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- EMDB-20100: B41 SOSIP.664 in complex with the silent-face antibody SF12 and V... -

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Entry
Database: EMDB / ID: EMD-20100
TitleB41 SOSIP.664 in complex with the silent-face antibody SF12 and V3-targeting antibody 10-1074
Map data
SampleComplex of B41 SOSIP.664 trimer with three SF12 Fabs and one 10-1074 Fab:
B41 SOSIP.664 trimer / 10-1074 Fab / SF12 Fab / (Envelope glycoprotein ...) x 2 / 10-1074 Heavy Chain,10-1074 Heavy Chain / 10-1074 Light Chain,10-1074 Light Chain / SF12 Heavy Chain,SF12 Heavy Chain / SF12 Light Chain,SF12 Light Chain / (ligand) x 3
Function / homology
Function and homology information


Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Cell surface interactions at the vascular wall / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / CD22 mediated BCR regulation / FCERI mediated NF-kB activation / Regulation of actin dynamics for phagocytic cup formation ...Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Cell surface interactions at the vascular wall / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / CD22 mediated BCR regulation / FCERI mediated NF-kB activation / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated Ca+2 mobilization / FCERI mediated MAPK activation / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / Fc epsilon receptor (FCERI) signaling / Role of LAT2/NTAL/LAB on calcium mobilization / positive regulation of plasma membrane raft polarization / positive regulation of establishment of T cell polarity / positive regulation of receptor clustering / host cell endosome membrane / actin filament reorganization / complement activation / evasion or tolerance by virus of host immune response / immunoglobulin complex, circulating / immunoglobulin receptor binding / phagocytosis, recognition / positive regulation of B cell activation / phagocytosis, engulfment / viral protein processing / complement activation, classical pathway / regulation of complement activation / antigen binding / Fc-epsilon receptor signaling pathway / B cell receptor signaling pathway / receptor-mediated endocytosis / Fc-gamma receptor signaling pathway involved in phagocytosis / retina homeostasis / fusion of virus membrane with host plasma membrane / regulation of immune response / clathrin-dependent endocytosis of virus by host cell / leukocyte migration / fusion of virus membrane with host endosome membrane / blood microparticle / viral envelope / immune response / virion attachment to host cell / external side of plasma membrane / host cell plasma membrane / defense response to bacterium / virion membrane / innate immune response / structural molecule activity / extracellular space / extracellular exosome / integral component of membrane / extracellular region / plasma membrane
Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Ig-like domain profile. / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin V-set domain / Immunoglobulin C1-set domain / Retroviral envelope protein GP41-like / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin C1-set / Immunoglobulin subtype ...Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Ig-like domain profile. / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin V-set domain / Immunoglobulin C1-set domain / Retroviral envelope protein GP41-like / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin C1-set / Immunoglobulin subtype / Immunoglobulin-like domain / Immunoglobulin V-set domain / Immunoglobulin-like fold / Immunoglobulin-like domain superfamily / Gp120 core superfamily / Envelope glycoprotein Gp160 / Retroviral envelope protein
Envelope glycoprotein gp160 / Envelope glycoprotein gp160 / Immunoglobulin kappa constant / IGL@ protein / IgG H chain
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsBarnes CO / Bjorkman PJ
CitationJournal: Immunity / Year: 2019
Title: Broad and Potent Neutralizing Antibodies Recognize the Silent Face of the HIV Envelope.
Authors: Till Schoofs / Christopher O Barnes / Nina Suh-Toma / Jovana Golijanin / Philipp Schommers / Henning Gruell / Anthony P West / Franziska Bach / Yu Erica Lee / Lilian Nogueira / Ivelin S Georgiev / Robert T Bailer / Julie Czartoski / John R Mascola / Michael S Seaman / M Juliana McElrath / Nicole A Doria-Rose / Florian Klein / Michel C Nussenzweig / Pamela J Bjorkman /
Abstract: Broadly neutralizing antibodies (bNAbs) against HIV-1 envelope (Env) inform vaccine design and are potential therapeutic agents. We identified SF12 and related bNAbs with up to 62% neutralization ...Broadly neutralizing antibodies (bNAbs) against HIV-1 envelope (Env) inform vaccine design and are potential therapeutic agents. We identified SF12 and related bNAbs with up to 62% neutralization breadth from an HIV-infected donor. SF12 recognized a glycan-dominated epitope on Env's silent face and was potent against clade AE viruses, which are poorly covered by V3-glycan bNAbs. A 3.3Å cryo-EM structure of a SF12-Env trimer complex showed additional contacts to Env protein residues by SF12 compared with VRC-PG05, the only other known donor-derived silentface antibody, explaining SF12's increased neutralization breadth, potency, and resistance to Env mutation routes. Asymmetric binding of SF12 was associated with distinct N-glycan conformations across Env protomers, demonstrating intra-Env glycan heterogeneity. Administrating SF12 to HIV-1-infected humanized mice suppressed viremia and selected for viruses lacking the N448 glycan. Effective bNAbs can therefore be raised against HIV-1 Env's silent face, suggesting their potential for HIV-1 prevention, therapy, and vaccine development.
Validation ReportPDB-ID: 6okp

SummaryFull reportAbout validation report
DateDeposition: Apr 14, 2019 / Header (metadata) release: May 8, 2019 / Map release: Jun 5, 2019 / Update: Jun 5, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.022
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6okp
  • Surface level: 0.022
  • 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_20100.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 256 pix.
= 279.04 Å
1.09 Å/pix.
x 256 pix.
= 279.04 Å
1.09 Å/pix.
x 256 pix.
= 279.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density
Contour LevelBy AUTHOR: 0.022 / Movie #1: 0.022
Minimum - Maximum-0.07658794 - 0.14188224
Average (Standard dev.)-0.000032784465 (±0.0046433927)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 279.04 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z279.040279.040279.040
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0770.142-0.000

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Supplemental data

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Mask #1

Fileemd_20100_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Complex of B41 SOSIP.664 trimer with three SF12 Fabs and one 10-1...

EntireName: Complex of B41 SOSIP.664 trimer with three SF12 Fabs and one 10-1074 Fab
Details: Fab fragment generated by recombinant expression and complexed with the B41 SOSIP.664 trimer
Number of components: 13

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Component #1: protein, Complex of B41 SOSIP.664 trimer with three SF12 Fabs and...

ProteinName: Complex of B41 SOSIP.664 trimer with three SF12 Fabs and one 10-1074 Fab
Details: Fab fragment generated by recombinant expression and complexed with the B41 SOSIP.664 trimer
Recombinant expression: No
MassTheoretical: 540 kDa

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Component #2: protein, B41 SOSIP.664 trimer

ProteinName: B41 SOSIP.664 trimer / Recombinant expression: No
SourceSpecies: Human immunodeficiency virus 1
Source (engineered)Expression System: Cricetulus griseus (Chinese hamster)

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Component #3: protein, 10-1074 Fab

ProteinName: 10-1074 Fab / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Vector: p3BNC / Strain: Expi293

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Component #4: protein, SF12 Fab

ProteinName: SF12 Fab / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Vector: p3BNC / Strain: Expi293

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Component #5: protein, Envelope glycoprotein gp41

ProteinName: Envelope glycoprotein gp41 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 17.357824 kDa
SourceSpecies: Human immunodeficiency virus 1 / Strain: B41
Source (engineered)Expression System: Cricetulus griseus (Chinese hamster)

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Component #6: protein, Envelope glycoprotein gp120

ProteinName: Envelope glycoprotein gp120 / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 57.702469 kDa
SourceSpecies: Human immunodeficiency virus 1 / Strain: B41
Source (engineered)Expression System: Cricetulus griseus (Chinese hamster)
Source (natural)Cell: B-Cell

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Component #7: protein, 10-1074 Heavy Chain,10-1074 Heavy Chain

ProteinName: 10-1074 Heavy Chain,10-1074 Heavy Chain / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.490568 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)
Source (natural)Cell: B-Cell

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Component #8: protein, 10-1074 Light Chain,10-1074 Light Chain

ProteinName: 10-1074 Light Chain,10-1074 Light Chain / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.18076 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)
Source (natural)Cell: B-Cell

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Component #9: protein, SF12 Heavy Chain,SF12 Heavy Chain

ProteinName: SF12 Heavy Chain,SF12 Heavy Chain / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 26.045205 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)
Source (natural)Cell: B-Cell

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Component #10: protein, SF12 Light Chain,SF12 Light Chain

ProteinName: SF12 Light Chain,SF12 Light Chain / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 23.236971 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #11: ligand, N-ACETYL-D-GLUCOSAMINE

LigandName: N-ACETYL-D-GLUCOSAMINEN-Acetylglucosamine / Number of Copies: 95 / Recombinant expression: No
MassTheoretical: 0.221208 kDa

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Component #12: ligand, BETA-D-MANNOSE

LigandName: BETA-D-MANNOSE / Number of Copies: 16 / Recombinant expression: No
MassTheoretical: 0.180156 kDa

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Component #13: ligand, ALPHA-D-MANNOSE

LigandName: ALPHA-D-MANNOSE / Number of Copies: 46 / 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.: 0.8 mg/mL / pH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 295 K / Humidity: 100 %
Details: 0 blot force, 3 second blot time, 3 uL sample added to freshly glow-discharged grids.

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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: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 130000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200.0 - 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: 2732

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 301920
3D reconstructionSoftware: RELION / Resolution: 3.28 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
Input PDB model: 6CH9, 6CH9
Chain ID: G, B
Output model

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