTIONf_chiral_restr0.043517
X-RAY DIFFRACTIONf_plane_restr0.005567
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6007-2.80140.34571320.28632695X-RAY DIFFRACTION95
2.8014-3.0830.33151610.26542836X-RAY DIFFRACTION100
3.083-3.52850.28161410.23632881X-RAY DIFFRACTION100
3.5285-4.44310.22121560.20152886X-RAY DIFFRACTION100
4.4431-29.52030.22211530.19863018X-RAY DIFFRACTION100

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