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- EMDB-9401: CH505 SOSIP.664 trimer in complex with DH522.2 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-9401
TitleCH505 SOSIP.664 trimer in complex with DH522.2 Fab
Map dataCH505 SOSIP.664 trimer in complex with DH522.2 Fab
Sample
  • Complex: CH505 SOSIP.664 in complex with DH522.2 Fab
    • Complex: CH505 SOSIP.664
      • Other: CH505 SOSIP.664
    • Complex: DH522.2 Fab
      • Other: DH522.2 Fab Heavy Chain
      • Other: DH522.2 Fab Light Chain
Biological speciesHomo sapiens (human) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / negative staining / Resolution: 28.1 Å
AuthorsFera D / Harrison SC
CitationJournal: Nat Commun / Year: 2017
Title: Initiation of HIV neutralizing B cell lineages with sequential envelope immunizations.
Authors: Wilton B Williams / Jinsong Zhang / Chuancang Jiang / Nathan I Nicely / Daniela Fera / Kan Luo / M Anthony Moody / Hua-Xin Liao / S Munir Alam / Thomas B Kepler / Akshaya Ramesh / Kevin ...Authors: Wilton B Williams / Jinsong Zhang / Chuancang Jiang / Nathan I Nicely / Daniela Fera / Kan Luo / M Anthony Moody / Hua-Xin Liao / S Munir Alam / Thomas B Kepler / Akshaya Ramesh / Kevin Wiehe / James A Holland / Todd Bradley / Nathan Vandergrift / Kevin O Saunders / Robert Parks / Andrew Foulger / Shi-Mao Xia / Mattia Bonsignori / David C Montefiori / Mark Louder / Amanda Eaton / Sampa Santra / Richard Scearce / Laura Sutherland / Amanda Newman / Hilary Bouton-Verville / Cindy Bowman / Howard Bomze / Feng Gao / Dawn J Marshall / John F Whitesides / Xiaoyan Nie / Garnett Kelsoe / Steven G Reed / Christopher B Fox / Kim Clary / Marguerite Koutsoukos / David Franco / John R Mascola / Stephen C Harrison / Barton F Haynes / Laurent Verkoczy /
Abstract: A strategy for HIV-1 vaccine development is to define envelope (Env) evolution of broadly neutralizing antibodies (bnAbs) in infection and to recreate those events by vaccination. Here, we report ...A strategy for HIV-1 vaccine development is to define envelope (Env) evolution of broadly neutralizing antibodies (bnAbs) in infection and to recreate those events by vaccination. Here, we report host tolerance mechanisms that limit the development of CD4-binding site (CD4bs), HCDR3-binder bnAbs via sequential HIV-1 Env vaccination. Vaccine-induced macaque CD4bs antibodies neutralize 7% of HIV-1 strains, recognize open Env trimers, and accumulate relatively modest somatic mutations. In naive CD4bs, unmutated common ancestor knock-in mice EnvB cell clones develop anergy and partial deletion at the transitional to mature B cell stage, but become Env upon receptor editing. In comparison with repetitive Env immunizations, sequential Env administration rescue anergic Env (non-edited) precursor B cells. Thus, stepwise immunization initiates CD4bs-bnAb responses, but immune tolerance mechanisms restrict their development, suggesting that sequential immunogen-based vaccine regimens will likely need to incorporate strategies to expand bnAb precursor pools.
History
DepositionSep 12, 2017-
Header (metadata) releaseOct 11, 2017-
Map releaseOct 11, 2017-
UpdateDec 6, 2017-
Current statusDec 6, 2017Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.13
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.13
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9401.png

Downloads & links

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Map

FileDownload / File: emd_9401.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCH505 SOSIP.664 trimer in complex with DH522.2 Fab
Voxel sizeX=Y=Z: 2.13 Å
Density
Contour LevelBy AUTHOR: 2.13 / Movie #1: 2.13
Minimum - Maximum-17.361639 - 14.903893999999999
Average (Standard dev.)-0.0074381735 (±0.9265896)
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
MAP C/R/S123
start NC/NR/NS-84-84-84
NC/NR/NS168168168
D min/max/mean-17.36214.904-0.007

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Supplemental data

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Sample components

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Entire : CH505 SOSIP.664 in complex with DH522.2 Fab

EntireName: CH505 SOSIP.664 in complex with DH522.2 Fab
Components
  • Complex: CH505 SOSIP.664 in complex with DH522.2 Fab
    • Complex: CH505 SOSIP.664
      • Other: CH505 SOSIP.664
    • Complex: DH522.2 Fab
      • Other: DH522.2 Fab Heavy Chain
      • Other: DH522.2 Fab Light Chain

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Supramolecule #1: CH505 SOSIP.664 in complex with DH522.2 Fab

SupramoleculeName: CH505 SOSIP.664 in complex with DH522.2 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: CH505 SOSIP.664

SupramoleculeName: CH505 SOSIP.664 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #3: DH522.2 Fab

SupramoleculeName: DH522.2 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: CH505 SOSIP.664

MacromoleculeName: CH505 SOSIP.664 / type: other / ID: 1 / Classification: other
Source (natural)Organism: Human immunodeficiency virus 1
SequenceString: AENLWVTVYY GVPVWKEAKT TLFCASDAKA YEKEVHNVWA THACVPTDPN PQEMVLKNVT ENFNMWKNDM VDQMHEDVIS LWDQSLKPCV KLTPLCVTLN CTNATASNSS IIEGMKNCSF NITTELRDKR EKKNALFYKL DIVQLDGNSS QYRLINCNTS VITQACPKVS ...String:
AENLWVTVYY GVPVWKEAKT TLFCASDAKA YEKEVHNVWA THACVPTDPN PQEMVLKNVT ENFNMWKNDM VDQMHEDVIS LWDQSLKPCV KLTPLCVTLN CTNATASNSS IIEGMKNCSF NITTELRDKR EKKNALFYKL DIVQLDGNSS QYRLINCNTS VITQACPKVS FDPIPIHYCA PAGYAILKCN NKTFTGTGPC NNVSTVQCTH GIKPVVSTQL LLNGSLAEGE IIIRSENITN NVKTIIVHLN ESVKIECTRP NNKTRTSIRI GPGQAFYATG QVIGDIREAY CNINESKWNE TLQRVSKKLK EYFPHKNITF QPSSGGDLEI TTHSFNCGGE FFYCNTSSLF NRTYMANSTD MANSTETNST RTITIHCRIK QIINMWQEVG RAMYAPPIAG NITCISNITG LLLTRDGGKN NTETFRPGGG NMKDNWRSEL YKYKVVKIEP LGVAPTRCKR RVVGRRRRRR AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEA QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSGK LICCTNVPWN SSWSNRNLSE IWDNMTWLQW DKEISNYTQI IYGLLEESQN QQEKNEQDLL ALD

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Macromolecule #2: DH522.2 Fab Heavy Chain

MacromoleculeName: DH522.2 Fab Heavy Chain / type: other / ID: 2 / Classification: other
Source (natural)Organism: Homo sapiens (human)
SequenceString: QVQLQESGPG LVKPSETLSL TCAVSGGSIG DDYYWNWIRQ SPGKGLEWIG SIYGSFGGTN FNPSLKNRVT ISMDTSNNQV SLKLNSVTAA DTAVYYCARG SHSIVVLFGY YFDYWGQGVL VTVSSASTKG PSVFPLAPSS RSTSESTAAL GCLVKD YFP EPVTVSWNSG ...String:
QVQLQESGPG LVKPSETLSL TCAVSGGSIG DDYYWNWIRQ SPGKGLEWIG SIYGSFGGTN FNPSLKNRVT ISMDTSNNQV SLKLNSVTAA DTAVYYCARG SHSIVVLFGY YFDYWGQGVL VTVSSASTKG PSVFPLAPSS RSTSESTAAL GCLVKD YFP EPVTVSWNSG SLTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYVCN VNHKPSN TK VDKRVEIKT

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Macromolecule #3: DH522.2 Fab Light Chain

MacromoleculeName: DH522.2 Fab Light Chain / type: other / ID: 3 / Classification: other
Source (natural)Organism: Homo sapiens (human)
SequenceString: QSALTQPPSV SKSLGQSVTI SCSGTTNDIG AYNGVS WYQ HHSDTAPRLL IYEVNKRPSG VSDRFSGSKS GNTASLTISG LQAEDEADYY CGSYRSG ST WVFGGGTRLT VLGQPKASPT VTLFPPSSEE LQANKATLVC LISDFYPGVV KVAWKADG S AVNAGVETTT ...String:
QSALTQPPSV SKSLGQSVTI SCSGTTNDIG AYNGVS WYQ HHSDTAPRLL IYEVNKRPSG VSDRFSGSKS GNTASLTISG LQAEDEADYY CGSYRSG ST WVFGGGTRLT VLGQPKASPT VTLFPPSSEE LQANKATLVC LISDFYPGVV KVAWKADG S AVNAGVETTT PSKQSNNKYA ASSYLSLTSD QWKSHKSYSC QVTHEGSTVE KTVAPAECS

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.01 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
5.0 mMC8H18N2O4SHEPES
150.0 mMNaClSodium chloridesodium chloride
StainingType: NEGATIVE / Material: uranyl formate

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Electron microscopy

MicroscopeFEI TECNAI 12
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 25.0 e/Å2

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Image processing

Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 28.1 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 15269

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