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- EMDB-9038: B41 SOSIP.664 in complex with soluble CD4 (D1-D2), the co-recepto... -

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Basic information

Entry
Database: EMDB / ID: 9038
TitleB41 SOSIP.664 in complex with soluble CD4 (D1-D2), the co-receptor mimicking antibody 21c and the broadly neutralizing antibody 8ANC195
Map dataSharpened map of complex used for model building and refinement.
SampleB41 SOSIP-sCD4-21c-8ANC195 complex:
(Envelope glycoprotein ...) x 2 / T-cell surface glycoprotein CD4 / 21c Fab VH domain / 21c Fab VL domain / (8ANC195 G52K5 Fab ...) x 2 / (ligand) x 3
Function / homologyGp120 core superfamily / Immunoglobulin subtype 2 / Immunoglobulin-like domain / Immunoglobulin C2-set domain / Retroviral envelope protein / Envelope glycoprotein GP120 / Immunoglobulin domain / Envelope glycoprotein Gp160 / Immunoglobulin-like domain superfamily / Ig-like domain profile. ...Gp120 core superfamily / Immunoglobulin subtype 2 / Immunoglobulin-like domain / Immunoglobulin C2-set domain / Retroviral envelope protein / Envelope glycoprotein GP120 / Immunoglobulin domain / Envelope glycoprotein Gp160 / Immunoglobulin-like domain superfamily / Ig-like domain profile. / Immunoglobulin C2-set / Immunoglobulin V-set domain / T cell CD4 receptor C-terminal region / Immunoglobulin / CD4, extracellular / Immunoglobulin-like fold / T cell CD4 receptor C terminal region / CD4, extracellular / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Phosphorylation of CD3 and TCR zeta chains / Clathrin-mediated endocytosis / Cargo recognition for clathrin-mediated endocytosis / Retroviral envelope protein GP41-like / Other interleukin signaling / Immunoglobulin subtype / T-cell surface antigen CD4 / Generation of second messenger molecules / Translocation of ZAP-70 to Immunological synapse / PD-1 signaling / Vpu mediated degradation of CD4 / Binding and entry of HIV virion / Downstream TCR signaling / Nef Mediated CD4 Down-regulation / Alpha-defensins / helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / induction by virus of host cell-cell fusion / maintenance of protein location in cell / T cell selection / regulation of T cell activation / MHC class II protein binding / immunoglobulin binding / positive regulation of monocyte differentiation / positive regulation of kinase activity / response to vitamin D / T cell receptor complex / positive regulation of viral entry into host cell / interleukin-15-mediated signaling pathway / positive regulation of interleukin-2 biosynthetic process / positive regulation of calcium ion transport into cytosol / enzyme linked receptor protein signaling pathway / positive regulation of calcium-mediated signaling / membrane fusion involved in viral entry into host cell / coreceptor activity / cellular response to granulocyte macrophage colony-stimulating factor stimulus / extracellular matrix structural constituent / regulation of calcium ion transport / T cell differentiation / cytokine production / protein tyrosine kinase binding / positive regulation of protein kinase activity / clathrin-coated vesicle membrane / host cell endosome membrane / positive regulation of T cell proliferation / entry into host cell / transmembrane receptor protein tyrosine kinase signaling pathway / regulation of defense response to virus by virus / transmembrane signaling receptor activity / virus receptor activity / signaling receptor activity / positive regulation of peptidyl-tyrosine phosphorylation / fusion of virus membrane with host plasma membrane / T cell receptor signaling pathway / membrane organization / positive regulation of MAPK cascade / adaptive immune response / response to estradiol / positive regulation of I-kappaB kinase/NF-kappaB signaling / early endosome / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / immune response / viral envelope / defense response to Gram-negative bacterium / cell adhesion / positive regulation of protein phosphorylation / virion attachment to host cell / external side of plasma membrane / membrane raft / host cell plasma membrane / endoplasmic reticulum lumen / virion membrane / cytokine-mediated signaling pathway / endoplasmic reticulum membrane / structural molecule activity / protein kinase binding / positive regulation of transcription, DNA-templated / integral component of plasma membrane / signal transduction
Function and homology information
SourceHomo sapiens (human) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / 4.06 Å resolution
AuthorsBarnes CO / Bjorkman PJ
CitationJournal: Cell Host Microbe / Year: 2018
Title: Partially Open HIV-1 Envelope Structures Exhibit Conformational Changes Relevant for Coreceptor Binding and Fusion.
Authors: Haoqing Wang / Christopher O Barnes / Zhi Yang / Michel C Nussenzweig / Pamela J Bjorkman
Abstract: HIV-1 Env, a trimer of gp120-gp41 heterodimers, mediates membrane fusion after binding host receptor CD4. Receptor binding displaces V1V2 loops from Env's apex, allowing coreceptor binding and ...HIV-1 Env, a trimer of gp120-gp41 heterodimers, mediates membrane fusion after binding host receptor CD4. Receptor binding displaces V1V2 loops from Env's apex, allowing coreceptor binding and opening Env to enable gp41-mediated fusion. We present 3.54 Å and 4.06 Å cryoelectron microscopy structures of partially open soluble native-like Env trimers (SOSIPs) bound to CD4. One structure, a complex with a coreceptor-mimicking antibody that binds both CD4 and gp120, stabilizes the displaced V1V2 and reveals its structure. Comparing partially and fully open Envs with closed Envs shows that gp41 rearrangements are independent of the CD4-induced rearrangements that result in V1V2 displacement and formation of a 4-stranded bridging sheet. These findings suggest ordered conformational changes before coreceptor binding: (1) gp120 opening inducing side-chain rearrangements and a compact gp41 central helix conformation, and (2) 4-stranded bridging-sheet formation and V1V2 displacement. These analyses illuminate potential receptor-induced Env changes and inform design of therapeutics disrupting viral entry.
Validation ReportPDB-ID: 6edu

SummaryFull reportAbout validation report
DateDeposition: Aug 11, 2018 / Header (metadata) release: Oct 17, 2018 / Map release: Oct 17, 2018 / Last update: Oct 24, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.041
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.041
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6edu
  • Surface level: 0.041
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9038.map.gz (map file in CCP4 format, 95552 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
288 pix
1.31 Å/pix.
= 377.28 Å
288 pix
1.31 Å/pix.
= 377.28 Å
288 pix
1.31 Å/pix.
= 377.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.31 Å
Density
Contour Level:0.041 (by author), 0.041 (movie #1):
Minimum - Maximum-0.13950668 - 0.2453407
Average (Standard dev.)0.0000070199203 (0.0057889447)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions288288288
Origin0.00.00.0
Limit287.0287.0287.0
Spacing288288288
CellA=B=C: 377.27997 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.311.311.31
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z377.280377.280377.280
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.1020.1940.000

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Supplemental data

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Mask #1

Fileemd_9038_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Mask #2

Fileemd_9038_msk_2.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire B41 SOSIP-sCD4-21c-8ANC195 complex

EntireName: B41 SOSIP-sCD4-21c-8ANC195 complex / Number of components: 11

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Component #1: protein, B41 SOSIP-sCD4-21c-8ANC195 complex

ProteinName: B41 SOSIP-sCD4-21c-8ANC195 complex / Recombinant expression: No
MassTheoretical: 700 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, Envelope glycoprotein gp160

ProteinName: Envelope glycoprotein gp160 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 17.357824 kDa
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Cricetulus griseus (Chinese hamster)

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Component #3: protein, Envelope glycoprotein gp160

ProteinName: Envelope glycoprotein gp160 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 57.702469 kDa
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Cricetulus griseus (Chinese hamster)

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Component #4: protein, T-cell surface glycoprotein CD4

ProteinName: T-cell surface glycoprotein CD4 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 20.50326 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: protein, 21c Fab VH domain

ProteinName: 21c Fab VH domain / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 24.61959 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #6: protein, 21c Fab VL domain

ProteinName: 21c Fab VL domain / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 22.815264 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #7: protein, 8ANC195 G52K5 Fab VH domain

ProteinName: 8ANC195 G52K5 Fab VH domain / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 26.12527 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #8: protein, 8ANC195 G52K5 Fab VL domain

ProteinName: 8ANC195 G52K5 Fab VL domain / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 23.401984 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #9: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 81 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Component #10: ligand, BETA-D-MANNOSE

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

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Component #11: ligand, ALPHA-D-MANNOSE

LigandName: ALPHA-D-MANNOSE / Number of Copies: 30 / 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 solutionSpecimen conc.: 0.35 mg/ml / pH: 8
Support film0.26 mA
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 293 K / Humidity: 95 %

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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: 6 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1700.0 - 3000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2531

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C3 (3 fold cyclic) / Number of projections: 305469
3D reconstructionSoftware: RELION / Resolution: 4.06 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Target criteria: Correlation coefficient / Refinement space: REAL
Output model

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