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- PDB-8tgo: Crystal structure of the BG505 triple tandem trimer gp140 HIV-1 E... -

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Basic information

Entry
Database: PDB / ID: 8tgo
TitleCrystal structure of the BG505 triple tandem trimer gp140 HIV-1 Env in complex with PGT124 and 35O22
Components
  • (Envelope glycoprotein ...) x 2
  • 35O22 scFv
  • PGT124 heavy chain
  • PGT124 light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HIV / envelope / antibody / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / identical protein binding / plasma 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
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 5.75 Å
AuthorsXian, Y. / Yuan, M. / Wilson, I.A.
Funding supportEuropean Union, United States, 6items
OrganizationGrant numberCountry
European Union (EU)681137European Union
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI110657 United States
International AIDS Vaccine Initiative United States
Bill & Melinda Gates FoundationOPP1111923 United States
Bill & Melinda Gates FoundationOPP1132237 United States
Bill & Melinda Gates FoundationOPP1115782 United States
CitationJournal: NPJ Vaccines / Year: 2024
Title: Triple tandem trimer immunogens for HIV-1 and influenza nucleic acid-based vaccines.
Authors: Iván Del Moral-Sánchez / Edmund G Wee / Yuejiao Xian / Wen-Hsin Lee / Joel D Allen / Alba Torrents de la Peña / Rebeca Fróes Rocha / James Ferguson / André N León / Sylvie Koekkoek / ...Authors: Iván Del Moral-Sánchez / Edmund G Wee / Yuejiao Xian / Wen-Hsin Lee / Joel D Allen / Alba Torrents de la Peña / Rebeca Fróes Rocha / James Ferguson / André N León / Sylvie Koekkoek / Edith E Schermer / Judith A Burger / Sanjeev Kumar / Robby Zwolsman / Mitch Brinkkemper / Aafke Aartse / Dirk Eggink / Julianna Han / Meng Yuan / Max Crispin / Gabriel Ozorowski / Andrew B Ward / Ian A Wilson / Tomáš Hanke / Kwinten Sliepen / Rogier W Sanders /
Abstract: Recombinant native-like HIV-1 envelope glycoprotein (Env) trimers are used in candidate vaccines aimed at inducing broadly neutralizing antibodies. While state-of-the-art SOSIP or single-chain Env ...Recombinant native-like HIV-1 envelope glycoprotein (Env) trimers are used in candidate vaccines aimed at inducing broadly neutralizing antibodies. While state-of-the-art SOSIP or single-chain Env designs can be expressed as native-like trimers, undesired monomers, dimers and malformed trimers that elicit non-neutralizing antibodies are also formed, implying that these designs could benefit from further modifications for gene-based vaccination approaches. Here, we describe the triple tandem trimer (TTT) design, in which three Env protomers are genetically linked in a single open reading frame and express as native-like trimers. Viral vectored Env TTT induced similar neutralization titers but with a higher proportion of trimer-specific responses. The TTT design was also applied to generate influenza hemagglutinin (HA) trimers without the need for trimerization domains. Additionally, we used TTT to generate well-folded chimeric Env and HA trimers that harbor protomers from three different strains. In summary, the TTT design is a useful platform for the design of HIV-1 Env and influenza HA immunogens for a multitude of vaccination strategies.
History
DepositionJul 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Envelope glycoprotein gp41
D: 35O22 scFv
C: PGT124 light chain
G: Envelope glycoprotein gp120
O: PGT124 heavy chain
H: Envelope glycoprotein gp41
L: 35O22 scFv
P: PGT124 light chain
R: Envelope glycoprotein gp120
S: PGT124 heavy chain
a: Envelope glycoprotein gp41
b: 35O22 scFv
c: PGT124 light chain
e: Envelope glycoprotein gp120
f: PGT124 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)476,17572
Polymers452,28415
Non-polymers23,89157
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)357.592, 212.044, 207.710
Angle α, β, γ (deg.)90.00, 125.07, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Envelope glycoprotein ... , 2 types, 6 molecules BHaGRe

#1: Protein Envelope glycoprotein gp41


Mass: 17855.959 Da / Num. of mol.: 3 / Fragment: UNP residues 509-661
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6
#4: Protein Envelope glycoprotein gp120


Mass: 54164.121 Da / Num. of mol.: 3 / Fragment: UNP residues 30-504
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6

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Protein , 1 types, 3 molecules OSf

#5: Protein PGT124 heavy chain


Mass: 25345.420 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Antibody , 2 types, 6 molecules DLbCPc

#2: Antibody 35O22 scFv


Mass: 30339.332 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody PGT124 light chain


Mass: 23056.605 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 6 types, 57 molecules

#6: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#7: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#8: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#9: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1721.527 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-i1_i2-j1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#10: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#11: Sugar...
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestN
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: 7.27 Å3/Da / Density % sol: 83.08 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium acetate, 0.2 M zinc acetate, 11.5 % w/v PEG3000, pH 4.83

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 5.75→60 Å / Num. obs: 33735 / % possible obs: 97.8 % / Redundancy: 6.8 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.221 / Rpim(I) all: 0.091 / Rrim(I) all: 0.239 / Χ2: 1.464 / Net I/σ(I): 5.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
5.8-5.95.71.76316230.6650.8940.7941.9410.84594
5.9-6.015.61.79516070.6210.8750.8191.980.82393.5
6.01-6.126.21.86216530.7710.9330.8082.0360.84196.7
6.12-6.257.11.78217280.8190.9490.7151.9220.84499.6
6.25-6.387.31.62316790.8510.9590.6411.7470.85699.5
6.38-6.537.41.38617090.8750.9660.5451.4910.89799.6
6.53-6.697.41.13417180.9420.9850.4451.220.9199.8
6.69-6.887.41.10617060.9150.9780.4351.1890.95299.5
6.88-7.087.40.9117030.9490.9870.3590.9790.97899.5
7.08-7.317.30.85316960.9390.9840.3370.9180.94499.5
7.31-7.577.30.57417230.9730.9930.2290.6191.12599.4
7.57-7.877.30.49117000.9730.9930.1950.5291.16899.4
7.87-8.237.20.3417270.9830.9960.1370.3671.41499.7
8.23-8.667.10.26417220.9880.9970.1070.2851.56499.7
8.66-9.270.19917040.9870.9970.0810.2151.79199.6
9.2-9.916.80.16217220.9880.9970.0670.1762.25998.8
9.91-10.96.40.1217000.9930.9980.0510.132.7198.2
10.9-12.465.70.09715800.9950.9990.0440.1072.98891.8
12.46-15.656.90.09917460.9940.9980.0410.1073.28399.9
15.65-6060.07415890.9960.9990.0320.0812.70789

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5CEZ

5cez


Resolution: 5.75→41.08 Å / SU ML: 0.8 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 36.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2916 1551 4.64 %
Rwork0.2418 --
obs0.2441 33412 92.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 5.75→41.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28076 0 1569 0 29645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00330312
X-RAY DIFFRACTIONf_angle_d0.58741251
X-RAY DIFFRACTIONf_dihedral_angle_d6.494742
X-RAY DIFFRACTIONf_chiral_restr0.0454988
X-RAY DIFFRACTIONf_plane_restr0.0045059
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
5.75-5.930.3448540.30061381X-RAY DIFFRACTION44
5.93-6.140.36571360.312896X-RAY DIFFRACTION93
6.14-6.390.38171840.28943046X-RAY DIFFRACTION99
6.39-6.680.33341400.28173108X-RAY DIFFRACTION99
6.68-7.030.31171380.27763082X-RAY DIFFRACTION99
7.03-7.470.33511640.25643123X-RAY DIFFRACTION99
7.47-8.040.33941340.23243090X-RAY DIFFRACTION99
8.04-8.840.3081660.22633078X-RAY DIFFRACTION99
8.84-10.10.22551630.18693099X-RAY DIFFRACTION99
10.1-12.660.24421270.20062989X-RAY DIFFRACTION94
12.67-41.080.29211450.26752969X-RAY DIFFRACTION92

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