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- PDB-6oo0: Crystal structure of bovine Fab NC-Cow1 -

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Basic information

Entry
Database: PDB / ID: 6oo0
TitleCrystal structure of bovine Fab NC-Cow1
Components
  • NC-Cow1 heavy chain
  • NC-Cow1 light chain
KeywordsIMMUNE SYSTEM / HIV-1 broadly neutralizing antibody / VIRAL PROTEIN-Immune System complex
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsStanfield, R.L. / Wilson, I.A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM105826 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI117675 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI084817 United States
CitationJournal: Sci Adv / Year: 2020
Title: Structural basis of broad HIV neutralization by a vaccine-induced cow antibody.
Authors: Robyn L Stanfield / Zachary T Berndsen / Ruiqi Huang / Devin Sok / Gabrielle Warner / Jonathan L Torres / Dennis R Burton / Andrew B Ward / Ian A Wilson / Vaughn V Smider /
Abstract: Potent broadly neutralizing antibodies (bnAbs) to HIV have been very challenging to elicit by vaccination in wild-type animals. Here, by x-ray crystallography, cryo-electron microscopy, and site- ...Potent broadly neutralizing antibodies (bnAbs) to HIV have been very challenging to elicit by vaccination in wild-type animals. Here, by x-ray crystallography, cryo-electron microscopy, and site-directed mutagenesis, we structurally and functionally elucidate the mode of binding of a potent bnAb (NC-Cow1) elicited in cows by immunization with the HIV envelope (Env) trimer BG505 SOSIP.664. The exceptionally long (60 residues) third complementarity-determining region of the heavy chain (CDR H3) of NC-Cow1 forms a mini domain (knob) on an extended stalk that navigates through the dense glycan shield on Env to target a small footprint on the gp120 CD4 receptor binding site with no contact of the other CDRs to the rest of the Env trimer. These findings illustrate, in molecular detail, how an unusual vaccine-induced cow bnAb to HIV Env can neutralize with high potency and breadth.
History
DepositionApr 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: NC-Cow1 light chain
H: NC-Cow1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3465
Polymers51,9912
Non-polymers3553
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-58 kcal/mol
Surface area22670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.060, 69.560, 95.610
Angle α, β, γ (deg.)90.00, 106.99, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody NC-Cow1 light chain


Mass: 22633.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)
#2: Antibody NC-Cow1 heavy chain


Mass: 29357.709 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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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: 2.54 Å3/Da / Density % sol: 51.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M sodium cacodylate, 40% methylpentanediol, 5% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.1→28.9 Å / Num. obs: 30513 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 40 Å2 / CC1/2: 0.991 / Rpim(I) all: 0.078 / Rrim(I) all: 0.162 / Rsym value: 0.142 / Net I/σ(I): 6
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1 / Num. unique obs: 2243 / CC1/2: 0.303 / Rpim(I) all: 0.693 / Rrim(I) all: 1.46 / Rsym value: 1.28 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ILT

5ilt


Resolution: 2.1→28.865 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.09
RfactorNum. reflection% reflection
Rfree0.238 1543 5.06 %
Rwork0.2019 --
obs0.2037 30507 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→28.865 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3607 0 24 66 3697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023728
X-RAY DIFFRACTIONf_angle_d0.5835092
X-RAY DIFFRACTIONf_dihedral_angle_d11.7972251
X-RAY DIFFRACTIONf_chiral_restr0.045576
X-RAY DIFFRACTIONf_plane_restr0.003649
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.16780.3531250.31722648X-RAY DIFFRACTION100
2.1678-2.24520.33941490.29872605X-RAY DIFFRACTION100
2.2452-2.33510.32761370.28712595X-RAY DIFFRACTION100
2.3351-2.44130.34831430.29062633X-RAY DIFFRACTION100
2.4413-2.56990.30431350.27832620X-RAY DIFFRACTION100
2.5699-2.73080.25931480.24242606X-RAY DIFFRACTION100
2.7308-2.94150.27641380.23332617X-RAY DIFFRACTION100
2.9415-3.23710.26281630.21442620X-RAY DIFFRACTION100
3.2371-3.70470.23141220.19122655X-RAY DIFFRACTION100
3.7047-4.66440.1851390.14952658X-RAY DIFFRACTION100
4.6644-28.86740.17331440.15122707X-RAY DIFFRACTION100

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