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- PDB-5tpp: Crystal Structure of DH270.5 (unliganded) from the DH270 Broadly ... -

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Basic information

Entry
Database: PDB / ID: 5tpp
TitleCrystal Structure of DH270.5 (unliganded) from the DH270 Broadly Neutralizing N332-glycan Dependent Lineage
Components
  • DH270.5 Fab heavy chain
  • DH270.5 Fab light chain
KeywordsIMMUNE SYSTEM / FAB FRAGMENT / HIV-1 / ANTIBODY
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / CITRIC ACID
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsFera, D. / Harrison, S.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1F32AI116355-01 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM-1- AI100645 United States
CitationJournal: Sci Transl Med / Year: 2017
Title: Staged induction of HIV-1 glycan-dependent broadly neutralizing antibodies.
Authors: Mattia Bonsignori / Edward F Kreider / Daniela Fera / R Ryan Meyerhoff / Todd Bradley / Kevin Wiehe / S Munir Alam / Baptiste Aussedat / William E Walkowicz / Kwan-Ki Hwang / Kevin O ...Authors: Mattia Bonsignori / Edward F Kreider / Daniela Fera / R Ryan Meyerhoff / Todd Bradley / Kevin Wiehe / S Munir Alam / Baptiste Aussedat / William E Walkowicz / Kwan-Ki Hwang / Kevin O Saunders / Ruijun Zhang / Morgan A Gladden / Anthony Monroe / Amit Kumar / Shi-Mao Xia / Melissa Cooper / Mark K Louder / Krisha McKee / Robert T Bailer / Brendan W Pier / Claudia A Jette / Garnett Kelsoe / Wilton B Williams / Lynn Morris / John Kappes / Kshitij Wagh / Gift Kamanga / Myron S Cohen / Peter T Hraber / David C Montefiori / Ashley Trama / Hua-Xin Liao / Thomas B Kepler / M Anthony Moody / Feng Gao / Samuel J Danishefsky / John R Mascola / George M Shaw / Beatrice H Hahn / Stephen C Harrison / Bette T Korber / Barton F Haynes /
Abstract: A preventive HIV-1 vaccine should induce HIV-1-specific broadly neutralizing antibodies (bnAbs). However, bnAbs generally require high levels of somatic hypermutation (SHM) to acquire breadth, and ...A preventive HIV-1 vaccine should induce HIV-1-specific broadly neutralizing antibodies (bnAbs). However, bnAbs generally require high levels of somatic hypermutation (SHM) to acquire breadth, and current vaccine strategies have not been successful in inducing bnAbs. Because bnAbs directed against a glycosylated site adjacent to the third variable loop (V3) of the HIV-1 envelope protein require limited SHM, the V3-glycan epitope is an attractive vaccine target. By studying the cooperation among multiple V3-glycan B cell lineages and their coevolution with autologous virus throughout 5 years of infection, we identify key events in the ontogeny of a V3-glycan bnAb. Two autologous neutralizing antibody lineages selected for virus escape mutations and consequently allowed initiation and affinity maturation of a V3-glycan bnAb lineage. The nucleotide substitution required to initiate the bnAb lineage occurred at a low-probability site for activation-induced cytidine deaminase activity. Cooperation of B cell lineages and an improbable mutation critical for bnAb activity defined the necessary events leading to breadth in this V3-glycan bnAb lineage. These findings may, in part, explain why initiation of V3-glycan bnAbs is rare, and suggest an immunization strategy for inducing similar V3-glycan bnAbs.
History
DepositionOct 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software
Item: _pdbx_audit_support.funding_organization / _software.name
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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
L: DH270.5 Fab heavy chain
H: DH270.5 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8686
Polymers48,6072
Non-polymers2614
Water7,440413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-57 kcal/mol
Surface area19920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.114, 68.798, 59.463
Angle α, β, γ (deg.)90.000, 113.210, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody DH270.5 Fab heavy chain


Mass: 22817.498 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC-8400 / Cell line (production host): HEK 293T / Production host: Homo sapiens (human)
#2: Antibody DH270.5 Fab light chain


Mass: 25789.676 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pVRC-8400 / Cell line (production host): HEK 293T / Production host: Homo sapiens (human)
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 413 / 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: 2.61 Å3/Da / Density % sol: 52.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 100 mM sodium citrate, pH 4.0 and 40% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.85→44.956 Å / Num. obs: 42441 / % possible obs: 97.1 % / Redundancy: 3 % / Biso Wilson estimate: 24.99 Å2 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.082 / Rrim(I) all: 0.153 / Χ2: 0.932 / Net I/av σ(I): 8.05 / Net I/σ(I): 5 / Num. measured all: 126544
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.85-1.882.10.560.546190.3
1.88-1.922.40.530.61195.1
1.92-1.952.60.4890.658197.4
1.95-1.992.70.440.702197.7
1.99-2.042.70.3920.751198.2
2.04-2.082.70.3580.781197.6
2.08-2.143.10.3380.83198.9
2.14-2.193.10.2990.85197.8
2.19-2.263.10.2740.871198.8
2.26-2.333.20.2650.874199.1
2.33-2.413.10.240.898198.5
2.41-2.5130.2220.892197.5
2.51-2.633.20.1920.935198.1
2.63-2.763.20.1730.931197.8
2.76-2.943.30.1490.952198.7
2.94-3.163.20.1340.958198
3.16-3.483.10.1140.968195.7
3.48-3.993.30.1020.975197.3
3.99-5.023.10.0880.98195.5
5.02-503.30.0870.984194.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.83 Å44.96 Å
Translation6.84 Å44.96 Å

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASER2.5.7phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.2data extraction
Cootmodel building
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TYG

3tyg


Resolution: 1.85→44.956 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.16
RfactorNum. reflection% reflection
Rfree0.2117 2007 4.81 %
Rwork0.1791 --
obs0.1807 42408 96.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 81.7 Å2 / Biso mean: 27.44 Å2 / Biso min: 11.9 Å2
Refinement stepCycle: final / Resolution: 1.85→44.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3303 0 16 415 3734
Biso mean--47.62 40.92 -
Num. residues----440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073421
X-RAY DIFFRACTIONf_angle_d1.2364668
X-RAY DIFFRACTIONf_chiral_restr0.087522
X-RAY DIFFRACTIONf_plane_restr0.006595
X-RAY DIFFRACTIONf_dihedral_angle_d15.7411194
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8325-1.87510.271220.24462138226077
1.8751-1.9220.27251410.22412663280496
1.922-1.9740.28281490.21162733288298
1.974-2.03210.2571410.20852700284198
2.0321-2.09760.22681410.20492715285698
2.0976-2.17260.25641280.19182772290098
2.1726-2.25960.27321210.19522744286599
2.2596-2.36240.21971210.18472798291999
2.3624-2.4870.24471370.19582719285698
2.487-2.64280.2231340.18782746288098
2.6428-2.84680.24351170.18932786290398
2.8468-3.13320.19321080.17642795290398
3.1332-3.58640.18441640.16432645280996
3.5864-4.51790.17171780.14572717289597
4.5179-44.96910.20861380.1752697283594
Refinement TLS params.Method: refined / Origin x: -26.0808 Å / Origin y: 8.5059 Å / Origin z: 36.7561 Å
111213212223313233
T0.1617 Å2-0.0023 Å20.0252 Å2-0.1329 Å20.0107 Å2--0.1018 Å2
L1.676 °2-0.4622 °20.3647 °2-0.6528 °2-0.0898 °2--0.4103 °2
S-0.0701 Å °-0.0359 Å °0.1477 Å °0.02 Å °0.0414 Å °0.0088 Å °-0.0312 Å °0.0785 Å °0.0292 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allS1 - 415
2X-RAY DIFFRACTION1allS416 - 419
3X-RAY DIFFRACTION1allL3 - 214
4X-RAY DIFFRACTION1allH1 - 228

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