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- EMDB-0485: Cryo-EM structure of T/F100 SOSIP.664 HIV-1 Env trimer in complex... -

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Entry
Database: EMDB / ID: 0485
TitleCryo-EM structure of T/F100 SOSIP.664 HIV-1 Env trimer in complex with 8ANC195 Fab
Map dataT/F100 SOSIP.664 HIV-1 Env trimer in complex with 8ANC195 Fab
SampleT/F100 Env trimer-8anc195 Fab complex:
T/F100 Env trimer / 8anc195 Fab / T/F100 Env gp120 / T/F100 Env gp41 / (8ANC195 G52K5 ...) x 2 / (ligand) x 3
Function / homologyRetroviral envelope protein GP41-like / Gp120 core superfamily / Immunoglobulin C1-set / Immunoglobulin/major histocompatibility complex, conserved site / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin V-set domain / Immunoglobulin-like fold / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Envelope glycoprotein Gp160 ...Retroviral envelope protein GP41-like / Gp120 core superfamily / Immunoglobulin C1-set / Immunoglobulin/major histocompatibility complex, conserved site / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin V-set domain / Immunoglobulin-like fold / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Envelope glycoprotein Gp160 / Envelope glycoprotein GP120 / Retroviral envelope protein / Immunoglobulin C1-set domain / Immunoglobulin V-set domain / Immunoglobulins and major histocompatibility complex proteins signature. / Ig-like domain profile. / Immunoglobulin subtype / 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 / antigen binding / adaptive immune response / 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 / extracellular region / plasma membrane / Envelope glycoprotein gp160 / Immunoglobulin kappa light chain / IgG H chain
Function and homology information
SourceHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 3.9 Å resolution
AuthorsFang Q / Rossmann MG
CitationJournal: Nat Commun / Year: 2019
Title: A sequestered fusion peptide in the structure of an HIV-1 transmitted founder envelope trimer.
Authors: Neeti Ananthaswamy / Qianglin Fang / Wadad AlSalmi / Swati Jain / Zhenguo Chen / Thomas Klose / Yingyuan Sun / Yue Liu / Marthandan Mahalingam / Subhash Chand / Sodsai Tovanabutra / Merlin L Robb / Michael G Rossmann / Venigalla B Rao
Validation ReportPDB-ID: 6nqd

SummaryFull reportAbout validation report
DateDeposition: Jan 21, 2019 / Header (metadata) release: Feb 20, 2019 / Map release: Mar 6, 2019 / Last update: Mar 6, 2019

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Structure visualization

Movie
  • Surface view colored by cylindrical radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6nqd
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0485.map.gz (map file in CCP4 format, 108001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
300 pix
1 Å/pix.
= 300. Å
300 pix
1 Å/pix.
= 300. Å
300 pix
1 Å/pix.
= 300. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density
Contour Level:0.01 (by author), 0.01 (movie #1):
Minimum - Maximum-0.052150786 - 0.07528584
Average (Standard dev.)-0.00003143784 (0.0021133777)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions300300300
Origin0.00.00.0
Limit299.0299.0299.0
Spacing300300300
CellA=B=C: 300.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z300.000300.000300.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0520.075-0.000

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Supplemental data

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Sample components

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Entire T/F100 Env trimer-8anc195 Fab complex

EntireName: T/F100 Env trimer-8anc195 Fab complex / Number of components: 10

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Component #1: protein, T/F100 Env trimer-8anc195 Fab complex

ProteinName: T/F100 Env trimer-8anc195 Fab complex / Recombinant expression: No

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Component #2: protein, T/F100 Env trimer

ProteinName: T/F100 Env trimer / Recombinant expression: No
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293S

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Component #3: protein, 8anc195 Fab

ProteinName: 8anc195 Fab / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: protein, T/F100 Env gp120

ProteinName: T/F100 Env gp120 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 54.739133 kDa
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: protein, T/F100 Env gp41

ProteinName: T/F100 Env gp41 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 20.333879 kDa
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Homo sapiens (human)

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Component #6: protein, 8ANC195 G52K5 heavy chain, IG gamma-1 chain

ProteinName: 8ANC195 G52K5 heavy chain, IG gamma-1 chain / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 26.153283 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #7: protein, 8ANC195 G52K5 light chain

ProteinName: 8ANC195 G52K5 light chain / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 23.460047 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #8: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 96 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Component #9: ligand, BETA-D-MANNOSE

LigandName: BETA-D-MANNOSE / Number of Copies: 12 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

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Component #10: ligand, ALPHA-D-MANNOSE

LigandName: ALPHA-D-MANNOSE / Number of Copies: 33 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 8
Support filmunspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 64 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 170716
3D reconstructionResolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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