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- PDB-5tkk: Structure of mouse vaccination-elicited HIV neutralizing antibody... -

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Basic information

Entry
Database: PDB / ID: 5tkk
TitleStructure of mouse vaccination-elicited HIV neutralizing antibody vFP5.01 in complex with HIV-1 fusion peptide residue 512-519
Components
  • HIV-1 fusion peptide residue 512-519
  • mouse antibody vFP5.01 heavy chain
  • mouse antibody vFP5.01 light chain
KeywordsIMMUNE SYSTEM / Neutralizing / mouse / antibody / fusion-peptide / complex
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / actin filament organization / host cell endosome membrane ...Synthesis and processing of ENV and VPU / symbiont-mediated evasion of host immune response / positive regulation of establishment of T cell polarity / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / actin filament organization / host cell endosome membrane / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / receptor ligand activity / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / symbiont entry into host cell / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / 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 speciesMus musculus (house mouse)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsXu, K. / Liu, K. / Kwong, P.D.
CitationJournal: Nat Med / Year: 2018
Title: Epitope-based vaccine design yields fusion peptide-directed antibodies that neutralize diverse strains of HIV-1.
Authors: Kai Xu / Priyamvada Acharya / Rui Kong / Cheng Cheng / Gwo-Yu Chuang / Kevin Liu / Mark K Louder / Sijy O'Dell / Reda Rawi / Mallika Sastry / Chen-Hsiang Shen / Baoshan Zhang / Tongqing Zhou ...Authors: Kai Xu / Priyamvada Acharya / Rui Kong / Cheng Cheng / Gwo-Yu Chuang / Kevin Liu / Mark K Louder / Sijy O'Dell / Reda Rawi / Mallika Sastry / Chen-Hsiang Shen / Baoshan Zhang / Tongqing Zhou / Mangaiarkarasi Asokan / Robert T Bailer / Michael Chambers / Xuejun Chen / Chang W Choi / Venkata P Dandey / Nicole A Doria-Rose / Aliaksandr Druz / Edward T Eng / S Katie Farney / Kathryn E Foulds / Hui Geng / Ivelin S Georgiev / Jason Gorman / Kurt R Hill / Alexander J Jafari / Young D Kwon / Yen-Ting Lai / Thomas Lemmin / Krisha McKee / Tiffany Y Ohr / Li Ou / Dongjun Peng / Ariana P Rowshan / Zizhang Sheng / John-Paul Todd / Yaroslav Tsybovsky / Elise G Viox / Yiran Wang / Hui Wei / Yongping Yang / Amy F Zhou / Rui Chen / Lu Yang / Diana G Scorpio / Adrian B McDermott / Lawrence Shapiro / Bridget Carragher / Clinton S Potter / John R Mascola / Peter D Kwong /
Abstract: A central goal of HIV-1 vaccine research is the elicitation of antibodies capable of neutralizing diverse primary isolates of HIV-1. Here we show that focusing the immune response to exposed N- ...A central goal of HIV-1 vaccine research is the elicitation of antibodies capable of neutralizing diverse primary isolates of HIV-1. Here we show that focusing the immune response to exposed N-terminal residues of the fusion peptide, a critical component of the viral entry machinery and the epitope of antibodies elicited by HIV-1 infection, through immunization with fusion peptide-coupled carriers and prefusion stabilized envelope trimers, induces cross-clade neutralizing responses. In mice, these immunogens elicited monoclonal antibodies capable of neutralizing up to 31% of a cross-clade panel of 208 HIV-1 strains. Crystal and cryoelectron microscopy structures of these antibodies revealed fusion peptide conformational diversity as a molecular explanation for the cross-clade neutralization. Immunization of guinea pigs and rhesus macaques induced similarly broad fusion peptide-directed neutralizing responses, suggesting translatability. The N terminus of the HIV-1 fusion peptide is thus a promising target of vaccine efforts aimed at eliciting broadly neutralizing antibodies.
History
DepositionOct 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
A: HIV-1 fusion peptide residue 512-519
H: mouse antibody vFP5.01 heavy chain
L: mouse antibody vFP5.01 light chain


Theoretical massNumber of molelcules
Total (without water)48,7893
Polymers48,7893
Non-polymers00
Water6,071337
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint-34 kcal/mol
Surface area18960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.237, 82.233, 72.264
Angle α, β, γ (deg.)90.000, 90.220, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide HIV-1 fusion peptide residue 512-519


Mass: 732.868 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04578*PLUS
#2: Antibody mouse antibody vFP5.01 heavy chain


Mass: 24360.387 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody mouse antibody vFP5.01 light chain


Mass: 23696.145 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.21 Å3/Da / Density % sol: 44.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.2M MgCl2, 0.1M Tris-HCl pH8.5, 20% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: liquid N3
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→25.469 Å / Num. obs: 59733 / % possible obs: 97.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.04 / Rrim(I) all: 0.077 / Χ2: 1.054 / Net I/av σ(I): 16.148 / Net I/σ(I): 13.1 / Num. measured all: 209617
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.55-1.582.10.4680.763177.3
1.58-1.612.30.4960.759193.7
1.61-1.642.80.5270.761197.2
1.64-1.673.20.530.79198.1
1.67-1.713.40.5120.821198.3
1.71-1.753.60.4320.893198.5
1.75-1.793.60.3380.931198.5
1.79-1.843.60.2650.951198.6
1.84-1.893.60.2020.966198.8
1.89-1.953.70.1570.979199.1
1.95-2.023.80.1350.981199.1
2.02-2.13.80.1150.987199.3
2.1-2.23.80.1010.987199.4
2.2-2.323.80.090.989199.5
2.32-2.463.80.0830.99199.6
2.46-2.653.80.0740.992199.8
2.65-2.923.80.0670.993199.9
2.92-3.343.80.0560.995199.8
3.34-4.213.70.0470.996199.4
4.21-503.50.0380.997191.8

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Processing

Software
NameVersionClassification
SERGUIdata collection
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→25.469 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.31
RfactorNum. reflection% reflection
Rfree0.2469 2929 4.91 %
Rwork0.209 --
obs0.2109 59675 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 106.72 Å2 / Biso mean: 37.5113 Å2 / Biso min: 9.87 Å2
Refinement stepCycle: final / Resolution: 1.55→25.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3356 0 0 337 3693
Biso mean---42.34 -
Num. residues----434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013439
X-RAY DIFFRACTIONf_angle_d1.2754683
X-RAY DIFFRACTIONf_chiral_restr0.077526
X-RAY DIFFRACTIONf_plane_restr0.008594
X-RAY DIFFRACTIONf_dihedral_angle_d17.3842052
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5501-1.57550.42771250.31312127225277
1.5755-1.60270.36551190.3062572269193
1.6027-1.63180.33841210.29482663278497
1.6318-1.66320.32581640.2862696286098
1.6632-1.69720.32271350.28042728286398
1.6972-1.73410.29941530.27422724287798
1.7341-1.77440.29511300.2642722285298
1.7744-1.81870.2981300.27182755288599
1.8187-1.86790.30131550.2582720287599
1.8679-1.92290.35521370.25282764290199
1.9229-1.98490.23741270.232714284199
1.9849-2.05580.29651640.23082757292199
2.0558-2.13810.24761610.22162767292899
2.1381-2.23530.26081210.23282760288199
2.2353-2.35310.26241610.2342711287299
2.3531-2.50040.26441330.226827982931100
2.5004-2.69330.25541460.226427742920100
2.6933-2.96390.24821420.208727992941100
2.9639-3.3920.23051580.192227562914100
3.392-4.27030.1911380.16212810294899
4.2703-25.47280.19581090.15892629273892
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0182-0.03540.00040.1172-0.00390.00030.0146-0.02650.01470.02380.01030.0042-0.03340.02610.02170.72320.05790.14650.62370.00690.240636.9558-7.660442.5224
20.35810.0715-0.39720.4547-0.13950.41230.0691-0.2113-0.06550.01570.0832-0.01280.0443-0.40340.29850.2195-0.0832-0.02270.41860.00640.128541.4641-21.298133.0662
30.39720.2819-0.44190.34270.00241.3445-0.0913-0.2083-0.02090.0974-0.1767-0.1430.32950.2657-0.35120.1351-0.0362-0.02380.11150.04990.221958.0069-21.30014.1415
40.02990.0234-0.06630.0264-0.07230.19670.1135-0.1654-0.08180.010.05430.1197-0.0024-0.13850.0080.44050.26410.16610.79420.29790.47229.9794-4.645918.8133
50.1212-0.0073-0.10080.0233-0.01660.20710.0076-0.0840.0451-0.07750.1059-0.0544-0.1392-0.06580.26610.78560.31440.4120.49360.19320.668634.31625.222418.7261
60.15110.00270.12970.10830.00750.11260.2708-0.11960.31040.33780.04470.2096-0.38760.05560.43020.6420.03420.26050.3697-0.04410.300839.6425-1.362629.1331
70.0992-0.0327-0.16190.3356-0.14520.43650.0792-0.04510.26950.09790.30130.2123-0.2989-0.07060.40610.68510.15790.30250.42770.07150.480637.38692.095523.3716
80.16650.1576-0.22250.1353-0.29051.08410.0038-0.0437-0.05340.02270.09660.0549-0.0697-0.44550.35690.2040.09460.04080.09170.03950.195645.7693-11.69564.683
90.01010.00970.00790.00890.00840.12050.00270.0682-0.0676-0.11540.06360.0460.0712-0.0980.04810.2262-0.0877-0.05470.5168-0.02230.163142.7372-18.6253-13.8477
100.0365-0.0998-0.19320.57260.40751.17140.0490.13080.04470.14950.0649-0.0269-0.2437-0.3330.16430.17-0.0003-0.0090.1513-0.02040.202646.0441-10.1242.9112
110.75570.0689-0.54360.37640.19380.5663-0.03820.46130.0807-0.2801-0.02330.0280.0848-0.52060.02620.2292-0.0529-0.04380.2553-0.04960.158248.7755-18.5823-13.165
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 512 through 519 )A512 - 519
2X-RAY DIFFRACTION2chain 'H' and (resid 2 through 109 )H2 - 109
3X-RAY DIFFRACTION3chain 'H' and (resid 110 through 215 )H110 - 215
4X-RAY DIFFRACTION4chain 'L' and (resid 1 through 13 )L1 - 13
5X-RAY DIFFRACTION5chain 'L' and (resid 14 through 25 )L14 - 25
6X-RAY DIFFRACTION6chain 'L' and (resid 26 through 61 )L26 - 61
7X-RAY DIFFRACTION7chain 'L' and (resid 62 through 90 )L62 - 90
8X-RAY DIFFRACTION8chain 'L' and (resid 91 through 144 )L91 - 144
9X-RAY DIFFRACTION9chain 'L' and (resid 145 through 155 )L145 - 155
10X-RAY DIFFRACTION10chain 'L' and (resid 156 through 174 )L156 - 174
11X-RAY DIFFRACTION11chain 'L' and (resid 175 through 213 )L175 - 213

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