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- PDB-5tqa: Crystal Structure of DH270.6 (unliganded) from the DH270 Broadly ... -

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Basic information

Entry
Database: PDB / ID: 5tqa
TitleCrystal Structure of DH270.6 (unliganded) from the DH270 Broadly Neutralizing N332-Glycan Dependent Lineage
Components
  • DH270.6 Fab heavy chain
  • DH270.6 Fab light chain
KeywordsIMMUNE SYSTEM / FAB FRAGMENT / HIV-1 / ANTIBODY
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.723 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 23, 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 18, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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
H: DH270.6 Fab heavy chain
L: DH270.6 Fab light chain
B: DH270.6 Fab light chain
A: DH270.6 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)97,3584
Polymers97,3584
Non-polymers00
Water1,928107
1
H: DH270.6 Fab heavy chain
L: DH270.6 Fab light chain


Theoretical massNumber of molelcules
Total (without water)48,6792
Polymers48,6792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-26 kcal/mol
Surface area19700 Å2
MethodPISA
2
B: DH270.6 Fab light chain
A: DH270.6 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)48,6792
Polymers48,6792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-24 kcal/mol
Surface area19730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.066, 73.718, 112.714
Angle α, β, γ (deg.)90.000, 107.180, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain H
12chain B
22chain L

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNCYSCYSchain AAD1 - 2301 - 230
21GLNGLNCYSCYSchain HHA1 - 2301 - 230
12ALAALATHRTHRchain BBC3 - 2133 - 213
22ALAALATHRTHRchain LLB3 - 2133 - 213

NCS ensembles :
ID
1
2

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Components

#1: Antibody DH270.6 Fab heavy chain


Mass: 25895.893 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HEK 293T / Plasmid: pVRC-8400 / Cell line (production host): HEK 293T / Production host: Homo sapiens (human)
#2: Antibody DH270.6 Fab light chain


Mass: 22783.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HEK 293T / Plasmid: pVRC-8400 / Cell line (production host): HEK 293T / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.73 Å3/Da / Density % sol: 55.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 30% PEG 4000, 100 mM PIPES pH 6, and 1M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97925 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 20, 2015
RadiationMonochromator: SINGLE CRYSTAL SI(220) SIDE BOUNCE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 2.73→48.36 Å / Num. obs: 27600 / % possible obs: 97.6 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.099 / Rrim(I) all: 0.15 / Χ2: 0.987 / Net I/av σ(I): 6.913 / Net I/σ(I): 5.7 / Num. measured all: 57894
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.73-2.782.10.64213510.4610.5650.8590.92996.6
2.78-2.832.10.57413840.5340.5050.7680.91397.3
2.83-2.882.10.45313410.6170.4010.6070.95797.4
2.88-2.942.10.40113840.7010.3550.5381.00596.7
2.94-32.20.34913470.7650.3060.4660.99997.2
3-3.072.10.31513730.8180.2760.4211.06597
3.07-3.152.10.29413500.7810.2610.3951.10697.3
3.15-3.242.10.22413730.8460.20.3011.08897.2
3.24-3.332.10.19613590.8970.1730.2621.13397.2
3.33-3.442.10.15613890.9310.1370.2091.04797.3
3.44-3.562.10.13413500.950.1180.1791.03897.8
3.56-3.72.10.12113820.9550.1050.161.05597.8
3.7-3.872.10.113970.9720.0880.1340.9698.4
3.87-4.082.10.08713710.9730.0760.1160.8998.1
4.08-4.332.10.07714160.980.0670.1020.92198.2
4.33-4.672.10.06713590.9840.060.090.96198.1
4.67-5.142.10.06414040.9830.0560.0851.04398.1
5.14-5.8820.06314020.9860.0570.0851.00998.3
5.88-7.420.05114200.9920.0470.070.63898.5
7.4-502.10.0314480.9970.0270.040.95598.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.36 Å48.36 Å
Translation6.36 Å48.36 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER2.5.7phasing
PDB_EXTRACT3.2data extraction
Cootmodel building
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TPP

5tpp


Resolution: 2.723→48.36 Å / FOM work R set: 0.7862 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.47 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.201 1288 4.8 %
Rwork0.1848 26261 -
obs0.1884 27590 97.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 149.52 Å2 / Biso mean: 55 Å2 / Biso min: 24.87 Å2
Refinement stepCycle: final / Resolution: 2.723→48.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6582 0 0 107 6689
Biso mean---42.01 -
Num. residues----882
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046757
X-RAY DIFFRACTIONf_angle_d0.9129206
X-RAY DIFFRACTIONf_chiral_restr0.0331038
X-RAY DIFFRACTIONf_plane_restr0.0061176
X-RAY DIFFRACTIONf_dihedral_angle_d13.4362380
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2038X-RAY DIFFRACTION9.86TORSIONAL
12H2038X-RAY DIFFRACTION9.86TORSIONAL
21B1866X-RAY DIFFRACTION9.86TORSIONAL
22L1866X-RAY DIFFRACTION9.86TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7273-2.83640.33071690.30832834300391
2.8364-2.96540.28191590.26832841300092
2.9654-3.12170.26191400.25132912305293
3.1217-3.31710.27411200.22242904302493
3.3171-3.57290.25171330.20122910304393
3.5729-3.9320.19071490.17952926307593
3.932-4.49980.17541440.15212940308493
4.4998-5.66480.14291310.14482972310394
5.6648-33.53540.16061430.16073022316594
Refinement TLS params.Method: refined / Origin x: -16.6741 Å / Origin y: 21.1325 Å / Origin z: -19.7133 Å
111213212223313233
T0.3422 Å2-0.034 Å20.0177 Å2-0.3932 Å2-0.0077 Å2--0.3196 Å2
L0.5631 °2-0.1732 °2-0.0933 °2-0.9729 °20.0552 °2--0.3354 °2
S0.0243 Å °0.2578 Å °-0.0157 Å °-0.2613 Å °-0.0288 Å °-0.0021 Å °-0.0072 Å °-0.0267 Å °0.0031 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allS1 - 72
2X-RAY DIFFRACTION1allS73 - 110
3X-RAY DIFFRACTION1allH1 - 230
4X-RAY DIFFRACTION1allL3 - 213
5X-RAY DIFFRACTION1allB3 - 213
6X-RAY DIFFRACTION1allA1 - 230

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