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- PDB-6n16: Vaccine-elicited NHP FP-targeting neutralizing antibody 0PV-b.01 ... -

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Basic information

Entry
Database: PDB / ID: 6n16
TitleVaccine-elicited NHP FP-targeting neutralizing antibody 0PV-b.01 in complex with HIV fusion peptide (residue 512-519)
Components
  • HIV fusion peptide (512-519)
  • antibody 0PV-b.01 Fab heavy chain
  • antibody 0PV-b.01 Fab light chain
KeywordsIMMUNE SYSTEM / HIV / neutralizing / NHP / FP / Fusion Peptide / vaccine
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane ...Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.302 Å
AuthorsXu, K. / Wang, Y. / Kwong, P.D.
CitationJournal: Cell / Year: 2019
Title: Antibody Lineages with Vaccine-Induced Antigen-Binding Hotspots Develop Broad HIV Neutralization.
Authors: Rui Kong / Hongying Duan / Zizhang Sheng / Kai Xu / Priyamvada Acharya / Xuejun Chen / Cheng Cheng / Adam S Dingens / Jason Gorman / Mallika Sastry / Chen-Hsiang Shen / Baoshan Zhang / ...Authors: Rui Kong / Hongying Duan / Zizhang Sheng / Kai Xu / Priyamvada Acharya / Xuejun Chen / Cheng Cheng / Adam S Dingens / Jason Gorman / Mallika Sastry / Chen-Hsiang Shen / Baoshan Zhang / Tongqing Zhou / Gwo-Yu Chuang / Cara W Chao / Ying Gu / Alexander J Jafari / Mark K Louder / Sijy O'Dell / Ariana P Rowshan / Elise G Viox / Yiran Wang / Chang W Choi / Martin M Corcoran / Angela R Corrigan / Venkata P Dandey / Edward T Eng / Hui Geng / Kathryn E Foulds / Yicheng Guo / Young D Kwon / Bob Lin / Kevin Liu / Rosemarie D Mason / Martha C Nason / Tiffany Y Ohr / Li Ou / Reda Rawi / Edward K Sarfo / Arne Schön / John P Todd / Shuishu Wang / Hui Wei / Winston Wu / / James C Mullikin / Robert T Bailer / Nicole A Doria-Rose / Gunilla B Karlsson Hedestam / Diana G Scorpio / Julie Overbaugh / Jesse D Bloom / Bridget Carragher / Clinton S Potter / Lawrence Shapiro / Peter D Kwong / John R Mascola /
Abstract: The vaccine-mediated elicitation of antibodies (Abs) capable of neutralizing diverse HIV-1 strains has been a long-standing goal. To understand how broadly neutralizing antibodies (bNAbs) can be ...The vaccine-mediated elicitation of antibodies (Abs) capable of neutralizing diverse HIV-1 strains has been a long-standing goal. To understand how broadly neutralizing antibodies (bNAbs) can be elicited, we identified, characterized, and tracked five neutralizing Ab lineages targeting the HIV-1-fusion peptide (FP) in vaccinated macaques over time. Genetic and structural analyses revealed two of these lineages to belong to a reproducible class capable of neutralizing up to 59% of 208 diverse viral strains. B cell analysis indicated each of the five lineages to have been initiated and expanded by FP-carrier priming, with envelope (Env)-trimer boosts inducing cross-reactive neutralization. These Abs had binding-energy hotspots focused on FP, whereas several FP-directed Abs induced by immunization with Env trimer-only were less FP-focused and less broadly neutralizing. Priming with a conserved subregion, such as FP, can thus induce Abs with binding-energy hotspots coincident with the target subregion and capable of broad neutralization.
History
DepositionNov 8, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 13, 2019Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: antibody 0PV-b.01 Fab heavy chain
B: antibody 0PV-b.01 Fab light chain
H: antibody 0PV-b.01 Fab heavy chain
J: antibody 0PV-b.01 Fab light chain
K: antibody 0PV-b.01 Fab heavy chain
L: antibody 0PV-b.01 Fab light chain
C: antibody 0PV-b.01 Fab heavy chain
D: antibody 0PV-b.01 Fab light chain
E: HIV fusion peptide (512-519)
F: HIV fusion peptide (512-519)
G: HIV fusion peptide (512-519)
I: HIV fusion peptide (512-519)


Theoretical massNumber of molelcules
Total (without water)192,11812
Polymers192,11812
Non-polymers00
Water0
1
A: antibody 0PV-b.01 Fab heavy chain
B: antibody 0PV-b.01 Fab light chain
E: HIV fusion peptide (512-519)


Theoretical massNumber of molelcules
Total (without water)48,0303
Polymers48,0303
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-33 kcal/mol
Surface area19180 Å2
MethodPISA
2
H: antibody 0PV-b.01 Fab heavy chain
L: antibody 0PV-b.01 Fab light chain
F: HIV fusion peptide (512-519)


Theoretical massNumber of molelcules
Total (without water)48,0303
Polymers48,0303
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-33 kcal/mol
Surface area19480 Å2
MethodPISA
3
J: antibody 0PV-b.01 Fab light chain
K: antibody 0PV-b.01 Fab heavy chain
G: HIV fusion peptide (512-519)


Theoretical massNumber of molelcules
Total (without water)48,0303
Polymers48,0303
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint-36 kcal/mol
Surface area19560 Å2
MethodPISA
4
C: antibody 0PV-b.01 Fab heavy chain
D: antibody 0PV-b.01 Fab light chain
I: HIV fusion peptide (512-519)


Theoretical massNumber of molelcules
Total (without water)48,0303
Polymers48,0303
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-34 kcal/mol
Surface area19270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.497, 84.204, 84.572
Angle α, β, γ (deg.)89.880, 111.430, 104.480
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
31chain H
41chain K
12chain B
22chain D
32chain J
42chain L
13chain E
23chain F
33chain G
43chain I

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA1 - 213
211chain CC1 - 213
311chain HH1 - 213
411chain KK1 - 213
112chain BB1 - 212
212chain DD1 - 212
312chain JJ1 - 212
412chain LL1 - 212
113chain EE512 - 519
213chain FF512 - 519
313chain GG512 - 519
413chain II512 - 519

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody
antibody 0PV-b.01 Fab heavy chain


Mass: 23685.500 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#2: Antibody
antibody 0PV-b.01 Fab light chain


Mass: 23611.219 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#3: Protein/peptide
HIV fusion peptide (512-519)


Mass: 732.868 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04578*PLUS

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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: 2.44 Å3/Da / Density % sol: 49.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.15 M Lithium sulfate monohydrate, 0.1 M Citric acid pH 3.5, 18% w/v Polyethylene glycol 6,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 68478 / % possible obs: 85.2 % / Redundancy: 1.8 % / Biso Wilson estimate: 24.82 Å2 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.08 / Rrim(I) all: 0.113 / Χ2: 0.653 / Net I/σ(I): 5.6 / Num. measured all: 126153
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.341.90.3336500.7230.330.4670.38990.7
2.34-2.381.90.30436470.7290.3040.430.37491
2.38-2.431.90.28836190.7670.2880.4070.39190
2.43-2.481.90.24735790.8120.2470.3490.40889.1
2.48-2.531.90.22535750.8610.2250.3180.4389.1
2.53-2.591.90.20335410.8630.2030.2870.43788.2
2.59-2.661.90.19235240.880.1920.2710.45787.6
2.66-2.731.90.15934830.9290.1590.2240.45786.7
2.73-2.811.90.1434470.9340.140.1980.50584.9
2.81-2.91.80.12233240.9490.1220.1720.53883.2
2.9-31.80.10632440.9590.1060.150.63181.4
3-3.121.80.08828530.9690.0880.1250.69670
3.12-3.261.80.08231570.9720.0820.1160.79379.5
3.26-3.441.80.06737140.9790.0670.0950.88892.1
3.44-3.651.80.05536380.9860.0550.0780.98790.5
3.65-3.931.80.05135380.9880.0510.0731.12688.6
3.93-4.331.80.04234390.9920.0420.0591.08585.4
4.33-4.951.80.03731890.9930.0370.0521.05578.8
4.95-6.241.80.03627680.9940.0360.0510.96169.2
6.24-501.90.02935490.9960.0290.0410.76788.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementResolution: 2.302→43.072 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 28.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.274 3355 4.9 %
Rwork0.2218 65084 -
obs0.2243 68439 84.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.95 Å2 / Biso mean: 27.3817 Å2 / Biso min: 10.88 Å2
Refinement stepCycle: final / Resolution: 2.302→43.072 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13377 0 0 0 13377
Num. residues----1774
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2628X-RAY DIFFRACTION6.165TORSIONAL
12C2628X-RAY DIFFRACTION6.165TORSIONAL
13H2628X-RAY DIFFRACTION6.165TORSIONAL
14K2628X-RAY DIFFRACTION6.165TORSIONAL
21B2612X-RAY DIFFRACTION6.165TORSIONAL
22D2612X-RAY DIFFRACTION6.165TORSIONAL
23J2612X-RAY DIFFRACTION6.165TORSIONAL
24L2612X-RAY DIFFRACTION6.165TORSIONAL
31E84X-RAY DIFFRACTION6.165TORSIONAL
32F84X-RAY DIFFRACTION6.165TORSIONAL
33G84X-RAY DIFFRACTION6.165TORSIONAL
34I84X-RAY DIFFRACTION6.165TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3021-2.3350.31311400.25822730287086
2.335-2.36990.31831350.26072918305391
2.3699-2.40690.35391530.26822884303791
2.4069-2.44640.2831450.27322858300390
2.4464-2.48850.32811630.25762835299889
2.4885-2.53380.36661470.25792835298289
2.5338-2.58250.33611670.26742757292488
2.5825-2.63520.34231500.26732874302488
2.6352-2.69250.37381550.27652735289087
2.6925-2.75510.27851410.25712723286486
2.7551-2.8240.33491240.26392738286284
2.824-2.90040.28161480.26342640278883
2.9004-2.98570.35451510.25552592274382
2.9857-3.0820.30241120.25072338245074
3.082-3.19210.29541200.24512223234369
3.1921-3.31990.31561410.23792836297789
3.3199-3.47090.26671620.22052923308592
3.4709-3.65380.2421270.21042904303190
3.6538-3.88260.24941290.21062861299089
3.8826-4.18220.23491390.18482754289387
4.1822-4.60260.211270.15842614274181
4.6026-5.26760.1681110.16412462257376
5.2676-6.63270.22671180.18662197231569
6.6327-43.07950.22071500.17822853300389

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