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- EMDB-7858: Ectodomain of full length, wild type HIV-1 glycoprotein clone PC6... -

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Entry
Database: EMDB / ID: EMD-7858
TitleEctodomain of full length, wild type HIV-1 glycoprotein clone PC64M18C043 in complex with PGT151 Fab
Map dataEctodomain of full length, wild type HIV-1 glycoprotein clone PC64M18C043 in complex with PGT151 Fab
Sample
  • Complex: Full length, wild type HIV-1 Envelope glycoprotein in complex with PGT151 Fab
    • Protein or peptide: Envelope glycoprotein gp160
    • Protein or peptide: Envelope glycoprotein gp160
    • Protein or peptide: Immunoglobulin G PGT151 Fab, Heavy chain
    • Protein or peptide: Immunoglobulin G PGT151 Fab, Light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV-1 / Glycoprotein / Env / VIRAL PROTEIN
Function / homology
Function and homology information


immunoglobulin complex / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / adaptive immune response / immune response / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / apoptotic process / host cell plasma membrane ...immunoglobulin complex / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / adaptive immune response / immune response / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / extracellular space / metal ion binding / 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 / Immunoglobulin V-Type / Immunoglobulin V-set domain ...: / Envelope glycoprotein Gp160 / : / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Envelope glycoprotein gp160 / Ig-like domain-containing protein / IgG H chain
Similarity search - Component
Biological speciesHomo sapiens (human) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsBerndsens ZB / Rantalainen KR / Ward AB
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)UM1 AI100663 United States
International AIDS Vaccine InitiativeOPP1084519 United States
Bill & Melinda Gates FoundationOPP1115782 United States
CitationJournal: Cell Rep / Year: 2018
Title: Co-evolution of HIV Envelope and Apex-Targeting Neutralizing Antibody Lineage Provides Benchmarks for Vaccine Design.
Authors: Kimmo Rantalainen / Zachary T Berndsen / Sasha Murrell / Liwei Cao / Oluwarotimi Omorodion / Jonathan L Torres / Mengyu Wu / Jeffrey Umotoy / Jeffrey Copps / Pascal Poignard / Elise Landais ...Authors: Kimmo Rantalainen / Zachary T Berndsen / Sasha Murrell / Liwei Cao / Oluwarotimi Omorodion / Jonathan L Torres / Mengyu Wu / Jeffrey Umotoy / Jeffrey Copps / Pascal Poignard / Elise Landais / James C Paulson / Ian A Wilson / Andrew B Ward /
Abstract: Broadly neutralizing antibodies (bnAbs) targeting the HIV envelope glycoprotein (Env) typically take years to develop. Longitudinal analyses of both neutralizing antibody lineages and viruses at ...Broadly neutralizing antibodies (bnAbs) targeting the HIV envelope glycoprotein (Env) typically take years to develop. Longitudinal analyses of both neutralizing antibody lineages and viruses at serial time points during infection provide a basis for understanding the co-evolutionary contest between HIV and the humoral immune system. Here, we describe the structural characterization of an apex-targeting antibody lineage and autologous clade A viral Env from a donor in the Protocol C cohort. Comparison of Ab-Env complexes at early and late time points reveals that, within the antibody lineage, the CDRH3 loop rigidifies, the bnAb angle of approach steepens, and surface charges are mutated to accommodate glycan changes. Additionally, we observed differences in site-specific glycosylation between soluble and full-length Env constructs, which may be important for tuning optimal immunogenicity in soluble Env trimers. These studies therefore provide important guideposts for design of immunogens that prime and mature nAb responses to the Env V2-apex.
History
DepositionMay 8, 2018-
Header (metadata) releaseJun 27, 2018-
Map releaseJun 27, 2018-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6dcq
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6dcq
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_7858.png

Downloads & links

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Map

FileDownload / File: emd_7858.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEctodomain of full length, wild type HIV-1 glycoprotein clone PC64M18C043 in complex with PGT151 Fab
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 320 pix.
= 329.6 Å		1.03 Å/pix.
x 320 pix.
= 329.6 Å		1.03 Å/pix.
x 320 pix.
= 329.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.0583 / Movie #1: 0.05
Minimum - Maximum-0.14663479 - 0.30068433
Average (Standard dev.)-0.00029263593 (±0.008385066)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 329.59998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z329.600329.600329.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ384384384
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.1470.301-0.000

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Supplemental data

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Mask #1

Fileemd_7858_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Ectodomain of full length, wild type HIV-1 glycoprotein...

Fileemd_7858_half_map_1.map
AnnotationEctodomain of full length, wild type HIV-1 glycoprotein clone PC64M18C043 in complex with PGT151 Fab
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Ectodomain of full length, wild type HIV-1 glycoprotein...

Fileemd_7858_half_map_2.map
AnnotationEctodomain of full length, wild type HIV-1 glycoprotein clone PC64M18C043 in complex with PGT151 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 : Full length, wild type HIV-1 Envelope glycoprotein in complex wit...

EntireName: Full length, wild type HIV-1 Envelope glycoprotein in complex with PGT151 Fab
Components
  • Complex: Full length, wild type HIV-1 Envelope glycoprotein in complex with PGT151 Fab
    • Protein or peptide: Envelope glycoprotein gp160
    • Protein or peptide: Envelope glycoprotein gp160
    • Protein or peptide: Immunoglobulin G PGT151 Fab, Heavy chain
    • Protein or peptide: Immunoglobulin G PGT151 Fab, Light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Full length, wild type HIV-1 Envelope glycoprotein in complex wit...

SupramoleculeName: Full length, wild type HIV-1 Envelope glycoprotein in complex with PGT151 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: Full length HIV-1 Envelope glycoprotein clone C043 collected 18 months post infection from donor 64 of Protocol C cohort study. Expressed as recombinant protein in HEK293F cell line.
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 389 KDa

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Macromolecule #1: Envelope glycoprotein gp160

MacromoleculeName: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 53.392359 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SAANNLWVTV YYGVPVWRDA ETTLFCASDA KAYDTEVHNV WATHACVPTD PSPQEIHLAN VTEKFDMWKN SMVEQMHTDI ISLWDESLK PCVKLTPLCI TLNCTNITRN VTGGNLTEEG KEELKNCSFN ATTELRDKIQ KVHSLFYRLD LVELNEGNSS D SNTSMYRL ...String:
SAANNLWVTV YYGVPVWRDA ETTLFCASDA KAYDTEVHNV WATHACVPTD PSPQEIHLAN VTEKFDMWKN SMVEQMHTDI ISLWDESLK PCVKLTPLCI TLNCTNITRN VTGGNLTEEG KEELKNCSFN ATTELRDKIQ KVHSLFYRLD LVELNEGNSS D SNTSMYRL INCNTSAITQ ACPKVSFEPI PIHYCAPAGF AILKCREKEF NGTGPCKKVS TVQCTHGIKP VVSTQLLLNG SL AEGKVKI RCENISNNAK TILVQLTTPV RINCTRPSNN TRTSIRIGPG QSFYATGDII GDIRKAYCNV SESEWKEALG KVV EQLRNH FNKTITFASS SGGDLEITTH SFNCGGEFFY CNTSSLFNST WDGNSATNST QVPNGTITLP CRIKQIINMW QRTG QAMYA PPIPGKIRCD SNITGLILIR DGGNNNNESE TFRPGGGDMR NNWRSELYKY KVVKIDPLGV APTGAKRRVV EREKR

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #2: Envelope glycoprotein gp160

MacromoleculeName: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 40.020207 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AVGIGAVLFG FLGAAGSTMG AASLTLTVQA RQLLSGIVQQ QSNLLRAIEA QQHLLRLTVW GIKQLQARVL AVERYLSDQQ LLGIWGCSG KLICTTNVPW NSSWSNKSQD EIWNNMTWLQ WDKEISNYTD TIYYLIEKSQ NQQEVNEKDL LALDKWTNLW N WFGISNWL ...String:
AVGIGAVLFG FLGAAGSTMG AASLTLTVQA RQLLSGIVQQ QSNLLRAIEA QQHLLRLTVW GIKQLQARVL AVERYLSDQQ LLGIWGCSG KLICTTNVPW NSSWSNKSQD EIWNNMTWLQ WDKEISNYTD TIYYLIEKSQ NQQEVNEKDL LALDKWTNLW N WFGISNWL WYIRIFIMIV GGLIGLRIIF AVLSVINRVR QGYSPVSFQT LTPNPRELDR PGGIEEGDGE LGKTRSIRLV GG FLALFWD DLRSLCLFSY HRLRDFILIA ARILELLGHN SLKGLRLGWE GLKYLGNLLL YWGRELKNSA VNLVDTIAIV VAG WTDRVI EVLQGIGRAF LHIPRRIRQG FERALL

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #3: Immunoglobulin G PGT151 Fab, Heavy chain

MacromoleculeName: Immunoglobulin G PGT151 Fab, Heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.087438 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RVQLVESGGG VVQPGKSVRL SCVVSDFPFS KYPMYWVRQA PGKGLEWVAA ISGDAWHVVY SNSVQGRFLV SRDNVKNTLY LEMNSLKIE DTAVYRCARM FQESGPPRLD RWSGRNYYYY SGMDVWGQGT TVTVSSASTK GPSVFPLAPS SKSTSGGTAA L GCLVKDYF ...String:
RVQLVESGGG VVQPGKSVRL SCVVSDFPFS KYPMYWVRQA PGKGLEWVAA ISGDAWHVVY SNSVQGRFLV SRDNVKNTLY LEMNSLKIE DTAVYRCARM FQESGPPRLD RWSGRNYYYY SGMDVWGQGT TVTVSSASTK GPSVFPLAPS SKSTSGGTAA L GCLVKDYF PEPVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VDKRVEPKSC DK

UniProtKB: IgG H chain

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Macromolecule #4: Immunoglobulin G PGT151 Fab, Light chain

MacromoleculeName: Immunoglobulin G PGT151 Fab, Light chain / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.057809 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVMTQTPLS LSVTPGQPAS ISCKSSESLR QSNGKTSLYW YRQKPGQSPQ LLVFEVSNRF SGVSDRFVGS GSGTDFTLRI SRVEAEDVG FYYCMQSKDF PLTFGGGTKV DLKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV ...String:
DIVMTQTPLS LSVTPGQPAS ISCKSSESLR QSNGKTSLYW YRQKPGQSPQ LLVFEVSNRF SGVSDRFVGS GSGTDFTLRI SRVEAEDVG FYYCMQSKDF PLTFGGGTKV DLKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRGE C

UniProtKB: Ig-like domain-containing protein

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Macromolecule #14: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 14 / Number of copies: 21 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

Concentration7 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMTris-HclTris(hydroxymethyl)aminomethane hydrochloride
150.0 mMNaClsodium chloride
0.1 %DDMn-Dodecyl-beta-Maltoside
0.03 %DeoxycholateSodium deoxycholate monohydrate

Details: Detergent removed with Biobeads prior to grid freezing
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force 0 Blot time 5 sec.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 4039 / Average electron dose: 1.885 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

3309

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Version: Relion / Number images used: 236179
Initial angle assignmentType: NOT APPLICABLE / Software - Version: Relion
Final angle assignmentType: NOT APPLICABLE / Software - Version: Relion
FSC plot (resolution estimation)

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