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- EMDB-20260: HIV Env 16055 NFL TD 2CC+ in complex with antibody 1C2 fragment a... -

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Basic information

Entry
Database: EMDB / ID: EMD-20260
TitleHIV Env 16055 NFL TD 2CC+ in complex with antibody 1C2 fragment antigen binding
Map datasharpened map
Sample
  • Complex: HIV Env 16055 NFL TD 2CC+ in complex with antibody 1C2 fragment antigen binding
    • Protein or peptide: HIV Env 16055 NFL TD 2CC+
    • Protein or peptide: Rabbit antibody 1C2 heavy chain fragment antigen binding
    • Protein or peptide: Rabbit antibody 1C2 kappa 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 / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / 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 / virus-mediated perturbation of host defense response / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / 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 / Oryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.94 Å
AuthorsOzorowski G / Torres JL / Ward AB
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM AI100663 United States
Bill & Melinda Gates FoundationOPP1084519 United States
Bill & Melinda Gates FoundationOPP1115782 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI136621 United States
CitationJournal: Immunity / Year: 2019
Title: Vaccination with Glycan-Modified HIV NFL Envelope Trimer-Liposomes Elicits Broadly Neutralizing Antibodies to Multiple Sites of Vulnerability.
Authors: Viktoriya Dubrovskaya / Karen Tran / Gabriel Ozorowski / Javier Guenaga / Richard Wilson / Shridhar Bale / Christopher A Cottrell / Hannah L Turner / Gemma Seabright / Sijy O'Dell / Jonathan ...Authors: Viktoriya Dubrovskaya / Karen Tran / Gabriel Ozorowski / Javier Guenaga / Richard Wilson / Shridhar Bale / Christopher A Cottrell / Hannah L Turner / Gemma Seabright / Sijy O'Dell / Jonathan L Torres / Lifei Yang / Yu Feng / Daniel P Leaman / Néstor Vázquez Bernat / Tyler Liban / Mark Louder / Krisha McKee / Robert T Bailer / Arlette Movsesyan / Nicole A Doria-Rose / Marie Pancera / Gunilla B Karlsson Hedestam / Michael B Zwick / Max Crispin / John R Mascola / Andrew B Ward / Richard T Wyatt /
Abstract: The elicitation of broadly neutralizing antibodies (bNAbs) against the HIV-1 envelope glycoprotein (Env) trimer remains a major vaccine challenge. Most cross-conserved protein determinants are ...The elicitation of broadly neutralizing antibodies (bNAbs) against the HIV-1 envelope glycoprotein (Env) trimer remains a major vaccine challenge. Most cross-conserved protein determinants are occluded by self-N-glycan shielding, limiting B cell recognition of the underlying polypeptide surface. The exceptions to the contiguous glycan shield include the conserved receptor CD4 binding site (CD4bs) and glycoprotein (gp)41 elements proximal to the furin cleavage site. Accordingly, we performed heterologous trimer-liposome prime:boosting in rabbits to drive B cells specific for cross-conserved sites. To preferentially expose the CD4bs to B cells, we eliminated proximal N-glycans while maintaining the native-like state of the cleavage-independent NFL trimers, followed by gradual N-glycan restoration coupled with heterologous boosting. This approach successfully elicited CD4bs-directed, cross-neutralizing Abs, including one targeting a unique glycan-protein epitope and a bNAb (87% breadth) directed to the gp120:gp41 interface, both resolved by high-resolution cryoelectron microscopy. This study provides proof-of-principle immunogenicity toward eliciting bNAbs by vaccination.
History
DepositionMay 31, 2019-
Header (metadata) releaseNov 20, 2019-
Map releaseNov 20, 2019-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6p65
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20260.png

Downloads & links

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Map

FileDownload / File: emd_20260.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Voxel sizeX=Y=Z: 1.15 Å
Density
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.15587336 - 0.2658922
Average (Standard dev.)0.00018898446 (±0.009513787)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 331.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.151.151.15
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z331.200331.200331.200
α/β/γ90.00090.00090.000
start NX/NY/NZ929262
NX/NY/NZ290290360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.1560.2660.000

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Supplemental data

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Mask #1

Fileemd_20260_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 1

Fileemd_20260_half_map_1.map
Annotationhalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map 2

Fileemd_20260_half_map_2.map
Annotationhalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HIV Env 16055 NFL TD 2CC+ in complex with antibody 1C2 fragment a...

EntireName: HIV Env 16055 NFL TD 2CC+ in complex with antibody 1C2 fragment antigen binding
Components
  • Complex: HIV Env 16055 NFL TD 2CC+ in complex with antibody 1C2 fragment antigen binding
    • Protein or peptide: HIV Env 16055 NFL TD 2CC+
    • Protein or peptide: Rabbit antibody 1C2 heavy chain fragment antigen binding
    • Protein or peptide: Rabbit antibody 1C2 kappa chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HIV Env 16055 NFL TD 2CC+ in complex with antibody 1C2 fragment a...

SupramoleculeName: HIV Env 16055 NFL TD 2CC+ in complex with antibody 1C2 fragment antigen binding
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 570 KDa

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Macromolecule #1: HIV Env 16055 NFL TD 2CC+

MacromoleculeName: HIV Env 16055 NFL TD 2CC+ / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 75.630539 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPMGSLQPLA TLYLLGMLVA SVLANGNLWV TVYYGVPVWK DAETTLFCAS DAKAYEKEKH NVWATHACVP TDPNPQEMVL ENVTENFNM WKNDMVEQMH TDVISLWDQS LKPCVKLTPL CVTLECRQVN TTNATSSVNV TNGEEIKNCS FNATTELRDK K QKVYALFY ...String:
MPMGSLQPLA TLYLLGMLVA SVLANGNLWV TVYYGVPVWK DAETTLFCAS DAKAYEKEKH NVWATHACVP TDPNPQEMVL ENVTENFNM WKNDMVEQMH TDVISLWDQS LKPCVKLTPL CVTLECRQVN TTNATSSVNV TNGEEIKNCS FNATTELRDK K QKVYALFY RLDIVPLEEE RKGNSSKYRL INCNTSACTQ ACPKVTFDPI PIHYCAPAGY AILKCNNKTF NGTGPCNNVS TV QCTHGIK PVVSTQLLLN GSLAEGEIII RSENLTNNVK TIIVHLNESV EIVCTRPNNY TRKSIRIGPG QTFYATGDII GNI RQAYCN ISKDDWIRTL QRVGKKLAEH FPRRIINFTS PAGGDLEITT HSFNCRGEFF YCNTSSLFNS TYNPNDTNSN SSSS NSSLD ITIPCRIKQI INMWQRVGQC MYAPPIEGNI TCKSNITGLL LVRDGGVESN ETEIFRPGGG DMRNNWRSEL YKYKV VEIK PLGIAPTRCK RRVVEGGGGS GGGGSDDDDK AVGLGAVRRG FLGAAGSTMG AASITLTVQA RQLLSGIVQQ QSNLLK APE AQQHLLQLGV WGIKQLQTRV LAIERYLKDQ QLLGIWGCSG KLICTTAVPW NSSWSNKSHD EIWGNMTWMQ WDREIGN YT NTIYRLLEDS QNQQEQNEKD LLACDGGGGS HHHHHHHH

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Macromolecule #2: Rabbit antibody 1C2 heavy chain fragment antigen binding

MacromoleculeName: Rabbit antibody 1C2 heavy chain fragment antigen binding
type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 27.476072 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MYRMQLLSCI ALSLALVTNS QCQSLEESGG DLVKPGASLT LTCTASGFSF GWNDYMSWVR QAPGKGLEWI GCIYAGSTRS TYYANWAKG RLTISKTSST AVTLQMTSLT AADTATYFCA RGAVTYDGLG GAYLKHFNLW GPGTLVTVSS GQPKAPSVFP L APCCGDTP ...String:
MYRMQLLSCI ALSLALVTNS QCQSLEESGG DLVKPGASLT LTCTASGFSF GWNDYMSWVR QAPGKGLEWI GCIYAGSTRS TYYANWAKG RLTISKTSST AVTLQMTSLT AADTATYFCA RGAVTYDGLG GAYLKHFNLW GPGTLVTVSS GQPKAPSVFP L APCCGDTP SSTVTLGCLV KGYLPEPVTV TWNSGTLTNG VRTFPSVRQS SGLYSLSSVV SVTSSSQPVT CNVAHPATNT KV DKTVAPS TCSKHHHHHH HH

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Macromolecule #3: Rabbit antibody 1C2 kappa chain

MacromoleculeName: Rabbit antibody 1C2 kappa chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 25.041023 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MYRMQLLSCI ALSLALVTNS AIKMTQTPSS VSAAVGGTVT VNCRASEDIE SYLAWYQQKP GQPPKLLIYD TSKLASGVPS RFKGSGSGT QFALTISGVQ CDDAATYYCL YGYISSDRID FGFGGGTELV VKGDPVAPSV LIFPPAADQV ATGTVTIVCV A NKYFPDVT ...String:
MYRMQLLSCI ALSLALVTNS AIKMTQTPSS VSAAVGGTVT VNCRASEDIE SYLAWYQQKP GQPPKLLIYD TSKLASGVPS RFKGSGSGT QFALTISGVQ CDDAATYYCL YGYISSDRID FGFGGGTELV VKGDPVAPSV LIFPPAADQV ATGTVTIVCV A NKYFPDVT VTWEVDGTTQ TTGIENSKTP QNSADCTYNL SSTLTLTSTQ YNSHKEYTCK VTQGTTSVVQ SFNRGDC

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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: 21 / 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

Concentration6 mg/mL
BufferpH: 7.4
Component:
ConcentrationName
50.0 mMTris
150.0 mMsodium chloride
0.06 mMn-Dodecyl-beta-D-Maltopyranoside

Details: DDM added to sample shortly (< 5 minutes) before vitrification
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 36000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number real images: 1690 / Average exposure time: 12.5 sec. / Average electron dose: 48.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 684522
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4zmj


Details: PDB coordinates converted to EM map and low pass filtered to 40 Angstrom
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.94 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 23702
FSC plot (resolution estimation)

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