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- PDB-6dcq: Ectodomain of full length, wild type HIV-1 glycoprotein clone PC6... -

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Basic information

Entry
Database: PDB / ID: 6dcq
TitleEctodomain of full length, wild type HIV-1 glycoprotein clone PC64M18C043 in complex with PGT151 Fab
Components
  • (Envelope glycoprotein ...) x 2
  • (Immunoglobulin G PGT151 Fab, ...) x 2
KeywordsVIRAL PROTEIN / HIV-1 / Glycoprotein / Env
Function / homologyImmunoglobulin V-set domain / Immunoglobulin-like domain / Immunoglobulin C1-set domain / Retroviral envelope protein / Envelope glycoprotein GP120 / Envelope glycoprotein Gp160 / Gp120 core superfamily / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Ig-like domain profile. ...Immunoglobulin V-set domain / Immunoglobulin-like domain / Immunoglobulin C1-set domain / Retroviral envelope protein / Envelope glycoprotein GP120 / Envelope glycoprotein Gp160 / Gp120 core superfamily / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Ig-like domain profile. / Immunoglobulin subtype / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C1-set / Immunoglobulin/major histocompatibility complex, conserved site / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Retroviral envelope protein GP41-like / Immunoglobulin V-set domain / membrane fusion involved in viral entry into host cell / host cell endosome membrane / viral envelope / virion attachment to host cell / virion membrane / structural molecule activity / integral component of membrane / Envelope glycoprotein gp160 / Uncharacterized protein / IgG H chain
Function and homology information
Specimen sourceHuman immunodeficiency virus 1
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.1 Å resolution
AuthorsRantalainen, K.
CitationJournal: Cell Rep / Year: 2018
Title: Co-evolution of HIV Envelope and Apex-Targeting Neutralizing Antibody Lineage Provides Benchmarks for Vaccine Design.
Authors: Kimmo Rantalainen / Zachary T Berndsen / Sasha Murrell / Liwei Cao / Oluwarotimi Omorodion / Jonathan L Torres / Mengyu Wu / Jeffrey Umotoy / Jeffrey Copps / Pascal Poignard / Elise Landais / James C Paulson / Ian A Wilson / Andrew B Ward
Abstract: Broadly neutralizing antibodies (bnAbs) targeting the HIV envelope glycoprotein (Env) typically take years to develop. Longitudinal analyses of both neutralizing antibody lineages and viruses at ...Broadly neutralizing antibodies (bnAbs) targeting the HIV envelope glycoprotein (Env) typically take years to develop. Longitudinal analyses of both neutralizing antibody lineages and viruses at serial time points during infection provide a basis for understanding the co-evolutionary contest between HIV and the humoral immune system. Here, we describe the structural characterization of an apex-targeting antibody lineage and autologous clade A viral Env from a donor in the Protocol C cohort. Comparison of Ab-Env complexes at early and late time points reveals that, within the antibody lineage, the CDRH3 loop rigidifies, the bnAb angle of approach steepens, and surface charges are mutated to accommodate glycan changes. Additionally, we observed differences in site-specific glycosylation between soluble and full-length Env constructs, which may be important for tuning optimal immunogenicity in soluble Env trimers. These studies therefore provide important guideposts for design of immunogens that prime and mature nAb responses to the Env V2-apex.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 8, 2018 / Release: Jun 27, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jun 27, 2018Structure modelrepositoryInitial release
1.1Jul 4, 2018Structure modelData collection / Database referencescitation_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

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Structure viewerMolecule:
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Assembly

Deposited unit
A: Envelope glycoprotein gp160
B: Envelope glycoprotein gp160
C: Envelope glycoprotein gp160
D: Envelope glycoprotein gp160
E: Envelope glycoprotein gp160
F: Envelope glycoprotein gp160
H: Immunoglobulin G PGT151 Fab, Heavy chain
L: Immunoglobulin G PGT151 Fab, Light chain
M: Immunoglobulin G PGT151 Fab, Heavy chain
N: Immunoglobulin G PGT151 Fab, Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)408,498143
Polyers380,52810
Non-polymers27,970133
Water0
1


  • idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Size exclusion chromatography peak retention volume corresponds to expected size, mass spectrometry, Presence of C-terminus in Env confirmed with mass spectrometry, native gel electrophoresis, Size of the complex confirmed with BN-PAGE
  • Download structure data
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)66850
ΔGint (kcal/M)225
Surface area (Å2)112960

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Components

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Envelope glycoprotein ... , 2 types, 6 molecules ACEBDF

#1: Protein/peptide Envelope glycoprotein gp160


Mass: 53392.359 Da / Num. of mol.: 3 / Fragment: GP120 domain residues 28-507 / Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Homo sapiens (human) / References: UniProt: A0A2H4K974
#2: Protein/peptide Envelope glycoprotein gp160


Mass: 40020.207 Da / Num. of mol.: 3 / Fragment: GP41 domain residues 508-859 / Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Homo sapiens (human) / References: UniProt: A0A2H4K974

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Immunoglobulin G PGT151 Fab, ... , 2 types, 4 molecules HMLN

#3: Protein/peptide Immunoglobulin G PGT151 Fab, Heavy chain


Mass: 26087.438 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: S6B291
#4: Protein/peptide Immunoglobulin G PGT151 Fab, Light chain


Mass: 24057.809 Da / Num. of mol.: 2 / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) / References: UniProt: Q8TCD0

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Non-polymers , 5 types, 133 molecules

#5: Chemical...
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 100 / Formula: C8H15NO6 / N-Acetylglucosamine
#6: Chemical
ChemComp-FUC / ALPHA-L-FUCOSE


Mass: 164.156 Da / Num. of mol.: 6 / Formula: C6H12O5
#7: Chemical
ChemComp-MAN / ALPHA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 16 / Formula: C6H12O6
#8: Chemical
ChemComp-BMA / BETA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 7 / Formula: C6H12O6
#9: Chemical
ChemComp-GAL / BETA-D-GALACTOSE


Mass: 180.156 Da / Num. of mol.: 4 / Formula: C6H12O6 / Galactose

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Full length, wild type HIV-1 Envelope glycoprotein in complex with PGT151 Fab
Type: COMPLEX
Details: Full length HIV-1 Envelope glycoprotein clone C043 collected 18 months post infection from donor 64 of Protocol C cohort study. Expressed as recombinant protein in HEK293F cell line.
Entity ID: 1, 2, 3, 4 / Source: NATURAL
Molecular weightValue: 0.389 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Details of virusVirus type: VIRION
Buffer solutionDetails: Detergent removed with Biobeads prior to grid freezing
pH: 7.4
Buffer component
IDConc.NameFormulaBuffer ID
150 mMTris(hydroxymethyl)aminomethane hydrochlorideTris-Hcl1
2150 mMsodium chlorideNaCl1
30.1 %n-Dodecyl-beta-MaltosideDDM1
40.03 %Sodium deoxycholate monohydrateDeoxycholate1
SpecimenConc.: 7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: C-flat-2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 kelvins / Details: Blot force 0 Blot time 5 sec

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / C2 aperture diameter: 100 mm
Image recordingElectron dose: 1.885 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1 / Number of real images: 4039
Image scansMovie frames/image: 40

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategory
2Leginonimage acquisition
4RelionCTF correction
10Relioninitial Euler assignment
11Relionfinal Euler assignment
12Relionclassification
13Relion3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 236179 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01120001
ELECTRON MICROSCOPYf_angle_d1.25527387
ELECTRON MICROSCOPYf_dihedral_angle_d8.22014234
ELECTRON MICROSCOPYf_chiral_restr0.0773429
ELECTRON MICROSCOPYf_plane_restr0.0083284

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