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- PDB-8e1p: Crystal structure of BG505 SOSIP.v4.1-GT1.2 trimer in complex wit... -

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Basic information

Entry
Database: PDB / ID: 8e1p
TitleCrystal structure of BG505 SOSIP.v4.1-GT1.2 trimer in complex with gl-PGV20 and PGT124 Fabs
Components
  • (germline PGV20 light ...) x 2
  • BG505-SOSIP.v4.1-GT1.2gp120
  • Envelope glycoprotein gp41
  • PGT124 Fab Heavy Chain
  • PGT124 Fab Light Chain
  • germline PGV20 heavy chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HIV envelope glycoprotein / antibody / CD4 antibody / VIRAL PROTEIN-IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / 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 ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / 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 / identical protein binding / 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 speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.82 Å
AuthorsSarkar, A. / Kumar, S. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Cell Rep Med / Year: 2023
Title: Germline-targeting HIV-1 Env vaccination induces VRC01-class antibodies with rare insertions.
Authors: Caniels, T.G. / Medina-Ramirez, M. / Zhang, J. / Sarkar, A. / Kumar, S. / LaBranche, A. / Derking, R. / Allen, J.D. / Snitselaar, J.L. / Capella-Pujol, J. / Sanchez, I.D.M. / Yasmeen, A. / ...Authors: Caniels, T.G. / Medina-Ramirez, M. / Zhang, J. / Sarkar, A. / Kumar, S. / LaBranche, A. / Derking, R. / Allen, J.D. / Snitselaar, J.L. / Capella-Pujol, J. / Sanchez, I.D.M. / Yasmeen, A. / Diaz, M. / Aldon, Y. / Bijl, T.P.L. / Venkatayogi, S. / Martin Beem, J.S. / Newman, A. / Jiang, C. / Lee, W.H. / Pater, M. / Burger, J.A. / van Breemen, M.J. / de Taeye, S.W. / Rantalainen, K. / LaBranche, C. / Saunders, K.O. / Montefiori, D. / Ozorowski, G. / Ward, A.B. / Crispin, M. / Moore, J.P. / Klasse, P.J. / Haynes, B.F. / Wilson, I.A. / Wiehe, K. / Verkoczy, L. / Sanders, R.W.
History
DepositionAug 11, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 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
F: germline PGV20 heavy chain
H: germline PGV20 heavy chain
I: germline PGV20 light chain
L: germline PGV20 light chain
N: germline PGV20 heavy chain
O: germline PGV20 light chain
A: PGT124 Fab Light Chain
C: PGT124 Fab Light Chain
E: BG505-SOSIP.v4.1-GT1.2gp120
G: BG505-SOSIP.v4.1-GT1.2gp120
J: PGT124 Fab Light Chain
M: BG505-SOSIP.v4.1-GT1.2gp120
B: PGT124 Fab Heavy Chain
D: PGT124 Fab Heavy Chain
K: PGT124 Fab Heavy Chain
Y: Envelope glycoprotein gp41
X: Envelope glycoprotein gp41
Z: Envelope glycoprotein gp41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)514,27665
Polymers497,06218
Non-polymers17,21547
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area75020 Å2
ΔGint-44 kcal/mol
Surface area200580 Å2
Unit cell
Length a, b, c (Å)146.057, 157.666, 158.558
Angle α, β, γ (deg.)90.000, 102.973, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 2 types, 6 molecules EGMYXZ

#5: Protein BG505-SOSIP.v4.1-GT1.2gp120


Mass: 53394.711 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Homo sapiens (human)
#7: Protein Envelope glycoprotein gp41 / Env polyprotein


Mass: 17146.482 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

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Antibody , 5 types, 12 molecules FHNILOACJBDK

#1: Antibody germline PGV20 heavy chain


Mass: 24399.408 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody germline PGV20 light chain


Mass: 22229.459 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 germline PGV20 light chain


Mass: 22229.459 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody PGT124 Fab 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)
#6: Antibody PGT124 Fab Heavy Chain


Mass: 25460.508 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 , 7 types, 47 molecules

#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.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
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
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.: 9
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
#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-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1WURCSPDB2Glycan 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]{}}}}LINUCSPDB-CARE
#11: 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-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]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


Type: oligosaccharide / Mass: 1600.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-1-2-2-2-2-2-2/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-i1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(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]{}}}}}LINUCSPDB-CARE
#12: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-beta-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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
DManpa1-3[DManpa1-6]DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_c6-d1_d3-e1_d6-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#13: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a1122h-1a_1-5]/1-1-1/a2-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Manp]{[(2+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}LINUCSPDB-CARE
#14: 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.: 30 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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 interestY
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: 3.58 Å3/Da / Density % sol: 65.63 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M ammonium sulfate, 0.1 M Tris, pH 8.5, 12% w/v PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.8→49.76 Å / Num. obs: 63948 / % possible obs: 95.7 % / Redundancy: 2.9 % / Biso Wilson estimate: 104.91 Å2 / CC1/2: 0.78 / Net I/σ(I): 4.3
Reflection shellResolution: 3.82→3.88 Å / Num. unique obs: 5699 / CC1/2: 0.31

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX1.19.2_4158refinement
HKL-2000data reduction
Cootmodel building
PHENIXphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5W6D

5w6d


Resolution: 3.82→49.76 Å / SU ML: 0.6141 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 31.5444
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3011 3180 4.97 %
Rwork0.2707 60748 -
obs0.2723 63928 94.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 122.39 Å2
Refinement stepCycle: LAST / Resolution: 3.82→49.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33286 0 1124 0 34410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002635188
X-RAY DIFFRACTIONf_angle_d0.530947888
X-RAY DIFFRACTIONf_chiral_restr0.04355646
X-RAY DIFFRACTIONf_plane_restr0.00425976
X-RAY DIFFRACTIONf_dihedral_angle_d10.187512824
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.82-3.880.37471010.33621911X-RAY DIFFRACTION68.58
3.88-3.940.39381460.34052704X-RAY DIFFRACTION95.96
3.94-4.010.35471260.33952614X-RAY DIFFRACTION95.47
4.01-4.080.36581420.34142706X-RAY DIFFRACTION95.99
4.08-4.150.32541440.32192694X-RAY DIFFRACTION96.07
4.15-4.230.35881400.31812662X-RAY DIFFRACTION96.42
4.23-4.320.33431390.29532701X-RAY DIFFRACTION96.3
4.32-4.410.34121550.28862676X-RAY DIFFRACTION96.36
4.41-4.510.31481400.26982675X-RAY DIFFRACTION96.5
4.51-4.630.30291390.26322674X-RAY DIFFRACTION95.75
4.63-4.750.28711380.26442699X-RAY DIFFRACTION95.88
4.75-4.890.28221400.25432637X-RAY DIFFRACTION95.07
4.89-5.050.30321450.25422682X-RAY DIFFRACTION95.51
5.05-5.230.29111370.25492677X-RAY DIFFRACTION96.21
5.23-5.440.29041420.25562680X-RAY DIFFRACTION95.79
5.44-5.680.26741390.26632684X-RAY DIFFRACTION96.32
5.68-5.980.33541410.26662677X-RAY DIFFRACTION95.72
5.98-6.360.28881380.26062704X-RAY DIFFRACTION95.56
6.36-6.850.30581360.26662665X-RAY DIFFRACTION95.14
6.85-7.530.28311380.2652641X-RAY DIFFRACTION94.14
7.53-8.620.27021330.24222686X-RAY DIFFRACTION94.66
8.62-10.840.21391330.21442651X-RAY DIFFRACTION93.9
10.84-49.760.30021480.2712648X-RAY DIFFRACTION91.64

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