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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 / homologyImmunoglobulin domain / Alpha-defensins / Immunoglobulin C2-set / Immunoglobulin-like domain / Immunoglobulin subtype / Immunoglobulin subtype 2 / Binding and entry of HIV virion / Nef Mediated CD4 Down-regulation / Ig-like domain profile. / Downstream TCR signaling ...Immunoglobulin domain / Alpha-defensins / Immunoglobulin C2-set / Immunoglobulin-like domain / Immunoglobulin subtype / Immunoglobulin subtype 2 / Binding and entry of HIV virion / Nef Mediated CD4 Down-regulation / Ig-like domain profile. / Downstream TCR signaling / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Retroviral envelope protein GP41-like / Envelope glycoprotein GP120 / T cell CD4 receptor C terminal region / CD4, extracellular / Immunoglobulin C2-set domain / Retroviral envelope protein / Vpu mediated degradation of CD4 / T-cell surface antigen CD4 / Phosphorylation of CD3 and TCR zeta chains / Generation of second messenger molecules / Envelope glycoprotein Gp160 / Gp120 core superfamily / Immunoglobulin-like domain superfamily / Clathrin-mediated endocytosis / Immunoglobulin V-set domain / Cargo recognition for clathrin-mediated endocytosis / Other interleukin signaling / PD-1 signaling / T cell CD4 receptor C-terminal region / CD4, extracellular / Immunoglobulin / Immunoglobulin-like fold / Translocation of ZAP-70 to Immunological synapse / 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 / regulation of T cell activation / T cell selection / 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 / enzyme linked receptor protein signaling pathway / positive regulation of calcium-mediated signaling / positive regulation of calcium ion transport into cytosol / cellular response to granulocyte macrophage colony-stimulating factor stimulus / coreceptor activity / regulation of calcium ion transport / T cell differentiation / cytokine production / extracellular matrix structural constituent / positive regulation of plasma membrane raft polarization / positive regulation of establishment of T cell polarity / positive regulation of receptor clustering / positive regulation of protein kinase activity / protein tyrosine kinase binding / actin filament reorganization / host cell endosome membrane / clathrin-coated vesicle membrane / evasion or tolerance by virus of host immune response / positive regulation of T cell proliferation / entry into host cell / T cell activation / transmembrane receptor protein tyrosine kinase signaling pathway / viral protein processing / regulation of defense response to virus by virus / virus receptor activity / membrane organization / positive regulation of peptidyl-tyrosine phosphorylation / adaptive immune response / positive regulation of MAPK cascade / fusion of virus membrane with host plasma membrane / T cell receptor signaling pathway / response to estradiol / clathrin-dependent endocytosis of virus by host cell / signaling receptor activity / positive regulation of I-kappaB kinase/NF-kappaB signaling / transmembrane signaling receptor activity / fusion of virus membrane with host endosome membrane / early endosome / cell surface receptor signaling pathway / viral envelope / immune response / defense response to Gram-negative bacterium / positive regulation of ERK1 and ERK2 cascade / cell adhesion / virion attachment to host cell / positive regulation of protein phosphorylation / membrane raft / external side of plasma membrane / host cell plasma membrane / endoplasmic reticulum lumen
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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