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- EMDB-8507: 92BR SOSIP.664 trimer in complex with DH270.1 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-8507
Title92BR SOSIP.664 trimer in complex with DH270.1 Fab
Map dataDH270.1 Fab in complex with 92BR SOSIP.664
Sample
  • Complex: 92BR HIV Env SOSIP and DH720.1 Fab
    • Other: 92BR SOSIP.664
    • Other: DH270.1 Fab Heavy Chain
    • Other: DH270.1 Fab Light Chain
Function / homology
Function and homology information


virus-mediated perturbation of host defense response => GO:0019049 / : / virion component => GO:0044423 / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / viral protein processing ...virus-mediated perturbation of host defense response => GO:0019049 / : / virion component => GO:0044423 / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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
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 / negative staining / Resolution: 29.4 Å
AuthorsFera D / Harrison SC
CitationJournal: Sci Transl Med / Year: 2017
Title: Staged induction of HIV-1 glycan-dependent broadly neutralizing antibodies.
Authors: Mattia Bonsignori / Edward F Kreider / Daniela Fera / R Ryan Meyerhoff / Todd Bradley / Kevin Wiehe / S Munir Alam / Baptiste Aussedat / William E Walkowicz / Kwan-Ki Hwang / Kevin O ...Authors: Mattia Bonsignori / Edward F Kreider / Daniela Fera / R Ryan Meyerhoff / Todd Bradley / Kevin Wiehe / S Munir Alam / Baptiste Aussedat / William E Walkowicz / Kwan-Ki Hwang / Kevin O Saunders / Ruijun Zhang / Morgan A Gladden / Anthony Monroe / Amit Kumar / Shi-Mao Xia / Melissa Cooper / Mark K Louder / Krisha McKee / Robert T Bailer / Brendan W Pier / Claudia A Jette / Garnett Kelsoe / Wilton B Williams / Lynn Morris / John Kappes / Kshitij Wagh / Gift Kamanga / Myron S Cohen / Peter T Hraber / David C Montefiori / Ashley Trama / Hua-Xin Liao / Thomas B Kepler / M Anthony Moody / Feng Gao / Samuel J Danishefsky / John R Mascola / George M Shaw / Beatrice H Hahn / Stephen C Harrison / Bette T Korber / Barton F Haynes /
Abstract: A preventive HIV-1 vaccine should induce HIV-1-specific broadly neutralizing antibodies (bnAbs). However, bnAbs generally require high levels of somatic hypermutation (SHM) to acquire breadth, and ...A preventive HIV-1 vaccine should induce HIV-1-specific broadly neutralizing antibodies (bnAbs). However, bnAbs generally require high levels of somatic hypermutation (SHM) to acquire breadth, and current vaccine strategies have not been successful in inducing bnAbs. Because bnAbs directed against a glycosylated site adjacent to the third variable loop (V3) of the HIV-1 envelope protein require limited SHM, the V3-glycan epitope is an attractive vaccine target. By studying the cooperation among multiple V3-glycan B cell lineages and their coevolution with autologous virus throughout 5 years of infection, we identify key events in the ontogeny of a V3-glycan bnAb. Two autologous neutralizing antibody lineages selected for virus escape mutations and consequently allowed initiation and affinity maturation of a V3-glycan bnAb lineage. The nucleotide substitution required to initiate the bnAb lineage occurred at a low-probability site for activation-induced cytidine deaminase activity. Cooperation of B cell lineages and an improbable mutation critical for bnAb activity defined the necessary events leading to breadth in this V3-glycan bnAb lineage. These findings may, in part, explain why initiation of V3-glycan bnAbs is rare, and suggest an immunization strategy for inducing similar V3-glycan bnAbs.
History
DepositionDec 5, 2016-
Header (metadata) releaseFeb 8, 2017-
Map releaseMar 15, 2017-
UpdateFeb 14, 2018-
Current statusFeb 14, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.28
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 3.28
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8507.png

Downloads & links

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Map

FileDownload / File: emd_8507.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDH270.1 Fab in complex with 92BR SOSIP.664
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.13 Å/pix.
x 168 pix.
= 357.84 Å		2.13 Å/pix.
x 168 pix.
= 357.84 Å		2.13 Å/pix.
x 168 pix.
= 357.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.13 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.28 / Movie #1: 3.28
Minimum - Maximum-31.809094999999999 - 25.922125000000001
Average (Standard dev.)-0.055014014 (±1.659475)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-84-84-84
Dimensions168168168
Spacing168168168
CellA=B=C: 357.84003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.132.132.13
M x/y/z168168168
origin x/y/z0.0000.0000.000
length x/y/z357.840357.840357.840
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS-84-84-84
NC/NR/NS168168168
D min/max/mean-31.80925.922-0.055

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Supplemental data

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Sample components

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Entire : 92BR HIV Env SOSIP and DH720.1 Fab

EntireName: 92BR HIV Env SOSIP and DH720.1 Fab
Components
  • Complex: 92BR HIV Env SOSIP and DH720.1 Fab
    • Other: 92BR SOSIP.664
    • Other: DH270.1 Fab Heavy Chain
    • Other: DH270.1 Fab Light Chain

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Supramolecule #1: 92BR HIV Env SOSIP and DH720.1 Fab

SupramoleculeName: 92BR HIV Env SOSIP and DH720.1 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293T / Recombinant plasmid: pVRC-8400

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Macromolecule #1: 92BR SOSIP.664

MacromoleculeName: 92BR SOSIP.664 / type: other / ID: 1 / Classification: other
Source (natural)Organism: Human immunodeficiency virus 1
SequenceString: KDNLWVTVYY GVPVWKEATT TLFCASDAKA YKAEVHNVWA THACVPTDPN PQEIVLENVT ENFNMWKNNM VEQMHEDIIS LWDQSLKPCV KLTPLCVTLN CIDLNNSTNN NNSSGVKTGI DKGEIKNCSF NTTTSVKDKE KKEYALFYNL DVVQIGNDNT SYRLTSCNTS ...String:
KDNLWVTVYY GVPVWKEATT TLFCASDAKA YKAEVHNVWA THACVPTDPN PQEIVLENVT ENFNMWKNNM VEQMHEDIIS LWDQSLKPCV KLTPLCVTLN CIDLNNSTNN NNSSGVKTGI DKGEIKNCSF NTTTSVKDKE KKEYALFYNL DVVQIGNDNT SYRLTSCNTS VITQACPKVT FEPIPIHYCT PAGYAILKCN GKKFNGTGPC TNVSTVQCTH GIKPVVSTQL LLNGSLAEED IVIRSENLTN NAKTIIVQLK DPVDINCTRP NNNTRKSIHI GPGRAFYATG DIIGDIRQAH CNLSRAQWND TLSKIVTKLR EQFENKTIKF QPPSGGDPEI VFHSFNCGGE FFYCNTTQLF NSTWTNNTEG TSNTTGNDTI TLPCRIKQIV NMWQEVGKAM YAPPIKGKIK CSSNITGLLL TRDGGNNEMN TTEIFRPGGG DMRDNWRSEL YKYKVVRIEP LGIAPTRCKR RVVGRRRRRR AVGTLGAMFL GFLGAAGSTM GAASVALTVQ ARQLLSGIVQ QQNNLLRAPE AQQHMLQLTV WGIKQLQARV LAVERYLGDQ QLLGIWGCSG KLICCTTVPW NTSWSNKSLD DIWTNMTWME WKREIDNYTS LIYTLIEESQ RQQEKNEQEL LELD
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #2: DH270.1 Fab Heavy Chain

MacromoleculeName: DH270.1 Fab Heavy Chain / type: other / ID: 2 / Classification: other
Source (natural)Organism: Homo sapiens (human)
SequenceString: QVQLVQSGAE MKKPGASVRV SCKASGYTFT DYYIHWVRQA PGQGPEWMGW INPSTGRTNS PQKFQGRVTM TRDTSISTAY MDLNRLTSDD TAMYYCTTGG WIGLYSDTSG YPNFDYWGQG TLVTVSGAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF PEPVTVSWNS ...String:
QVQLVQSGAE MKKPGASVRV SCKASGYTFT DYYIHWVRQA PGQGPEWMGW INPSTGRTNS PQKFQGRVTM TRDTSISTAY MDLNRLTSDD TAMYYCTTGG WIGLYSDTSG YPNFDYWGQG TLVTVSGAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF PEPVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VDKRVEPKSC DKHHHHHH
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #3: DH270.1 Fab Light Chain

MacromoleculeName: DH270.1 Fab Light Chain / type: other / ID: 3 / Classification: other
Source (natural)Organism: Homo sapiens (human)
SequenceString: QSALTQPASV SGSPGQSITI SCTGTNYDVG SYNLVSWYQQ HPGKVPKYII YEVNKRPSGV SNRFSGSKSG NTASLTISGL QAEDEATYYC CSYAGSSIIF FGGGTKLTVI GQPKGAPSVT LFPPSSEELQ ANKATLVCLI SDFYPGAVTV AWKADSSPVK AGVETTTPSK ...String:
QSALTQPASV SGSPGQSITI SCTGTNYDVG SYNLVSWYQQ HPGKVPKYII YEVNKRPSGV SNRFSGSKSG NTASLTISGL QAEDEATYYC CSYAGSSIIF FGGGTKLTVI GQPKGAPSVT LFPPSSEELQ ANKATLVCLI SDFYPGAVTV AWKADSSPVK AGVETTTPSK QSNNKYAASS YLSLTPEQWK SHRSYSCQVT HEGSTVEKTV APTECS
Recombinant expressionOrganism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation state2D array

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Sample preparation

Concentration0.01 mg/mL
BufferpH: 8
Details: 10 mM HEPES, pH 8.0, 150 mM NaCl, 0.02% sodium azide
StainingType: NEGATIVE / Material: 2% uranyl formate
GridModel: Electron Microscopy Sciences / Material: COPPER

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Electron microscopy

MicroscopeFEI TECNAI 12
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: OTHER / Average electron dose: 25.0 e/Å2

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Image processing

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 29.4 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 5419

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