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- EMDB-0485: Cryo-EM structure of T/F100 SOSIP.664 HIV-1 Env trimer in complex... -

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Basic information

Entry
Database: EMDB / ID: EMD-0485
TitleCryo-EM structure of T/F100 SOSIP.664 HIV-1 Env trimer in complex with 8ANC195 Fab
Map dataT/F100 SOSIP.664 HIV-1 Env trimer in complex with 8ANC195 Fab
Sample
  • Complex: T/F100 Env trimer-8anc195 Fab complex
    • Complex: T/F100 Env trimer
      • Protein or peptide: T/F100 Env gp120
      • Protein or peptide: T/F100 Env gp41
    • Complex: 8anc195 Fab
      • Protein or peptide: 8ANC195 G52K5 heavy chain, IG gamma-1 chain
      • Protein or peptide: 8ANC195 G52K5 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


immunoglobulin complex / 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 / adaptive immune response / viral protein processing / fusion of virus membrane with host plasma membrane ...immunoglobulin complex / 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 / adaptive immune response / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / extracellular region / 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 / Immunoglobulin V-set domain / Immunoglobulin subtype ...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 / Immunoglobulin kappa light chain / IgG H chain
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsFang Q / Rossmann MG
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI011219 United States
CitationJournal: Nat Commun / Year: 2019
Title: A sequestered fusion peptide in the structure of an HIV-1 transmitted founder envelope trimer.
Authors: Neeti Ananthaswamy / Qianglin Fang / Wadad AlSalmi / Swati Jain / Zhenguo Chen / Thomas Klose / Yingyuan Sun / Yue Liu / Marthandan Mahalingam / Subhash Chand / Sodsai Tovanabutra / Merlin L ...Authors: Neeti Ananthaswamy / Qianglin Fang / Wadad AlSalmi / Swati Jain / Zhenguo Chen / Thomas Klose / Yingyuan Sun / Yue Liu / Marthandan Mahalingam / Subhash Chand / Sodsai Tovanabutra / Merlin L Robb / Michael G Rossmann / Venigalla B Rao /
Abstract: The envelope protein of human immunodeficiency virus-1 (HIV-1) and its fusion peptide are essential for cell entry and vaccine design. Here, we describe the 3.9-Å resolution structure of an envelope ...The envelope protein of human immunodeficiency virus-1 (HIV-1) and its fusion peptide are essential for cell entry and vaccine design. Here, we describe the 3.9-Å resolution structure of an envelope protein trimer from a very early transmitted founder virus (CRF01_AE T/F100) complexed with Fab from the broadly neutralizing antibody (bNAb) 8ANC195. The overall T/F100 trimer structure is similar to other reported "closed" state prefusion trimer structures. In contrast, the fusion peptide, which is exposed to solvent in reported closed structures, is sequestered (buried) in the hydrophobic core of the T/F100 trimer. A buried conformation has previously been observed in "open" state structures formed after CD4 receptor binding. The T/F100 trimer binds poorly to bNAbs including the fusion peptide-specific bNAbs PGT151 and VRC34.01. The T/F100 structure might represent a prefusion state, intermediate between the closed and open states. These observations are relevant to mechanisms of HIV-1 transmission and vaccine design.
History
DepositionJan 21, 2019-
Header (metadata) releaseFeb 20, 2019-
Map releaseMar 6, 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: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6nqd
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0485.png

Downloads & links

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Map

FileDownload / File: emd_0485.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationT/F100 SOSIP.664 HIV-1 Env trimer in complex with 8ANC195 Fab
Voxel sizeX=Y=Z: 1 Å
Density
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.052150786 - 0.07528584
Average (Standard dev.)-0.0000314378 (±0.0021133777)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 300.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z300.000300.000300.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0520.075-0.000

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Supplemental data

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Sample components

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Entire : T/F100 Env trimer-8anc195 Fab complex

EntireName: T/F100 Env trimer-8anc195 Fab complex
Components
  • Complex: T/F100 Env trimer-8anc195 Fab complex
    • Complex: T/F100 Env trimer
      • Protein or peptide: T/F100 Env gp120
      • Protein or peptide: T/F100 Env gp41
    • Complex: 8anc195 Fab
      • Protein or peptide: 8ANC195 G52K5 heavy chain, IG gamma-1 chain
      • Protein or peptide: 8ANC195 G52K5 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: T/F100 Env trimer-8anc195 Fab complex

SupramoleculeName: T/F100 Env trimer-8anc195 Fab complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

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Supramolecule #2: T/F100 Env trimer

SupramoleculeName: T/F100 Env trimer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293S

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Supramolecule #3: 8anc195 Fab

SupramoleculeName: 8anc195 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: T/F100 Env gp120

MacromoleculeName: T/F100 Env gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 54.739133 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ATNNLWVTVY YGVPVWRDAD TTLFCASDAK AHETEVHNVW ATHACVPTDP NPQEMHLKNV TENFNMWKNN MVEQMQEDVI SLWDQSLKP CVKLTPLCVT LNCTSATVTN YTKVNDTSDI IGNITDDVRN CSFNMTTELR DKQQKVYALF YKLDIVPIDD S SNNGSSNF ...String:
ATNNLWVTVY YGVPVWRDAD TTLFCASDAK AHETEVHNVW ATHACVPTDP NPQEMHLKNV TENFNMWKNN MVEQMQEDVI SLWDQSLKP CVKLTPLCVT LNCTSATVTN YTKVNDTSDI IGNITDDVRN CSFNMTTELR DKQQKVYALF YKLDIVPIDD S SNNGSSNF SEYRLINCNT SVIKQACPKV SFDPIPIHYC TPAGYAILRC NDKKFNGTGP CKNVSSVQCT HGIKPVVSTQ LL LNGSLAE EGIIIRSENL TNNAKTIIVH FNESVKINCT RPSNNTRTGI HIGPGQVFYK TGDIIGDIRK AYCNISGAQW HKV LGRVAN KLKEHFNNKT IVFKPSSGGD PEITMHHFNC RGEFFYCNTT KLFNSTWGGN KNETRDNGTI TIPCRIKQII NMWQ GVGQA MYAPPIKGVI KCLSNITGIL LTRDGGNDST ENNETFRPGG GNIKDNWRNE LYKYKVVQIE PLGIAPTKCK RRVVE RRRR RR

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Macromolecule #2: T/F100 Env gp41

MacromoleculeName: T/F100 Env gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 20.333879 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGLGAMIFG FLGAAGSTMG AASITLTVQA RQLLSGIVQQ QSNLLRAPEA QQHLLQLTVW GIKQLQARVL AVERYLQDQK FLGLWGCSG KIICCTAVPW NSSWSNKTFE EIWNNMTWIE WEREISNYTS QIYDILTISQ TQQEKNEKDL LELDAAAWSH P QFEKGGGS GGGSGGSAWS HPQFEK

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Macromolecule #3: 8ANC195 G52K5 heavy chain, IG gamma-1 chain

MacromoleculeName: 8ANC195 G52K5 heavy chain, IG gamma-1 chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.153283 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QIHLVQSGTE VKKPGSSVTV SCKAYGVNTF GLYAVNWVRQ APGQSLEYIG QIWRWKSSAS HHFRGRVLIS AVDLTGSSPP ISSLEIKNL TSDDTAVYFC TTTSTYDRWS GLHHDGVMAF SSWGQGTLIS VSAASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP ...String:
QIHLVQSGTE VKKPGSSVTV SCKAYGVNTF GLYAVNWVRQ APGQSLEYIG QIWRWKSSAS HHFRGRVLIS AVDLTGSSPP ISSLEIKNL TSDDTAVYFC TTTSTYDRWS GLHHDGVMAF SSWGQGTLIS VSAASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK RVEPKSCDKT HH HHHH

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Macromolecule #4: 8ANC195 G52K5 light chain

MacromoleculeName: 8ANC195 G52K5 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.460047 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPST LSASTGDTVR ISCRASQSIT GNWVAWYQQR PGKAPRLLIY RGAALLGGVP SRFRGSAAGT DFTLTIGNLQ AEDFGTFYC QQYDTYPGTF GQGTKVEVKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
DIQMTQSPST LSASTGDTVR ISCRASQSIT GNWVAWYQQR PGKAPRLLIY RGAALLGGVP SRFRGSAAGT DFTLTIGNLQ AEDFGTFYC QQYDTYPGTF GQGTKVEVKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #10: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 10 / Number of copies: 30 / 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: 8
GridPretreatment - Type: GLOW DISCHARGE / Details: unspecified
VitrificationCryogen name: ETHANE

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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
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 64.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 170716

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