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- PDB-8d53: Crystal Structure of Mosaic HIV-1 Envelope (MosM3.3) in Complex w... -

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Basic information

Entry
Database: PDB / ID: 8d53
TitleCrystal Structure of Mosaic HIV-1 Envelope (MosM3.3) in Complex with antibodies PGT124 and 35O22 at 3.25 Angstrom
Components
  • (Envelope glycoprotein ...) x 2
  • 35O22scFV Heavy chain variable
  • 35O22scFv Light Chain Variable
  • PGT124 Fab Heavy Chain
  • PGT124 Fab Light Chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HIV-1 Envelop Protein / B cell targeting / Mosaic design / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.24 Å
AuthorsXian, Y. / Wilson, I.A.
Funding support United States, 3items
OrganizationGrant numberCountry
International AIDS Vaccine InitiativeINV-008352/OPP1153692 United States
Consortia for HIV/AIDS Vaccine DevelopmentCHAVD 1UM1 AI144462 United States
Other private2 P01 AI110657
CitationJournal: To Be Published
Title: Structural and Antigenic Characterization of B Cell Mosaic Env Trimers
Authors: Xian, Y. / Wilson, I.A.
History
DepositionJun 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 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
G: Envelope glycoprotein gp120
B: Envelope glycoprotein gp41
L: PGT124 Fab Light Chain
H: PGT124 Fab Heavy Chain
D: 35O22scFV Heavy chain variable
E: 35O22scFv Light Chain Variable
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,70724
Polymers138,0036
Non-polymers9,70418
Water00
1
G: Envelope glycoprotein gp120
B: Envelope glycoprotein gp41
L: PGT124 Fab Light Chain
H: PGT124 Fab Heavy Chain
D: 35O22scFV Heavy chain variable
E: 35O22scFv Light Chain Variable
hetero molecules

G: Envelope glycoprotein gp120
B: Envelope glycoprotein gp41
L: PGT124 Fab Light Chain
H: PGT124 Fab Heavy Chain
D: 35O22scFV Heavy chain variable
E: 35O22scFv Light Chain Variable
hetero molecules

G: Envelope glycoprotein gp120
B: Envelope glycoprotein gp41
L: PGT124 Fab Light Chain
H: PGT124 Fab Heavy Chain
D: 35O22scFV Heavy chain variable
E: 35O22scFv Light Chain Variable
hetero molecules


  • defined by author
  • Evidence: gel filtration
  • 443 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)443,12272
Polymers414,01018
Non-polymers29,11254
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Unit cell
Length a, b, c (Å)139.266, 139.266, 320.332
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number149
Space group name H-MP312

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Components

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Envelope glycoprotein ... , 2 types, 2 molecules GB

#1: Protein Envelope glycoprotein gp120


Mass: 50556.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MosM3.3 gp120 / Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Homo sapiens (human)
#2: Protein Envelope glycoprotein gp41


Mass: 15221.087 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MosM3.3 gp41 / Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Homo sapiens (human)

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Antibody , 4 types, 4 molecules LHDE

#3: Antibody PGT124 Fab Light Chain


Mass: 22898.451 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody PGT124 Fab Heavy Chain


Mass: 24750.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Antibody 35O22scFV Heavy chain variable


Mass: 12905.351 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#6: Antibody 35O22scFv Light Chain Variable


Mass: 11670.933 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 7 types, 18 molecules

#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.: 6
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#8: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-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: 1559.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6[DManpa1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+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
#9: 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.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#11: Polysaccharide alpha-D-mannopyranose-(5-4)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(5-4)-alpha-D-mannopyranose-(1-6)-[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: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa5-4DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(4+2)][b-D-Frup]{}}}}}}LINUCSPDB-CARE
#12: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(6-3)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(6-3)-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
DManpa1-3DManpb1-4DManpa6-3DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-ManpA]{}}}}}LINUCSPDB-CARE
#13: 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.: 5 / 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: 6.5 Å3/Da / Density % sol: 81.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.825M ammonium sulfate, 2% PGE 400, 0.1M HEPES, pH 7.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03316 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03316 Å / Relative weight: 1
ReflectionResolution: 3.24→50 Å / Num. obs: 47686 / % possible obs: 83.6 % / Redundancy: 5 % / Biso Wilson estimate: 98.22 Å2 / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.07 / Rrim(I) all: 0.173 / Χ2: 1.098 / Net I/σ(I): 5.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.25-3.315.91.28511180.6210.5051.3861.08139.8
3.31-3.375.61.14912480.550.4631.2451.10144.2
3.37-3.435.30.9814720.6610.4081.0671.08851.9
3.43-3.54.80.83816410.7250.3770.9251.11957.3
3.5-3.585.20.85618000.7070.3680.9371.14264
3.58-3.665.40.76819570.7750.3240.8381.12669.9
3.66-3.755.20.60121690.8310.2590.6591.14476.7
3.75-3.854.70.55624090.8570.2520.6141.14784.7
3.85-3.974.80.44925900.9390.20.4951.21591.6
3.97-4.0950.37527380.9340.1660.4131.25495.8
4.09-4.2450.30628180.9530.1370.3381.1698.9
4.24-4.414.90.21328210.9820.0960.2361.17199.7
4.41-4.614.70.18828380.9830.0870.2081.15699.8
4.61-4.855.20.15228420.9880.0660.1671.10799.4
4.85-5.164.90.13928350.990.0620.1531.08298.7
5.16-5.565.10.12428170.9920.0540.1361.04299.4
5.56-6.115.10.1228570.9910.0530.1321.02799.4
6.11-74.80.09729010.9940.0440.1080.9899.8
7-8.814.90.07528680.9950.0340.0830.91999.2
8.81-504.80.05829470.9950.0280.0650.96298.2

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.19.1_4122refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5cez

5cez


Resolution: 3.24→42.79 Å / SU ML: 0.61 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 42.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3308 2293 4.82 %
Rwork0.317 45270 -
obs0.3176 47563 83.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 256.83 Å2 / Biso mean: 123.6762 Å2 / Biso min: 66.84 Å2
Refinement stepCycle: final / Resolution: 3.24→42.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9690 0 331 0 10021
Biso mean--165.67 --
Num. residues----1243
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.24-3.310.5084760.42731304138039
3.31-3.380.4112830.40581580166347
3.38-3.470.45551150.38771839195455
3.47-3.560.42331060.38682130223663
3.56-3.670.39591260.39232368249470
3.67-3.790.36411200.37842718283881
3.79-3.920.38511460.37432976312288
3.92-4.080.40221580.34753241339995
4.08-4.260.36261580.33033336349499
4.26-4.490.27991930.32263360355399
4.49-4.770.31881590.297233553514100
4.77-5.140.32491790.28973371355099
5.14-5.650.28281370.30743394353199
5.65-6.470.30971830.32043383356699
6.47-8.140.35211810.30973428360999
8.14-42.790.28661730.27613487366098

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