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- EMDB-20813: Structure of full-length, fully glycosylated, non-modified HIV-1 ... -

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Basic information

Entry
Database: EMDB / ID: EMD-20813
TitleStructure of full-length, fully glycosylated, non-modified HIV-1 gp160 bound to PG16 Fab at a nominal resolution of 4.6 Angstrom
Map dataHIV-1 gp160 bound to PG16 Fab, recommended contour level (absolute as displayed in Chimera): 0.01-0.03
Sample
  • Complex: HIV-1 GP160 trimer:PG16 Fab complex
    • Complex: HIV envelope glycoprotein GP160 (mature)
      • Protein or peptide: envelope glycoprotein gp120,envelope glycoprotein gp120
      • Protein or peptide: Envelope glycoprotein gp41
    • Complex: Antibody PG16 Fab
      • Protein or peptide: antibody PG16 Fab heavy chain
      • Protein or peptide: antibody PG16 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV-1 / ENV / gp160 / PG16 / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / 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: 4.6 Å
AuthorsPan J / Chen B
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI-100645 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI129721 United States
CitationJournal: J Mol Biol / Year: 2020
Title: Cryo-EM Structure of Full-length HIV-1 Env Bound With the Fab of Antibody PG16.
Authors: Junhua Pan / Hanqin Peng / Bing Chen / Stephen C Harrison /
Abstract: The HIV-1 envelope protein (Env) is the target of neutralizing antibodies and the template for vaccine immunogen design. The dynamic conformational equilibrium of trimeric Env influences its ...The HIV-1 envelope protein (Env) is the target of neutralizing antibodies and the template for vaccine immunogen design. The dynamic conformational equilibrium of trimeric Env influences its antigenicity and potential immunogenicity. Antibodies that bind at the trimer apex stabilize a "closed" conformation characteristic of the most difficult to neutralize isolates. A goal of vaccine development is therefore to mimic the closed conformation in a designed immunogen. A disulfide-stabilized, trimeric Env ectodomain-the "SOSIP" construct-has many of the relevant properties; it is also particularly suitable for structure determination. Some single-molecule studies have, however, suggested that the SOSIP trimer is not a good representation of Env on the surface of a virion or an infected cell. We isolated Env (fully cleaved to gp120 and gp41) from the surface of expressing cells using tagged, apex-binding Fab PG16 and determined the structure of the PG16-Env complex by cryo-EM to an overall resolution of 4.6 Å. Placing the only purification tag on the Fab ensured that the isolated Env was continuously stabilized in its closed, native conformation. The Env structure in this complex corresponds closely to the SOSIP structures determined by both x-ray crystallography and cryo-EM. Although the membrane-interacting elements are not resolved in our reconstruction, we can make inferences about the connection between ectodomain and membrane-proximal external region (MPER) by reference to the published cryo-tomography structure of an Env "spike" and the NMR structure of the MPER-transmembrane segment. We discuss these results in view of the conflicting interpretations in the literature.
History
DepositionOct 7, 2019-
Header (metadata) releaseDec 25, 2019-
Map releaseApr 29, 2020-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ulc
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20813.png

Downloads & links

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Map

FileDownload / File: emd_20813.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHIV-1 gp160 bound to PG16 Fab, recommended contour level (absolute as displayed in Chimera): 0.01-0.03
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.64 Å/pix.
x 192 pix.
= 314.88 Å		1.64 Å/pix.
x 192 pix.
= 314.88 Å		1.64 Å/pix.
x 192 pix.
= 314.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.64 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.032849714 - 0.08716195
Average (Standard dev.)0.000115782364 (±0.0034224354)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 314.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.641.641.64
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z314.880314.880314.880
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ500500500
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.0330.0870.000

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Supplemental data

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Sample components

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Entire : HIV-1 GP160 trimer:PG16 Fab complex

EntireName: HIV-1 GP160 trimer:PG16 Fab complex
Components
  • Complex: HIV-1 GP160 trimer:PG16 Fab complex
    • Complex: HIV envelope glycoprotein GP160 (mature)
      • Protein or peptide: envelope glycoprotein gp120,envelope glycoprotein gp120
      • Protein or peptide: Envelope glycoprotein gp41
    • Complex: Antibody PG16 Fab
      • Protein or peptide: antibody PG16 Fab heavy chain
      • Protein or peptide: antibody PG16 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HIV-1 GP160 trimer:PG16 Fab complex

SupramoleculeName: HIV-1 GP160 trimer:PG16 Fab complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: recombinant protein complex of mature HIV-1 gp160 (cleaved into the receptor/coreceptor binding domain gp120 and the fusogen domain gp41) and antibody PG16 Fab fragment
Molecular weightTheoretical: 530 KDa

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Supramolecule #2: HIV envelope glycoprotein GP160 (mature)

SupramoleculeName: HIV envelope glycoprotein GP160 (mature) / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Details: cleaved form consisting of receptor binding domain GP120 and fusogenic domain GP41
Source (natural)Organism: Human immunodeficiency virus 1

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Supramolecule #3: Antibody PG16 Fab

SupramoleculeName: Antibody PG16 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: envelope glycoprotein gp120,envelope glycoprotein gp120

MacromoleculeName: envelope glycoprotein gp120,envelope glycoprotein gp120
type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 57.173941 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRVRGIQRNC QHLWRWGTLI LGMLMICSAA ENLWVTVYYG VPVWKDAETT LFCASDAKAY DTEVHNVWAT HACVPTDPNP QEIYMENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPCV QLTPLCVTLD CSYNITNNIT NSITNSSVNM REEIKNCSFN M TTELRDKN ...String:
MRVRGIQRNC QHLWRWGTLI LGMLMICSAA ENLWVTVYYG VPVWKDAETT LFCASDAKAY DTEVHNVWAT HACVPTDPNP QEIYMENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPCV QLTPLCVTLD CSYNITNNIT NSITNSSVNM REEIKNCSFN M TTELRDKN RKVYSLFYKL DVVQINNGNN SSNLYRLINC NTSALTQACP KVTFEPIPIR YCAPAGYAIL KCNDKEFNGT GL CKNVSTV QCTHGIRPVV STQLLLNGSL AEGKVMIRSE NITNNVKNII VQLNETVTIN CTRPNNNTRK SVRIGPGQTF YAT GDIIGD IRQAHCNVSG SQWNRALHQV VGQLREYWNT TIIFKNSSGG DLEITTHSFN CGGEFFYCNT SGLFNSNWTH NDTA SMKPN DTITLPCRIK QIINMWQRVG QAIYAPPIQG VIRCESNITG LILTRDGGGN INESQIFRPG GGDMRDNWRS ELYKY KVVR IEPLGVAPTK AKRRVVEREK R

UniProtKB: Envelope glycoprotein gp160

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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: 40.404629 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AVVELGAVFI GFLGTAGSTM GAASITLTVQ VRKLLSGIVQ QQSNLLRAIE AQQHLLKLTV WGIKQLQARV LAVERYLRDQ QLLGIWGCS GKLICTTNVP WNSSWSNKSE REIWENMTWL QWDKEISNYT HIIYELIEES QKQQEKNEQE LLELDKWANL W NWFDISNW ...String:
AVVELGAVFI GFLGTAGSTM GAASITLTVQ VRKLLSGIVQ QQSNLLRAIE AQQHLLKLTV WGIKQLQARV LAVERYLRDQ QLLGIWGCS GKLICTTNVP WNSSWSNKSE REIWENMTWL QWDKEISNYT HIIYELIEES QKQQEKNEQE LLELDKWANL W NWFDISNW LWYIKIFIMI VGGLIGLRIV FAVLSVINRV RQGYSPLSFQ TLTPNPRDPD RPGRIEGEGG EQDRGRSIRL VS GFLALAW DDLRNLCLSS YHQLRDFILI VARTVELLGH SSLKGLRLGW EGLKYLGNLL LYWGRELKTS AINLFDTIAI VVA GWTDRV IEVGQRLGRA ILNIPRRIRQ GLERALL

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #3: antibody PG16 Fab heavy chain

MacromoleculeName: antibody PG16 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31.952703 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEFGLSWVFL VALLRGVQCQ EQLVESGGGV VQPGGSLRLS CLASGFTFHK YGMHWVRQAP GKGLEWVALI SDDGMRKYHS DSMWGRVTI SRDNSKNTLY LQFSSLKVED TAMFFCAREA GGPIWHDDVK YYDFNDGYYN YHYMDVWGKG TTVTVSSAST K GPSVFPLA ...String:
MEFGLSWVFL VALLRGVQCQ EQLVESGGGV VQPGGSLRLS CLASGFTFHK YGMHWVRQAP GKGLEWVALI SDDGMRKYHS DSMWGRVTI SRDNSKNTLY LQFSSLKVED TAMFFCAREA GGPIWHDDVK YYDFNDGYYN YHYMDVWGKG TTVTVSSAST K GPSVFPLA PSSKSTSGGT AALGCLVKDY FPEPVTVSWN SGALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CN VNHKPSN TKVDKRVEPK SCDKASGGGS AWSHPQFEKG GGSGGGSGGS SAWSHPQFEK

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Macromolecule #4: antibody PG16 Fab light chain

MacromoleculeName: antibody PG16 Fab light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.424229 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAWALLLLTL LTQGTGSWAQ SALTQPASVS GSPGQTITIS CNGTSSDVGG FDSVSWYQQS PGKAPKVMVF DVSHRPSGIS NRFSGSKSG NTASLTISGL HIEDEGDYFC SSLTDRSHRI FGGGTKVTVL GQPKAAPSVT LFPPSSEELQ ANKATLVCLI S DFYPGAVT ...String:
MAWALLLLTL LTQGTGSWAQ SALTQPASVS GSPGQTITIS CNGTSSDVGG FDSVSWYQQS PGKAPKVMVF DVSHRPSGIS NRFSGSKSG NTASLTISGL HIEDEGDYFC SSLTDRSHRI FGGGTKVTVL GQPKAAPSVT LFPPSSEELQ ANKATLVCLI S DFYPGAVT VAWKADSSPV KAGVETTTPS KQSNNKYAAS SYLSLTPEQW KSHKSYSCQV THEGSTVEKT VAPTECSGGS GG HHHHHHH HHH

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Macromolecule #12: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 12 / Number of copies: 44 / 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

Concentration0.3 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mM(HOCH2)3CNH2Tris
150.0 mMNaClsodium chloride
0.05 %H(C2H4O)nO(C6H4)C9H19NP40
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 3 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK I / Details: 4.2 second blot before plunging.
DetailsThis sample was monodisperse (stoichiometry of 3:1 gp160:Fab).

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-40 / Number grids imaged: 2 / Number real images: 8138 / Average exposure time: 0.125 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus min: 0.8 µm / Calibrated magnification: 30488 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Details: de novo initial model generated using e2initialmodel.py from selected 2D class images
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.4) / Number images used: 492995
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 2.0) / Software - details: from 2D classification
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.4)
Final 3D classificationNumber classes: 6 / Avg.num./class: 82165 / Software - Name: RELION (ver. 3.0.4)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 300
Output model

PDB-6ulc:
Structure of full-length, fully glycosylated, non-modified HIV-1 gp160 bound to PG16 Fab at a nominal resolution of 4.6 Angstrom

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