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- PDB-6mn7: Cryo-EM structure of BG505.SOSIP.664 in complex with BF520.1 anti... -

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Basic information

Entry
Database: PDB / ID: 6mn7
TitleCryo-EM structure of BG505.SOSIP.664 in complex with BF520.1 antigen binding fragment
Components
  • (Envelope Glycoprotein ...) x 2
  • BF520.1 Fab variable region
KeywordsVIRAL PROTEIN / Complex / Broadly neutralizing antibody
Function / homologyGp120 core superfamily / Envelope glycoprotein Gp160 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Retroviral envelope protein GP41-like / Envelope glycoprotein GP120 / Retroviral envelope protein / positive regulation of plasma membrane raft polarization / positive regulation of establishment of T cell polarity / positive regulation of receptor clustering / actin filament reorganization ...Gp120 core superfamily / Envelope glycoprotein Gp160 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Retroviral envelope protein GP41-like / Envelope glycoprotein GP120 / Retroviral envelope protein / positive regulation of plasma membrane raft polarization / positive regulation of establishment of T cell polarity / positive regulation of receptor clustering / actin filament reorganization / host cell endosome membrane / evasion or tolerance by virus of host immune response / viral protein processing / fusion of virus membrane with host plasma membrane / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / integral component of membrane / identical protein binding / Envelope glycoprotein gp160 / Envelope glycoprotein gp160
Function and homology information
Specimen sourceHuman immunodeficiency virus 1
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.8 Å resolution
AuthorsWilliams, J.A. / Lee, K.K. / Overbaugh, J.
CitationJournal: To Be Published
Title: Rapid development of an infant-derived HIV-1 broadly neutralizing antibody lineage
Authors: Simonich, C.A. / Doepker, L. / Ralph, D. / Williams, J.A. / Dhar, A. / Yaffe, Z. / Gentles, L. / Small, C.T. / Oliver, B. / Vigdorovich, V. / Mangala Prasad, V. / Nduati, R. / Sather, D.N. / Lee, K.K. / Matsen, F.A. / Overbaugh, J.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 1, 2018 / Release: Mar 6, 2019

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Structure visualization

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Assembly

Deposited unit
A: Envelope Glycoprotein gp120
B: Envelope Glycoprotein gp41
C: Envelope Glycoprotein gp120
D: Envelope Glycoprotein gp120
E: Envelope Glycoprotein gp41
F: Envelope Glycoprotein gp41
G: BF520.1 Fab variable region
H: BF520.1 Fab variable region
I: BF520.1 Fab variable region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)328,346201
Polyers289,1999
Non-polymers39,147192
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Envelope Glycoprotein ... , 2 types, 6 molecules ACDBEF

#1: Protein/peptide Envelope Glycoprotein gp120 /


Mass: 53278.301 Da / Num. of mol.: 3 / Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6
#2: Protein/peptide Envelope Glycoprotein gp41


Mass: 17146.482 Da / Num. of mol.: 3 / Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Homo sapiens (human) / References: UniProt: Q2N0S7

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Protein/peptide , 1 types, 3 molecules GHI

#3: Protein/peptide BF520.1 Fab variable region


Mass: 25974.941 Da / Num. of mol.: 3 / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 192 molecules

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


Mass: 221.208 Da / Num. of mol.: 111 / Formula: C8H15NO6 / N-Acetylglucosamine
#5: Chemical...
ChemComp-BMA / BETA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 30 / Formula: C6H12O6
#6: Chemical...
ChemComp-MAN / ALPHA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 51 / Formula: C6H12O6

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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: Cryo-EM structure of BF520.1 Fab in complex with BG505.SOSIP.664
Type: COMPLEX / Entity ID: 1, 2, 3 / Source: MULTIPLE SOURCES
Source (natural)Organism: Human immunodeficiency virus 1
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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
Image recordingElectron dose: 66 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3
3D reconstructionResolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 67174 / Symmetry type: POINT

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