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- PDB-8top: Cryo-EM structure of HIV-1 Env BG505 DS-SOSIP in complex with ant... -

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Basic information

Entry
Database: PDB / ID: 8top
TitleCryo-EM structure of HIV-1 Env BG505 DS-SOSIP in complex with antibody GPZ6-b.01 targeting the fusion peptide
Components
  • (HIV-1 BG505 DS-SOSIP ...) x 2
  • Heavy chain of antibody GPZ6-b.01
  • Light chain of antibody GPZ6-b.01
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HIV-1 Envelope / antibody / GPZ6-b.01 / SHIV / BG505 DS-SOSIP / neutralization / immunization / 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
Macaca mulatta (Rhesus monkey)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsZhou, T. / Morano, N.C. / Roark, R.S. / Kwong, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Cryo-EM structure of HIV-1 Env BG505 DS-SOSIP in complex with antibody GPZ6-b.01 targeting the fusion peptide
Authors: Wang, H.
History
DepositionAug 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _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
O: HIV-1 BG505 DS-SOSIP gp120
P: HIV-1 BG505 DS-SOSIP glycoprotein gp41
Q: HIV-1 BG505 DS-SOSIP gp120
R: HIV-1 BG505 DS-SOSIP glycoprotein gp41
S: HIV-1 BG505 DS-SOSIP gp120
T: HIV-1 BG505 DS-SOSIP glycoprotein gp41
H: Heavy chain of antibody GPZ6-b.01
J: Heavy chain of antibody GPZ6-b.01
K: Light chain of antibody GPZ6-b.01
L: Light chain of antibody GPZ6-b.01
M: Heavy chain of antibody GPZ6-b.01
N: Light chain of antibody GPZ6-b.01
U: Heavy chain of antibody GPZ6-b.01
V: Light chain of antibody GPZ6-b.01
W: Heavy chain of antibody GPZ6-b.01
X: Light chain of antibody GPZ6-b.01
Y: Heavy chain of antibody GPZ6-b.01
Z: Light chain of antibody GPZ6-b.01
A: HIV-1 BG505 DS-SOSIP gp120
B: HIV-1 BG505 DS-SOSIP glycoprotein gp41
C: HIV-1 BG505 DS-SOSIP gp120
D: HIV-1 BG505 DS-SOSIP glycoprotein gp41
E: HIV-1 BG505 DS-SOSIP gp120
F: HIV-1 BG505 DS-SOSIP glycoprotein gp41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)744,590121
Polymers718,13924
Non-polymers26,45197
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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HIV-1 BG505 DS-SOSIP ... , 2 types, 12 molecules OQSACEPRTBDF

#1: Protein
HIV-1 BG505 DS-SOSIP gp120


Mass: 54086.324 Da / Num. of mol.: 6 / Fragment: UNP residues 30-505
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
#2: Protein
HIV-1 BG505 DS-SOSIP glycoprotein gp41 / Env polyproten


Mass: 17146.482 Da / Num. of mol.: 6 / Fragment: UNP residues 509-661
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Cell (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6

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Antibody , 2 types, 12 molecules HJMUWYKLNVXZ

#3: Antibody
Heavy chain of antibody GPZ6-b.01


Mass: 25294.381 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell (production host): HEK293F / Production host: Homo sapiens (human)
#4: Antibody
Light chain of antibody GPZ6-b.01


Mass: 23162.631 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Cell (production host): HEK293F / Production host: Homo sapiens (human)

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Sugars , 3 types, 97 molecules

#5: 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
#6: 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.: 6
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
#7: 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.: 82 / 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: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex between HIV-1 Env BG505 DS-SOSIP and antibody GPZ6-b.01
Type: COMPLEX / Entity ID: #1-#4 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.720 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK 293F / Plasmid: pVRC8400
Buffer solutionpH: 7.4
Details: 137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, and 1.8 mM KH2PO4
Buffer componentConc.: 137 mM / Name: PBS
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Purified complex by FPLC and concentrated to final concentration.
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 103000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 100 K / Temperature (min): 70 K
Image recordingElectron dose: 58.06 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3particle selection
2Leginonimage acquisition
4cryoSPARC3CTF correction
7Cootmodel fitting
9PHENIXmodel refinement
12cryoSPARC3classification
13cryoSPARC33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 566072 / Details: Blob pick in cryoSparc
3D reconstructionResolution: 3.52 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 199205 / Symmetry type: POINT
Atomic model buildingB value: 82.9 / Protocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 7LPN

7lpn


Accession code: 7LPN / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00541055
ELECTRON MICROSCOPYf_angle_d0.78755731
ELECTRON MICROSCOPYf_dihedral_angle_d6.2536081
ELECTRON MICROSCOPYf_chiral_restr0.0776705
ELECTRON MICROSCOPYf_plane_restr0.0086921

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