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- PDB-6xrj: Crystal structure of the disulfide linked DH717.1 Fab dimer, deri... -

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Basic information

Entry
Database: PDB / ID: 6xrj
TitleCrystal structure of the disulfide linked DH717.1 Fab dimer, derived from a macaque HIV-1 vaccine-induced Env glycan-reactive neutralizing antibody B cell lineage
Components
  • DH717.1 heavy chain Fab fragment
  • DH717.1 light chain Fab fragment
KeywordsIMMUNE SYSTEM / Fab-dimerized / glycan-reactive / antibodies / HIV
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsManne, K. / Nicely, N.I. / Acharya, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI145687 United States
Citation
Journal: Cell / Year: 2021
Title: Fab-dimerized glycan-reactive antibodies are a structural category of natural antibodies.
Authors: Wilton B Williams / R Ryan Meyerhoff / R J Edwards / Hui Li / Kartik Manne / Nathan I Nicely / Rory Henderson / Ye Zhou / Katarzyna Janowska / Katayoun Mansouri / Sophie Gobeil / Tyler ...Authors: Wilton B Williams / R Ryan Meyerhoff / R J Edwards / Hui Li / Kartik Manne / Nathan I Nicely / Rory Henderson / Ye Zhou / Katarzyna Janowska / Katayoun Mansouri / Sophie Gobeil / Tyler Evangelous / Bhavna Hora / Madison Berry / A Yousef Abuahmad / Jordan Sprenz / Margaret Deyton / Victoria Stalls / Megan Kopp / Allen L Hsu / Mario J Borgnia / Guillaume B E Stewart-Jones / Matthew S Lee / Naomi Bronkema / M Anthony Moody / Kevin Wiehe / Todd Bradley / S Munir Alam / Robert J Parks / Andrew Foulger / Thomas Oguin / Gregory D Sempowski / Mattia Bonsignori / Celia C LaBranche / David C Montefiori / Michael Seaman / Sampa Santra / John Perfect / Joseph R Francica / Geoffrey M Lynn / Baptiste Aussedat / William E Walkowicz / Richard Laga / Garnett Kelsoe / Kevin O Saunders / Daniela Fera / Peter D Kwong / Robert A Seder / Alberto Bartesaghi / George M Shaw / Priyamvada Acharya / Barton F Haynes /
Abstract: Natural antibodies (Abs) can target host glycans on the surface of pathogens. We studied the evolution of glycan-reactive B cells of rhesus macaques and humans using glycosylated HIV-1 envelope (Env) ...Natural antibodies (Abs) can target host glycans on the surface of pathogens. We studied the evolution of glycan-reactive B cells of rhesus macaques and humans using glycosylated HIV-1 envelope (Env) as a model antigen. 2G12 is a broadly neutralizing Ab (bnAb) that targets a conserved glycan patch on Env of geographically diverse HIV-1 strains using a unique heavy-chain (V) domain-swapped architecture that results in fragment antigen-binding (Fab) dimerization. Here, we describe HIV-1 Env Fab-dimerized glycan (FDG)-reactive bnAbs without V-swapped domains from simian-human immunodeficiency virus (SHIV)-infected macaques. FDG Abs also recognized cell-surface glycans on diverse pathogens, including yeast and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike. FDG precursors were expanded by glycan-bearing immunogens in macaques and were abundant in HIV-1-naive humans. Moreover, FDG precursors were predominately mutated IgMIgDCD27, thus suggesting that they originated from a pool of antigen-experienced IgM or marginal zone B cells.
#1: Journal: bioRxiv / Year: 2020
Title: Fab-dimerized glycan-reactive antibodies neutralize HIV and are prevalent in humans and rhesus macaques
Authors: Acharya, P. / Williams, W. / Henderson, R. / Janowska, K. / Manne, K. / Parks, R. / Deyton, M. / Sprenz, J. / Stalls, V. / Kopp, M. / Mansouri, K. / Edwards, R.J. / Meyerhoff, R.R. / Oguin, ...Authors: Acharya, P. / Williams, W. / Henderson, R. / Janowska, K. / Manne, K. / Parks, R. / Deyton, M. / Sprenz, J. / Stalls, V. / Kopp, M. / Mansouri, K. / Edwards, R.J. / Meyerhoff, R.R. / Oguin, T. / Sempowski, G. / Saunders, K. / Haynes, B.F.
History
DepositionJul 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation / citation_author
Revision 1.2Jun 9, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI ..._citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DH717.1 heavy chain Fab fragment
B: DH717.1 light chain Fab fragment
C: DH717.1 heavy chain Fab fragment
D: DH717.1 light chain Fab fragment
E: DH717.1 heavy chain Fab fragment
F: DH717.1 light chain Fab fragment
H: DH717.1 heavy chain Fab fragment
L: DH717.1 light chain Fab fragment


Theoretical massNumber of molelcules
Total (without water)185,3028
Polymers185,3028
Non-polymers00
Water0
1
A: DH717.1 heavy chain Fab fragment
B: DH717.1 light chain Fab fragment


Theoretical massNumber of molelcules
Total (without water)46,3252
Polymers46,3252
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-27 kcal/mol
Surface area19320 Å2
MethodPISA
2
C: DH717.1 heavy chain Fab fragment
D: DH717.1 light chain Fab fragment


Theoretical massNumber of molelcules
Total (without water)46,3252
Polymers46,3252
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-25 kcal/mol
Surface area20800 Å2
MethodPISA
3
E: DH717.1 heavy chain Fab fragment
F: DH717.1 light chain Fab fragment


Theoretical massNumber of molelcules
Total (without water)46,3252
Polymers46,3252
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-21 kcal/mol
Surface area20720 Å2
MethodPISA
4
H: DH717.1 heavy chain Fab fragment
L: DH717.1 light chain Fab fragment


Theoretical massNumber of molelcules
Total (without water)46,3252
Polymers46,3252
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-27 kcal/mol
Surface area20700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)201.587, 201.587, 154.327
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Space group name HallP4cw2c
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+1/4
#8: -y,-x,-z+3/4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLNGLNSERSERchain 'A'AA1 - 1381 - 138
121GLUGLUILEILEchain 'A'AA144 - 224144 - 224
211GLNGLNSERSER(chain 'C' and (resid 1 through 138 or resid 144 through 224))CC1 - 1381 - 138
221GLUGLUILEILE(chain 'C' and (resid 1 through 138 or resid 144 through 224))CC144 - 224144 - 224
311GLNGLNSERSER(chain 'E' and (resid 1 through 138 or resid 144 through 224))EE1 - 1381 - 138
321GLUGLUILEILE(chain 'E' and (resid 1 through 138 or resid 144 through 224))EE144 - 224144 - 224
411GLNGLNSERSER(chain 'H' and (resid 1 through 138 or resid 144 through 224))HG1 - 1381 - 138
421GLUGLUILEILE(chain 'H' and (resid 1 through 138 or resid 144 through 224))HG144 - 224144 - 224
112ALAALAPROPROchain 'B'BB3 - 2121 - 210
212ALAALAPROPROchain 'D'DD3 - 2121 - 210
312ALAALAPROPROchain 'F'FF3 - 2121 - 210
412ALAALAPROPROchain 'L'LH3 - 2121 - 210

NCS ensembles :
ID
1
2

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Components

#1: Antibody
DH717.1 heavy chain Fab fragment


Mass: 24092.014 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody
DH717.1 light chain Fab fragment


Mass: 22233.449 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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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: 4.23 Å3/Da / Density % sol: 70.93 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: 0.1M Citric acid pH3.5, 14% PEG 1000

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Data collection

DiffractionMean temperature: 193.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.147→41.71 Å / Num. obs: 55412 / % possible obs: 99.72 % / Redundancy: 9 % / Biso Wilson estimate: 82.54 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.166 / Net I/σ(I): 13.4
Reflection shellResolution: 3.147→3.26 Å / Redundancy: 9.6 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 5393 / CC1/2: 0.525 / % possible all: 98.94

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ukn

5ukn


Resolution: 3.15→41.71 Å / SU ML: 0.305 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.5962
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2822 1999 3.61 %1999
Rwork0.245 53413 --
obs0.2464 55412 99.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 113.53 Å2
Refinement stepCycle: LAST / Resolution: 3.15→41.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12965 0 0 0 12965
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012113260
X-RAY DIFFRACTIONf_angle_d2.033818086
X-RAY DIFFRACTIONf_chiral_restr0.11192077
X-RAY DIFFRACTIONf_plane_restr0.01262322
X-RAY DIFFRACTIONf_dihedral_angle_d16.66044680
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.230.34981380.32123683X-RAY DIFFRACTION98.53
3.23-3.310.29961400.29773776X-RAY DIFFRACTION99.95
3.31-3.410.33031410.28023769X-RAY DIFFRACTION100
3.41-3.520.29331420.26593772X-RAY DIFFRACTION99.95
3.52-3.650.30261400.2723767X-RAY DIFFRACTION100
3.65-3.790.29441430.26453790X-RAY DIFFRACTION99.9
3.79-3.960.27351410.25323783X-RAY DIFFRACTION99.7
3.97-4.170.31681420.23273792X-RAY DIFFRACTION99.97
4.17-4.440.25211410.2183789X-RAY DIFFRACTION99.97
4.44-4.780.24741430.20933820X-RAY DIFFRACTION100
4.78-5.260.22441440.22093836X-RAY DIFFRACTION99.92
5.26-6.010.32421450.24033866X-RAY DIFFRACTION100
6.02-7.570.26771450.26483895X-RAY DIFFRACTION99.7
7.57-41.710.29251540.2384075X-RAY DIFFRACTION99.41

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