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- PDB-6vtu: DH717.1 Fab monomer in complex with man9 glycan -

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Basic information

Entry
Database: PDB / ID: 6vtu
TitleDH717.1 Fab monomer in complex with man9 glycan
Components
  • DH717.1 heavy chain
  • DH717.1 light chain
KeywordsIMMUNE SYSTEM / FAB FRAGMENT / HIV-1 / ANTIBODY
Function / homology
Function and homology information


immunoglobulin complex / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
IGL@ protein / IgG H chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.61 Å
AuthorsFera, D. / Bronkema, N.
CitationJournal: 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.
History
DepositionFeb 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
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jun 9, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Oct 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

Downloads & links

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Assembly

Deposited unit
H: DH717.1 heavy chain
L: DH717.1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2144
Polymers46,6182
Non-polymers5972
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4290 Å2
ΔGint-12 kcal/mol
Surface area19830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.238, 115.238, 98.476
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein DH717.1 heavy chain


Mass: 23812.766 Da / Num. of mol.: 1 / Fragment: FAB,FAB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HEK293T / Plasmid: pVRC-8400 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: S6B291
#2: Antibody DH717.1 light chain


Mass: 22805.055 Da / Num. of mol.: 1 / Fragment: FAB,FAB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: Q6IPQ0
#3: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a1122h-1a_1-5]/1-1-1/a2-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.54 Å3/Da / Density % sol: 65.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 100 mM sodium citrate, pH 5.0, 30% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97927 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 15, 2017
RadiationMonochromator: single crystal Si(220) side bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 2.61→50 Å / Num. obs: 20471 / % possible obs: 98 % / Redundancy: 4.4 % / Biso Wilson estimate: 49.17 Å2 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.075 / Rrim(I) all: 0.168 / Χ2: 0.947 / Net I/σ(I): 5.8 / Num. measured all: 90397
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.61-2.663.30.8849480.5050.5451.0430.76193.3
2.66-2.73.60.9159700.5240.5391.0670.7496.1
2.7-2.763.90.87710140.60.4911.0090.77497.5
2.76-2.814.30.74810200.6990.3920.8490.75698.9
2.81-2.874.60.6419940.7890.3240.7210.82499.7
2.87-2.944.60.59110270.7910.3010.6670.82199.5
2.94-3.014.70.4610190.8670.2310.5170.89699.4
3.01-3.094.60.38810240.8920.1960.4370.99499.4
3.09-3.194.60.30110310.9280.1530.341.02499.5
3.19-3.294.60.24310260.9510.1230.2741.03299.3
3.29-3.414.60.19410360.9710.0970.2181.0499.3
3.41-3.544.60.17210150.9740.0870.1931.03599.3
3.54-3.74.60.1510280.9750.0760.1691.07699
3.7-3.94.60.12210260.9820.0610.1371.06898.9
3.9-4.144.60.110240.9860.0510.1130.96798.3
4.14-4.464.60.08910500.9910.0430.0990.95298.3
4.46-4.914.60.08510310.9890.0420.0950.97598.1
4.91-5.624.50.09310430.990.0460.1040.96497.3
5.62-7.084.40.09610430.990.0480.1081.05996
7.08-504.30.08311020.9910.0410.0930.97593.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.78 Å81.56 Å
Translation2.78 Å81.56 Å

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8.2refinement
Cootmodel building
PHASER2.8.2phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5TPP

5tpp


Resolution: 2.61→49.732 Å / FOM work R set: 0.8495 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2243 993 4.88 %
Rwork0.1909 19345 -
obs0.1926 20338 98.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 120.3 Å2 / Biso mean: 46.94 Å2 / Biso min: 18.1 Å2
Refinement stepCycle: final / Resolution: 2.61→49.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3170 0 39 155 3364
Biso mean--68.91 43.55 -
Num. residues----433
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033288
X-RAY DIFFRACTIONf_angle_d0.8114489
X-RAY DIFFRACTIONf_chiral_restr0.053524
X-RAY DIFFRACTIONf_plane_restr0.004572
X-RAY DIFFRACTIONf_dihedral_angle_d13.3071155
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.61-2.74760.30241450.282261295
2.7476-2.91970.28051410.2508273199
2.9197-3.14510.27991510.24032759100
3.1451-3.46160.24681540.2008276199
3.4616-3.96230.21261410.1777278199
3.9623-4.99130.17181310.149281498
4.9913-49.7320.21061300.1828288796
Refinement TLS params.Method: refined / Origin x: -15.9227 Å / Origin y: 52.8128 Å / Origin z: -23.2067 Å
111213212223313233
T0.1835 Å2-0.0064 Å20.0013 Å2-0.1563 Å2-0.0166 Å2--0.1674 Å2
L0.2644 °2-0.0848 °20.2814 °2-0.4994 °2-0.5136 °2--0.5477 °2
S-0.0722 Å °-0.016 Å °-0.008 Å °0.1355 Å °0.0383 Å °-0.0553 Å °-0.0855 Å °-0.0708 Å °-0.0004 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allS2 - 160
2X-RAY DIFFRACTION1allH1 - 209
3X-RAY DIFFRACTION1allL1 - 209
4X-RAY DIFFRACTION1allG1
5X-RAY DIFFRACTION1allP79 - 81

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