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- EMDB-20118: Full length HIV-1 Env AMC011 in complex with PGT151 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-20118
TitleFull length HIV-1 Env AMC011 in complex with PGT151 Fab
Map dataFull length AMC011 HIV-1 Env in complex with PGT151 Fab
Sample
  • Complex: PGT151 Fab in complex with full length AMC011 HIV-1 Env
    • Complex: AMC011 Glycoprotein 120
      • Protein or peptide: Envelope glycoprotein gp120
    • Complex: AMC011 Glycoprotein 41
      • Protein or peptide: Envelope glycoprotein gp41
    • Complex: PGT151 Fab
      • 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
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsRantalainen K / Torrents de la Pena A / Ward AB
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI110657 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)F31 AI131873 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI100663 United States
Bill & Melinda Gates FoundationOPP1115782 United States
Bill & Melinda Gates FoundationOPP1084519 United States
CitationJournal: PLoS Pathog / Year: 2019
Title: Similarities and differences between native HIV-1 envelope glycoprotein trimers and stabilized soluble trimer mimetics.
Authors: Alba Torrents de la Peña / Kimmo Rantalainen / Christopher A Cottrell / Joel D Allen / Marit J van Gils / Jonathan L Torres / Max Crispin / Rogier W Sanders / Andrew B Ward /
Abstract: The HIV-1 envelope glycoprotein (Env) trimer is located on the surface of the virus and is the target of broadly neutralizing antibodies (bNAbs). Recombinant native-like soluble Env trimer mimetics, ...The HIV-1 envelope glycoprotein (Env) trimer is located on the surface of the virus and is the target of broadly neutralizing antibodies (bNAbs). Recombinant native-like soluble Env trimer mimetics, such as SOSIP trimers, have taken a central role in HIV-1 vaccine research aimed at inducing bNAbs. We therefore performed a direct and thorough comparison of a full-length unmodified Env trimer containing the transmembrane domain and the cytoplasmic tail, with the sequence matched soluble SOSIP trimer, both based on an early Env sequence (AMC011) from an HIV+ individual that developed bNAbs. The structures of the full-length AMC011 trimer bound to either bNAb PGT145 or PGT151 were very similar to the structures of SOSIP trimers. Antigenically, the full-length and SOSIP trimers were comparable, but in contrast to the full-length trimer, the SOSIP trimer did not bind at all to non-neutralizing antibodies, most likely as a consequence of the intrinsic stabilization of the SOSIP trimer. Furthermore, the glycan composition of full-length and SOSIP trimers was similar overall, but the SOSIP trimer possessed slightly less complex and less extensively processed glycans, which may relate to the intrinsic stabilization as well as the absence of the membrane tether. These data provide insights into how to best use and improve membrane-associated full-length and soluble SOSIP HIV-1 Env trimers as immunogens.
History
DepositionApr 16, 2019-
Header (metadata) releaseJul 31, 2019-
Map releaseJul 31, 2019-
UpdateJul 29, 2020-
Current statusJul 29, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0218
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0218
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6olp
  • Surface level: 0.0218
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6olp
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20118.png

Downloads & links

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Map

FileDownload / File: emd_20118.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull length AMC011 HIV-1 Env in complex with PGT151 Fab
Voxel sizeX=Y=Z: 1.03 Å
Density
Contour LevelBy AUTHOR: 0.0218 / Movie #1: 0.0218
Minimum - Maximum-0.034411278 - 0.067403115
Average (Standard dev.)0.0001558608 (±0.0027043528)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 360.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z350350350
origin x/y/z0.0000.0000.000
length x/y/z360.500360.500360.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS350350350
D min/max/mean-0.0340.0670.000

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Supplemental data

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Mask #1

Fileemd_20118_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Full length AMC011 HIV-1 Env in complex with PGT151 Fab - half map 2

Fileemd_20118_half_map_1.map
AnnotationFull length AMC011 HIV-1 Env in complex with PGT151 Fab - half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Full length AMC011 HIV-1 Env in complex with PGT151 Fab - half map 1

Fileemd_20118_half_map_2.map
AnnotationFull length AMC011 HIV-1 Env in complex with PGT151 Fab - half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PGT151 Fab in complex with full length AMC011 HIV-1 Env

EntireName: PGT151 Fab in complex with full length AMC011 HIV-1 Env
Components
  • Complex: PGT151 Fab in complex with full length AMC011 HIV-1 Env
    • Complex: AMC011 Glycoprotein 120
      • Protein or peptide: Envelope glycoprotein gp120
    • Complex: AMC011 Glycoprotein 41
      • Protein or peptide: Envelope glycoprotein gp41
    • Complex: PGT151 Fab
      • 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: PGT151 Fab in complex with full length AMC011 HIV-1 Env

SupramoleculeName: PGT151 Fab in complex with full length AMC011 HIV-1 Env
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

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Supramolecule #2: AMC011 Glycoprotein 120

SupramoleculeName: AMC011 Glycoprotein 120 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #3: AMC011 Glycoprotein 41

SupramoleculeName: AMC011 Glycoprotein 41 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #4: PGT151 Fab

SupramoleculeName: PGT151 Fab / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)
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: 56.973098 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRVKEIRKNY QHLWKWGIML LGILMICSAA EQLWVTVYYG VPVWKEATTT LFCASDARAY DTEVHNVWAT HACVPTDPNP QEVVLENVT ENFNMWKNNM VEQMHEDIIS LWDQSLKPCV KLTPLCVTLN CTDLRNATNT NATNTTSSSR GTMEGGEIKN C SFNITTSM ...String:
MRVKEIRKNY QHLWKWGIML LGILMICSAA EQLWVTVYYG VPVWKEATTT LFCASDARAY DTEVHNVWAT HACVPTDPNP QEVVLENVT ENFNMWKNNM VEQMHEDIIS LWDQSLKPCV KLTPLCVTLN CTDLRNATNT NATNTTSSSR GTMEGGEIKN C SFNITTSM RDKVQKEYAL FYKLDVVPIK NDNTSYRLIS CNTSVITQAC PKVSFEPIPI HYCAPAGFAI LKCNDKKFNG TG PCTNVST VQCTHGIRPV VSTQLLLNGS LAEEEVVIRS ANFTDNAKII IVQLNKSVEI NCTRPNNNTR KSIHIGPGRA FYT TGEIIG DIRQAHCNIS GTKWNDTLKQ IVVKLKEQFG NKTIVFNHSS GGDPEIVMHS FNCGGEFFYC NSTQLFNSTW NDTT GSNYT GTIVLPCRIK QIVNMWQEVG KAMYAPPIKG QIRCSSNITG LILIRDGGKN RSENTEIFRP GGGDMRDNWR SELYK YKVV KIEPLGIAPT KAKRRVVQRE KR

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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: 39.677762 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RLLLSGIVQQ QNNLLRAIEA QQHLLQLTVW GIKQLQARVL AVERYLKDQQ LLGIWGCSG KLICTTAVPW NTSWSNKSYN QIWNNMTWME WEREIDNYTS LIYTLIEDSQ NQQEKNEQEL LELDKWASLW N WFDITKWL ...String:
AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RLLLSGIVQQ QNNLLRAIEA QQHLLQLTVW GIKQLQARVL AVERYLKDQQ LLGIWGCSG KLICTTAVPW NTSWSNKSYN QIWNNMTWME WEREIDNYTS LIYTLIEDSQ NQQEKNEQEL LELDKWASLW N WFDITKWL WYIKIFIMIV GGLIGLRIVF TVLSIVNRIR QGYSPLSFQT PLPTPRGPDR PEGIEEEGGE RDRDRSDRLV TG FLALIWV DLRSLCLFSY HRLRDLLLIV TRIVELLGRR GWGVLKYWWN LLQYWSQELR NSAVSLLNAT AIAVAEGTDR VIE VSQRAF RAILHVPVRI RQGLERALV

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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

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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

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Macromolecule #15: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 15 / Number of copies: 41 / 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

Concentration6 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMTrisTris base
150.0 mMNaClSodium Chloride
0.1 %DDMn-Dodecyl-B-D-Maltoside
0.03 mg/mlDeoxycholateSodium Deoxycholate

Details: Detergent removed with biobeads prior to grid preparation
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot force 0 No wait Blot time 6 sec.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-32 / Number grids imaged: 1 / Number real images: 3076 / Average exposure time: 8.0 sec. / Average electron dose: 51.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf (ver. 1.06)
Startup modelType of model: NONE / Details: Ab initio model generated with CRYOSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 74889
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-6olp:
Full length HIV-1 Env AMC011 in complex with PGT151 Fab

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