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- PDB-8d50: Crystal Structure of Mosaic HIV-1 Envelope (MosM3.1) in Complex w... -

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Basic information

Entry
Database: PDB / ID: 8d50
TitleCrystal Structure of Mosaic HIV-1 Envelope (MosM3.1) in Complex with antibodies PGT124 and 35O22 at 4.3 Angstrom
Components
  • (Envelope glycoprotein ...) x 2
  • 35O22 Fab heavy chain
  • 35O22 Fab light chain
  • PGT124 Fab heavy chain
  • PGT124 Fab light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HIV-1 envelop protein / B cell targeting / mosaic design / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homologyalpha-D-mannopyranose
Function and homology information
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.32 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 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Nov 13, 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
D: 35O22 Fab heavy chain
E: 35O22 Fab light chain
L: PGT124 Fab light chain
H: PGT124 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,45823
Polymers138,9646
Non-polymers7,49417
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)132.189, 132.189, 315.415
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

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

#1: Protein Envelope glycoprotein gp120


Mass: 48934.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MosM3.1 / Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Homo sapiens (human)
#2: Protein Envelope glycoprotein gp41


Mass: 15716.788 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MosM3.1 / Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Homo sapiens (human)

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Antibody , 4 types, 4 molecules DELH

#3: Antibody 35O22 Fab heavy chain


Mass: 15584.698 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 35O22 Fab light chain


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)
#5: Antibody PGT124 Fab light chain


Mass: 22650.193 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 PGT124 Fab heavy chain


Mass: 24406.371 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, 17 molecules

#7: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...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: 910.823 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpa1-2DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_d2-e1WURCSPDB2Glycan 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]{}}}}}LINUCSPDB-CARE
#8: 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.: 3
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
#9: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-3)-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: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d3-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#10: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...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: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#11: 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-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
#12: 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.: 7 / 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
#13: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG 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: 5.73 Å3/Da / Density % sol: 78.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M imidazole (pH=7.33), 0.2M lithium sulfate, 8.545%(w/v) PEG3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03321 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 4.3→50.27 Å / Num. obs: 19809 / % possible obs: 95.3 % / Redundancy: 5.4 % / Biso Wilson estimate: 123.47 Å2 / Rmerge(I) obs: 0.228 / Rpim(I) all: 0.104 / Rrim(I) all: 0.252 / Χ2: 1.148 / Net I/σ(I): 4.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
4.3-4.374.20.8998740.5010.4281.0021.16583.7
4.37-4.454.30.8928650.6260.4260.9960.92685.1
4.45-4.544.11.0198800.6330.491.1390.93885.2
4.54-4.634.20.8989070.6490.4381.0070.92987.5
4.63-4.734.10.8749360.5950.4290.9820.92488.9
4.73-4.8440.5929370.7470.2990.6690.85690.6
4.84-4.963.90.6019290.7870.3130.6830.87892.5
4.96-5.13.90.82110070.6430.450.9430.96194.7
5.1-5.254.40.69310320.6760.3560.7850.92298.1
5.25-5.424.50.65210070.7440.3360.7380.96799.2
5.42-5.6150.69310320.7680.3420.7760.94199.8
5.61-5.835.80.79410440.7540.3580.8740.926100
5.83-6.16.20.7210260.8280.3130.7870.939100
6.1-6.426.50.60410520.8750.2530.6560.938100
6.42-6.826.60.53410460.8990.2210.5791.086100
6.82-7.356.40.43810350.9330.1850.4761.065100
7.35-8.086.70.2510420.9770.1020.271.16499.9
8.08-9.257.10.1310470.9920.0520.141.37100
9.25-11.637.30.07810400.9970.0310.0841.88399.9
11.63-506.80.04410710.9990.0180.0481.9199.4

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Processing

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

5cez


Resolution: 4.32→50.27 Å / SU ML: 0.94 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 51.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3691 975 4.95 %
Rwork0.3229 18728 -
obs0.3252 19703 94.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 401.23 Å2 / Biso mean: 188.2294 Å2 / Biso min: 45.54 Å2
Refinement stepCycle: final / Resolution: 4.32→50.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9797 0 454 0 10251
Biso mean--222.08 --
Num. residues----1255
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.32-4.540.39821210.38682261238279
4.55-4.830.40041390.35862441258087
4.83-5.20.38191250.34822662278793
5.2-5.720.36921320.35522842297499
5.73-6.550.37771580.352728192977100
6.55-8.250.35751660.34528302996100
8.25-50.270.35431340.269328733007100

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