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- EMDB-23424: Cryo-EM map of Q23.17_DS-SOSIP in complex with Glycan276-Dependen... -

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Basic information

Entry
Database: EMDB / ID: EMD-23424
TitleCryo-EM map of Q23.17_DS-SOSIP in complex with Glycan276-Dependent Broadly Neutralizing Antibody 179NC75 Fab
Map dataCryo-EM map of Q23.17_DS-SOSIP in complex with Glycan276-Dependent Broadly Neutralizing Antibody 179NC75 Fab
Sample
  • Complex: Trimeric HIV-1 Env in complex with VRC33.01 Fab
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: Envelope glycoprotein gp41
    • Protein or peptide: 179NC75 Fab Heavy chain
    • Protein or peptide: 179NC75 Fab Light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / plasma membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsManne K / Acharya P
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI45687 United States
CitationJournal: Cell Rep / Year: 2021
Title: Structural basis of glycan276-dependent recognition by HIV-1 broadly neutralizing antibodies.
Authors: Christopher A Cottrell / Kartik Manne / Rui Kong / Shuishu Wang / Tongqing Zhou / Gwo-Yu Chuang / Robert J Edwards / Rory Henderson / Katarzyna Janowska / Megan Kopp / Bob C Lin / Mark K ...Authors: Christopher A Cottrell / Kartik Manne / Rui Kong / Shuishu Wang / Tongqing Zhou / Gwo-Yu Chuang / Robert J Edwards / Rory Henderson / Katarzyna Janowska / Megan Kopp / Bob C Lin / Mark K Louder / Adam S Olia / Reda Rawi / Chen-Hsiang Shen / Justin D Taft / Jonathan L Torres / Nelson R Wu / Baoshan Zhang / Nicole A Doria-Rose / Myron S Cohen / Barton F Haynes / Lawrence Shapiro / Andrew B Ward / Priyamvada Acharya / John R Mascola / Peter D Kwong /
Abstract: Recognition of N-linked glycan at residue N276 (glycan276) at the periphery of the CD4-binding site (CD4bs) on the HIV-envelope trimer is a formidable challenge for many CD4bs-directed antibodies. To ...Recognition of N-linked glycan at residue N276 (glycan276) at the periphery of the CD4-binding site (CD4bs) on the HIV-envelope trimer is a formidable challenge for many CD4bs-directed antibodies. To understand how this glycan can be recognized, here we isolate two lineages of glycan276-dependent CD4bs antibodies. Antibody CH540-VRC40.01 (named for donor-lineage.clone) neutralizes 81% of a panel of 208 diverse strains, while antibody CH314-VRC33.01 neutralizes 45%. Cryo-electron microscopy (cryo-EM) structures of these two antibodies and 179NC75, a previously identified glycan276-dependent CD4bs antibody, in complex with HIV-envelope trimer reveal substantially different modes of glycan276 recognition. Despite these differences, binding of glycan276-dependent antibodies maintains a glycan276 conformation similar to that observed in the absence of glycan276-binding antibodies. By contrast, glycan276-independent CD4bs antibodies, such as VRC01, displace glycan276 upon binding. These results provide a foundation for understanding antibody recognition of glycan276 and suggest its presence may be crucial for priming immunogens seeking to initiate broad CD4bs recognition.
History
DepositionFeb 4, 2021-
Header (metadata) releaseJun 2, 2021-
Map releaseJun 2, 2021-
UpdateNov 17, 2021-
Current statusNov 17, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.9
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.9
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7llk
  • Surface level: 0.9
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7llk
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23424.png

Downloads & links

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Map

FileDownload / File: emd_23424.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of Q23.17_DS-SOSIP in complex with Glycan276-Dependent Broadly Neutralizing Antibody 179NC75 Fab
Voxel sizeX=Y=Z: 1.00065 Å
Density
Contour LevelBy AUTHOR: 1.05 / Movie #1: 0.9
Minimum - Maximum-0.72330743 - 2.335317
Average (Standard dev.)0.004384784 (±0.111316994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 320.2083 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.000651.000651.00065
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z320.208320.208320.208
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.7232.3350.004

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Supplemental data

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Additional map: Cryo-EM sharpened-map of Q23.17 DS-SOSIP in complex with Glycan276-Dependent...

Fileemd_23424_additional_1.map
AnnotationCryo-EM sharpened-map of Q23.17_DS-SOSIP in complex with Glycan276-Dependent Broadly Neutralizing Antibody 179NC75 Fab
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM half map B Q23.17 DS-SOSIP in complex with...

Fileemd_23424_half_map_1.map
AnnotationCryo-EM half map B Q23.17_DS-SOSIP in complex with Glycan276-Dependent Broadly Neutralizing Antibody 179NC75 Fab
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM half map A Q23.17 DS-SOSIP in complex with...

Fileemd_23424_half_map_2.map
AnnotationCryo-EM half map A Q23.17_DS-SOSIP in complex with Glycan276-Dependent Broadly Neutralizing Antibody 179NC75 Fab
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Trimeric HIV-1 Env in complex with VRC33.01 Fab

EntireName: Trimeric HIV-1 Env in complex with VRC33.01 Fab
Components
  • Complex: Trimeric HIV-1 Env in complex with VRC33.01 Fab
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: Envelope glycoprotein gp41
    • Protein or peptide: 179NC75 Fab Heavy chain
    • Protein or peptide: 179NC75 Fab Light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Trimeric HIV-1 Env in complex with VRC33.01 Fab

SupramoleculeName: Trimeric HIV-1 Env in complex with VRC33.01 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: Envelope glycoprotein gp120

MacromoleculeName: Envelope glycoprotein gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 53.62793 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AENLWVTVYY GVPVWRDADT TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLDNVT EKFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL HCTNVTSVNT TGDREGLKNC SFNMTTELRD KRQKVYSLFY RLDIVPINEN QGSEYRLINC N TSACTQAC ...String:
AENLWVTVYY GVPVWRDADT TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLDNVT EKFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL HCTNVTSVNT TGDREGLKNC SFNMTTELRD KRQKVYSLFY RLDIVPINEN QGSEYRLINC N TSACTQAC PKVSFEPIPI HYCAPAGFAI LKCKDEGFNG TGLCKNVSTV QCTHGIKPVV STQLLLNGSL AEKNITIRSE NI TNNAKII IVQLVQPVTI KCIRPNNNTR KSIRIGPGQA FYATGDIIGD IRQAHCNVSR SRWNKTLQEV AEKLRTYFGN KTI IFANSS GGDLEITTHS FNCGGEFFYC NTSGLFNSTW YVNSTWNDTD STQESNDTIT LPCRIKQIIN MWQRAGQCMY APPI PGVIK CESNITGLLL TRDGGKDNNV NETFRPGGGD MRDNWRSELY KYKVVKIEPL GVAPTRCKRR VVERRRRRR

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Macromolecule #2: Envelope glycoprotein gp41

MacromoleculeName: Envelope glycoprotein gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.211594 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASNTLTVQA RQLLSGIVQQ QNNLPRAPEA QQHLLKLTVW GIKQLQARVL AVERYLEVQQ LLGIWGCSG KLICCTNVPW NSSWSNKSLD EIWNNMTWLQ WDKEINNYTQ LIYRLIEESQ FQQEINEVEL LALD

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Macromolecule #3: 179NC75 Fab Heavy chain

MacromoleculeName: 179NC75 Fab Heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.897457 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EMRLEESGGA LVKPGGSLRL SCVASGFKLS EWSLMWVRQA PGKGLQWVSS ISLNQDYISY AGSVRGRFDV FRDRTQTSLL LNMNKLKTE DTGVYFCARV HAWRYFDWVN RRSPVEKVLS IDLWGRGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG C LVKDYFPE ...String:
EMRLEESGGA LVKPGGSLRL SCVASGFKLS EWSLMWVRQA PGKGLQWVSS ISLNQDYISY AGSVRGRFDV FRDRTQTSLL LNMNKLKTE DTGVYFCARV HAWRYFDWVN RRSPVEKVLS IDLWGRGTLV TVSSASTKGP SVFPLAPSSK STSGGTAALG C LVKDYFPE PVTVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSCDK

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Macromolecule #4: 179NC75 Fab Light chain

MacromoleculeName: 179NC75 Fab Light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.042402 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SVTSGATQPP SVSVSKGETA RITCSGVELS SQYVSWYRQR PGQSPVLVMF HNNSRASRIP ERFSASDSGD TATLTIAGAQ DVDEAEYYC QTWDSKNYVT FGGGTKLTVL GQPKAAPSVT LFPPSSEELQ ANKATLVCLI SDFYPGAVTV AWKADSSPVK A GVETTTPS ...String:
SVTSGATQPP SVSVSKGETA RITCSGVELS SQYVSWYRQR PGQSPVLVMF HNNSRASRIP ERFSASDSGD TATLTIAGAQ DVDEAEYYC QTWDSKNYVT FGGGTKLTVL GQPKAAPSVT LFPPSSEELQ ANKATLVCLI SDFYPGAVTV AWKADSSPVK A GVETTTPS KQSNNKYAAS SYLSLTPEQW KSHRSYSCQV THEGSTVEKT VAPTECS

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 10 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293 K / Instrument: LEICA EM GP / Details: Blot for 2.5 S before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 93.15 K / Max: 93.15 K
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.5 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6vkn

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 489824

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Atomic model buiding 1

Initial modelPDB ID:

6vkn

RefinementProtocol: AB INITIO MODEL
Output model

PDB-7llk:
Cryo-EM structure of Q23.17_DS-SOSIP in complex with Glycan276-Dependent Broadly Neutralizing Antibody 179NC75 Fab

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