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- PDB-6wix: Crystal Structure of HIV-1 MI369 RnS-DS.SOSIP Prefusion Env Trime... -

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Basic information

Entry
Database: PDB / ID: 6wix
TitleCrystal Structure of HIV-1 MI369 RnS-DS.SOSIP Prefusion Env Trimer in Complex with Human Antibodies 3H109L and 35O22 at 3.5 Angstrom
Components
  • (Envelope glycoprotein ...) x 2
  • 35O22 scFv heavy chain
  • 35O22 scFv light chain
  • 3H109L Fab heavy chain
  • 3H109L Fab light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HIV-1 Envelope Prefusion Trimer / VIRAL PROTEIN / 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 / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane ...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 / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / 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 / Glycoprotein 120
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsLai, Y.-T. / Olia, A. / Kwong, P.D.
CitationJournal: Cell Rep / Year: 2020
Title: Automated Design by Structure-Based Stabilization and Consensus Repair to Achieve Prefusion-Closed Envelope Trimers in a Wide Variety of HIV Strains.
Authors: Rawi, R. / Rutten, L. / Lai, Y.T. / Olia, A.S. / Blokland, S. / Juraszek, J. / Shen, C.H. / Tsybovsky, Y. / Verardi, R. / Yang, Y. / Zhang, B. / Zhou, T. / Chuang, G.Y. / Kwong, P.D. / Langedijk, J.P.M.
History
DepositionApr 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _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 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Envelope glycoprotein gp41
D: 35O22 scFv heavy chain
E: 35O22 scFv light chain
G: Envelope glycoprotein gp120
H: 3H109L Fab heavy chain
L: 3H109L Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,61320
Polymers150,0116
Non-polymers7,60214
Water0
1
B: Envelope glycoprotein gp41
D: 35O22 scFv heavy chain
E: 35O22 scFv light chain
G: Envelope glycoprotein gp120
H: 3H109L Fab heavy chain
L: 3H109L Fab light chain
hetero molecules

B: Envelope glycoprotein gp41
D: 35O22 scFv heavy chain
E: 35O22 scFv light chain
G: Envelope glycoprotein gp120
H: 3H109L Fab heavy chain
L: 3H109L Fab light chain
hetero molecules

B: Envelope glycoprotein gp41
D: 35O22 scFv heavy chain
E: 35O22 scFv light chain
G: Envelope glycoprotein gp120
H: 3H109L Fab heavy chain
L: 3H109L Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)472,84060
Polymers450,03418
Non-polymers22,80642
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Unit cell
Length a, b, c (Å)131.860, 131.860, 316.390
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 BG

#1: Protein Envelope glycoprotein gp41


Mass: 17211.594 Da / Num. of mol.: 1 / Fragment: ectodomain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Homo sapiens (human) / References: UniProt: O55774*PLUS
#4: Protein Envelope glycoprotein gp120 /


Mass: 56106.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Homo sapiens (human) / References: UniProt: Q0H5Z3*PLUS

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Antibody , 4 types, 4 molecules DEHL

#2: Antibody 35O22 scFv heavy chain


Mass: 14663.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody 35O22 scFv light chain


Mass: 12358.635 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 3H109L Fab heavy chain


Mass: 26255.498 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 3H109L Fab light chain


Mass: 23416.145 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 , 6 types, 14 molecules

#7: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-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
DManpa1-3DManpa1-6[DManpa1-3]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-e1_e3-f1WURCSPDB2Glycan 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]{[(3+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.: 5
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 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.: 2
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
#10: 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.: 1
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
#11: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose


Type: oligosaccharide / Mass: 627.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
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

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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: 5.29 Å3/Da / Density % sol: 76.76 %
Crystal growTemperature: 298 K / Method: evaporation
Details: 0.18M LiSO4, 0.09M Imidazole pH 6.5, 4.5% MPD, 7.425% PEG3350

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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: RAYONIX MX300-HS / Detector: CCD / Date: Dec 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.56→50 Å / Num. obs: 62697 / % possible obs: 62.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.053 / Rrim(I) all: 0.111 / Χ2: 0.809 / Net I/σ(I): 5.9 / Num. measured all: 236565
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.56-2.622.17290.1411.382.5260.82414.6
2.6-2.652.32.9549490.1621.7933.4750.8119.1
2.65-2.72.72.35110890.1141.3182.7110.84321.8
2.7-2.763.12.11812160.2651.1422.4210.79524.3
2.76-2.823.21.49413760.4770.7951.7020.77727.5
2.82-2.883.21.32315930.5260.7041.5060.81732.1
2.88-2.963.21.14518310.5520.6241.3110.79236.6
2.96-3.043.21.06220600.6410.5951.2250.84241.5
3.04-3.123.20.86623260.710.4870.9990.82346.3
3.12-3.233.40.74625590.7690.4240.8630.78451.2
3.23-3.343.50.64130230.860.3630.740.82760.8
3.34-3.473.50.62940850.8820.360.7290.80681.3
3.47-3.633.80.53148260.9330.3040.6140.81596.7
3.63-3.824.10.44249360.9650.2470.5080.81399.3
3.82-4.064.20.28950100.9850.1560.330.83799.9
4.06-4.384.20.17850180.9930.0970.2040.861100
4.38-4.823.90.09649710.9950.0540.1110.93699.8
4.82-5.514.10.07650420.9960.0410.0860.885100
5.51-6.944.50.05550320.9950.0280.0620.742100
6.94-5040.02750260.9970.0150.0310.59499.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TVP

4tvp


Resolution: 2.67→42.39 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 28.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2697 1724 4.99 %
Rwork0.2249 32838 -
obs0.2271 34562 39.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.16 Å2 / Biso mean: 47.4968 Å2 / Biso min: 1.43 Å2
Refinement stepCycle: final / Resolution: 2.67→42.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9448 0 504 0 9952
Biso mean--68.58 --
Num. residues----1215
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.67-2.750.58870.33651481552
2.75-2.840.2832200.32513073275
2.84-2.940.3712210.31034404616
2.94-3.060.3002360.31386006369
3.06-3.20.393430.314686690912
3.2-3.370.3377650.26751241130618
3.37-3.580.292830.24111661174424
3.58-3.850.28831410.22462596273737
3.85-4.240.31142170.20884240445761
4.24-4.850.2553590.19896796715598
4.85-6.110.25593600.224469677327100
6.11-42.390.24063720.23746976734899

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