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- PDB-5v8m: A broadly neutralizing antibody targets the dynamic HIV Envelope ... -

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Basic information

Entry
Database: PDB / ID: 5v8m
TitleA broadly neutralizing antibody targets the dynamic HIV Envelope trimer apex via a long, rigidified, and anionic beta-hairpin structure
Descriptorgp120
gp41
antibody 3BNC117
heavy chain
antibody 3BNC117
light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HIV / broadly neutralizing antibody / 3BNC117 / VIRAL PROTEIN-IMMUNE SYSTEM complex
Specimen sourceHuman immunodeficiency virus 1 / virus / HIV-1 / ヒト免疫不全ウイルス 1
Homo sapiens / human
MethodElectron microscopy (4.4 Å resolution / Particle / Single particle)
AuthorsLee, J.H. / Cottrell, C.A. / Ward, A.B.
CitationImmunity, 2017, 46, 690-702

Immunity, 2017, 46, 690-702 StrPapers
A Broadly Neutralizing Antibody Targets the Dynamic HIV Envelope Trimer Apex via a Long, Rigidified, and Anionic β-Hairpin Structure.
Jeong Hyun Lee / Raiees Andrabi / Ching-Yao Su / Anila Yasmeen / Jean-Philippe Julien / Leopold Kong / Nicholas C Wu / Ryan McBride / Devin Sok / Matthias Pauthner / Christopher A Cottrell / Travis Nieusma / Claudia Blattner / James C Paulson / Per Johan Klasse / Ian A Wilson / Dennis R Burton / Andrew B Ward

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 22, 2017 / Release: May 3, 2017

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Assembly

Deposited unit
A: gp120
B: gp41
H: antibody 3BNC117, heavy chain
L: antibody 3BNC117, light chain
F: gp120
I: gp41
R: antibody 3BNC117, heavy chain
T: antibody 3BNC117, light chain
G: gp120
J: gp41
S: antibody 3BNC117, heavy chain
U: antibody 3BNC117, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)388,298165
Polyers356,67012
Non-polymers31,628153
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)71360
ΔGint (kcal/M)314
Surface area (Å2)118300

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Components

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Polypeptide(L) , 2 types, 6 molecules AFGBIJ

#1: Polypeptide(L)gp120 / envelope glycoprotein gp120


Mass: 54064.277 Da / Num. of mol.: 3 / Fragment: UNP residues 30-505 / Source: (gene. exp.) Human immunodeficiency virus 1 / References: UniProt: Q2N0S6

Cellular component

Molecular function

Biological process

  • membrane fusion involved in viral entry into host cell (GO: 0039663)
  • virion attachment to host cell (GO: 0019062)
#2: Polypeptide(L)gp41 / envelope glycoprotein gp41


Mass: 17146.482 Da / Num. of mol.: 3 / Fragment: UNP residues 509-661 / Source: (gene. exp.) Human immunodeficiency virus 1 / References: UniProt: Q2N0S6

Cellular component

Molecular function

Biological process

  • membrane fusion involved in viral entry into host cell (GO: 0039663)
  • virion attachment to host cell (GO: 0019062)

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Antibody 3BNC117, ... , 2 types, 6 molecules HRSLTU

#3: Polypeptide(L)antibody 3BNC117, heavy chain


Mass: 24656.484 Da / Num. of mol.: 3 / Fragment: Fab / Source: (gene. exp.) Homo sapiens
#4: Polypeptide(L)antibody 3BNC117, light chain


Mass: 23022.658 Da / Num. of mol.: 3 / Fragment: Fab / Source: (gene. exp.) Homo sapiens

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Non-polymers , 3 types, 153 molecules

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


Mass: 221.208 Da / Num. of mol.: 99 / Formula: C8H15NO6
#6: Chemical
ChemComp-BMA / BETA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 15 / Formula: C6H12O6
#7: Chemical...
ChemComp-MAN / ALPHA-D-MANNOSE


Mass: 180.156 Da / Num. of mol.: 39 / Formula: C6H12O6

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: BG505 SOSIP.664 soluble Env trimer in complex with 3BNC117 Fab
Type: COMPLEX / Entity ID: 1,2,3,4 / Source: RECOMBINANT
Molecular weightValue: 0.51 deg. / Units: MEGADALTONS / Experimental flag: NO
Source (natural)Organism: Homo sapiens
Source (recombinant)Cell: HEK293F / Organism: Homo sapiens
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 FIELD
Image recordingElectron dose: 32 e/Å2 / Detector mode: COUNTING / 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: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 22625 / Symmetry type: POINT

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