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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: EMD-9038
TitleB41 SOSIP.664 in complex with soluble CD4 (D1-D2), the co-receptor mimicking antibody 21c and the broadly neutralizing antibody 8ANC195
Map data
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 / homology
Function and homology information


interleukin-16 binding / interleukin-16 receptor activity / helper T cell enhancement of adaptive immune response / induction by virus of host cell-cell fusion / maintenance of protein location in cell / positive regulation of kinase activity / T cell selection / MHC class II protein binding / positive regulation of monocyte differentiation / positive regulation of viral entry into host cell ...interleukin-16 binding / interleukin-16 receptor activity / helper T cell enhancement of adaptive immune response / induction by virus of host cell-cell fusion / maintenance of protein location in cell / positive regulation of kinase activity / T cell selection / MHC class II protein binding / positive regulation of monocyte differentiation / positive regulation of viral entry into host cell / regulation of T cell activation / response to vitamin D / interleukin-15-mediated signaling pathway / enzyme linked receptor protein signaling pathway / positive regulation of interleukin-2 biosynthetic process / positive regulation of calcium-mediated signaling / positive regulation of calcium ion transport into cytosol / macrophage differentiation / extracellular matrix structural constituent / coreceptor activity / cellular response to granulocyte macrophage colony-stimulating factor stimulus / T cell receptor complex / cytokine production / T cell differentiation / regulation of calcium ion transport / immunoglobulin binding / positive regulation of plasma membrane raft polarization / positive regulation of establishment of T cell polarity / positive regulation of protein kinase activity / positive regulation of receptor clustering / clathrin-coated vesicle membrane / host cell endosome membrane / protein tyrosine kinase binding / actin filament reorganization / positive regulation of T cell proliferation / go:0030260: / mitigation of host immune response by virus / T cell activation / viral protein processing / regulation of defense response to virus by virus / virus receptor activity / transmembrane signaling receptor activity / membrane organization / positive regulation of peptidyl-tyrosine phosphorylation / transmembrane receptor protein tyrosine kinase signaling pathway / positive regulation of MAPK cascade / clathrin-dependent endocytosis of virus by host cell / response to estradiol / fusion of virus membrane with host plasma membrane / positive regulation of I-kappaB kinase/NF-kappaB signaling / signaling receptor activity / T cell receptor signaling pathway / adaptive immune response / fusion of virus membrane with host endosome membrane / cell surface receptor signaling pathway / early endosome / positive regulation of ERK1 and ERK2 cascade / viral envelope / immune response / external side of plasma membrane / cell adhesion / defense response to Gram-negative bacterium / positive regulation of protein phosphorylation / virion attachment to host cell / endoplasmic reticulum lumen / membrane raft / host cell plasma membrane / cytokine-mediated signaling pathway / virion membrane / endoplasmic reticulum membrane / structural molecule activity / protein kinase binding / positive regulation of transcription, DNA-templated / signal transduction / integral component of plasma membrane / enzyme binding / protein homodimerization activity / cell / zinc ion binding / integral component of membrane / identical protein binding / plasma membrane
Immunoglobulin V-set domain / Immunoglobulin subtype 2 / Envelope glycoprotein Gp160 / Gp120 core superfamily / Immunoglobulin-like domain superfamily / T cell CD4 receptor C-terminal region / Retroviral envelope protein GP41-like / CD4, extracellular / Immunoglobulin-like fold / Immunoglobulin ...Immunoglobulin V-set domain / Immunoglobulin subtype 2 / Envelope glycoprotein Gp160 / Gp120 core superfamily / Immunoglobulin-like domain superfamily / T cell CD4 receptor C-terminal region / Retroviral envelope protein GP41-like / CD4, extracellular / Immunoglobulin-like fold / Immunoglobulin / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin C2-set / Immunoglobulin-like domain / T-cell surface antigen CD4 / Immunoglobulin subtype
Envelope glycoprotein gp160 / Envelope glycoprotein gp160 / T-cell surface glycoprotein CD4
Biological speciesHomo sapiens (human) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 4.06 Å
AuthorsBarnes CO / Bjorkman PJ
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P50 GM082545-06 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI100148 United States
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.
History
DepositionAug 11, 2018-
Header (metadata) releaseOct 17, 2018-
Map releaseOct 17, 2018-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: RCSB / Status: Released

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Structure visualization

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

Downloads & links

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Map

FileDownload / File: emd_9038.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 288 pix.
= 377.28 Å
1.31 Å/pix.
x 288 pix.
= 377.28 Å
1.31 Å/pix.
x 288 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 LevelBy AUTHOR: 0.041 / Movie #1: 0.041
Minimum - Maximum-0.13950668 - 0.2453407
Average (Standard dev.)0.00000701992 (±0.0057889447)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 377.27997 Å
α=β=γ: 90.0 °

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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Segmentation: #2

Fileemd_9038_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Segmentation: #1

Fileemd_9038_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: Sharpened map of focused refinement of 21c, gp120,...

Fileemd_9038_additional.map
AnnotationSharpened map of focused refinement of 21c, gp120, and sCD4. Used for model building and refinement of V1V2 region, 21c-gp120 interface, and 21c-sCD4 interface.
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: 60 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

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