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- EMDB-8573: HIV-1 CH505 Transmitted Founder SOSIP.664 Env trimer in Complex w... -

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Basic information

Entry
Database: EMDB / ID: EMD-8573
TitleHIV-1 CH505 Transmitted Founder SOSIP.664 Env trimer in Complex with the DH576 Fab from the RV305 Trial
Map dataNegative Stain EM Reconstruction of the DH576 Fab in complex with the HIV CH505 SOSIP.664 trimer
Sample
  • Complex: HIV-1 CH505 Transmitted Founder SOSIP.664 Env trimer in Complex with the DH576 Fab from the RV305 Trial
    • Complex: CH505 Transmitted Founder Envelope
      • Protein or peptide: DH576 Fab Light Chain
    • Complex: DH576 Fab
      • Protein or peptide: DH576 Fab Heavy Chain
    • Protein or peptide: HIV EnvelopeEnv (gene)
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 28.1 Å
AuthorsFera D / Harrison SC
CitationJournal: PLoS Pathog / Year: 2017
Title: Boosting of HIV envelope CD4 binding site antibodies with long variable heavy third complementarity determining region in the randomized double blind RV305 HIV-1 vaccine trial.
Authors: David Easterhoff / M Anthony Moody / Daniela Fera / Hao Cheng / Margaret Ackerman / Kevin Wiehe / Kevin O Saunders / Justin Pollara / Nathan Vandergrift / Rob Parks / Jerome Kim / Nelson L ...Authors: David Easterhoff / M Anthony Moody / Daniela Fera / Hao Cheng / Margaret Ackerman / Kevin Wiehe / Kevin O Saunders / Justin Pollara / Nathan Vandergrift / Rob Parks / Jerome Kim / Nelson L Michael / Robert J O'Connell / Jean-Louis Excler / Merlin L Robb / Sandhya Vasan / Supachai Rerks-Ngarm / Jaranit Kaewkungwal / Punnee Pitisuttithum / Sorachai Nitayaphan / Faruk Sinangil / James Tartaglia / Sanjay Phogat / Thomas B Kepler / S Munir Alam / Hua-Xin Liao / Guido Ferrari / Michael S Seaman / David C Montefiori / Georgia D Tomaras / Stephen C Harrison / Barton F Haynes /
Abstract: The canary pox vector and gp120 vaccine (ALVAC-HIV and AIDSVAX B/E gp120) in the RV144 HIV-1 vaccine trial conferred an estimated 31% vaccine efficacy. Although the vaccine Env AE.A244 gp120 is ...The canary pox vector and gp120 vaccine (ALVAC-HIV and AIDSVAX B/E gp120) in the RV144 HIV-1 vaccine trial conferred an estimated 31% vaccine efficacy. Although the vaccine Env AE.A244 gp120 is antigenic for the unmutated common ancestor of V1V2 broadly neutralizing antibody (bnAbs), no plasma bnAb activity was induced. The RV305 (NCT01435135) HIV-1 clinical trial was a placebo-controlled randomized double-blinded study that assessed the safety and efficacy of vaccine boosting on B cell repertoires. HIV-1-uninfected RV144 vaccine recipients were reimmunized 6-8 years later with AIDSVAX B/E gp120 alone, ALVAC-HIV alone, or a combination of ALVAC-HIV and AIDSVAX B/E gp120 in the RV305 trial. Env-specific post-RV144 and RV305 boost memory B cell VH mutation frequencies increased from 2.9% post-RV144 to 6.7% post-RV305. The vaccine was well tolerated with no adverse events reports. While post-boost plasma did not have bnAb activity, the vaccine boosts expanded a pool of envelope CD4 binding site (bs)-reactive memory B cells with long third heavy chain complementarity determining regions (HCDR3) whose germline precursors and affinity matured B cell clonal lineage members neutralized the HIV-1 CRF01 AE tier 2 (difficult to neutralize) primary isolate, CNE8. Electron microscopy of two of these antibodies bound with near-native gp140 trimers showed that they recognized an open conformation of the Env trimer. Although late boosting of RV144 vaccinees expanded a novel pool of neutralizing B cell clonal lineages, we hypothesize that boosts with stably closed trimers would be necessary to elicit antibodies with greater breadth of tier 2 HIV-1 strains.
TRIAL REGISTRATION: ClinicalTrials.gov NCT01435135.
History
DepositionJan 23, 2017-
Header (metadata) releaseFeb 15, 2017-
Map releaseMar 8, 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: 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_8573.png

Downloads & links

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Map

FileDownload / File: emd_8573.map.gz / Format: CCP4 / Size: 18.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative Stain EM Reconstruction of the DH576 Fab in complex with the HIV CH505 SOSIP.664 trimer
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: 2.13 / Movie #1: 2.13
Minimum - Maximum-17.58503 - 15.786918999999999
Average (Standard dev.)-0.024374684 (±1.0161787)
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-17.58515.787-0.024

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Supplemental data

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Sample components

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Entire : HIV-1 CH505 Transmitted Founder SOSIP.664 Env trimer in Complex w...

EntireName: HIV-1 CH505 Transmitted Founder SOSIP.664 Env trimer in Complex with the DH576 Fab from the RV305 Trial
Components
  • Complex: HIV-1 CH505 Transmitted Founder SOSIP.664 Env trimer in Complex with the DH576 Fab from the RV305 Trial
    • Complex: CH505 Transmitted Founder Envelope
      • Protein or peptide: DH576 Fab Light Chain
    • Complex: DH576 Fab
      • Protein or peptide: DH576 Fab Heavy Chain
    • Protein or peptide: HIV EnvelopeEnv (gene)

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Supramolecule #1: HIV-1 CH505 Transmitted Founder SOSIP.664 Env trimer in Complex w...

SupramoleculeName: HIV-1 CH505 Transmitted Founder SOSIP.664 Env trimer in Complex with the DH576 Fab from the RV305 Trial
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK 293T
Molecular weightTheoretical: 50 KDa

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Supramolecule #2: CH505 Transmitted Founder Envelope

SupramoleculeName: CH505 Transmitted Founder Envelope / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK 293T

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Supramolecule #3: DH576 Fab

SupramoleculeName: DH576 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3 / Details: fab fragment
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK 293T

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Macromolecule #1: HIV Envelope

MacromoleculeName: HIV Envelope / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VENLWVTVYY GVPVWKEAKT TLFCASDAKA YEKEVHNVWA THACVPTDPS PQELVLENVT ENFNMWKNDM VDQMHEDIIS LWDQSLKPCV KLTPLCVTLN CSNATVDSSK VYDTRSNVNV TSINNTIMGE MKNCSFNTTT EIRDKEKKEY ALFYRPDVVP LDETSNTSEY ...String:
VENLWVTVYY GVPVWKEAKT TLFCASDAKA YEKEVHNVWA THACVPTDPS PQELVLENVT ENFNMWKNDM VDQMHEDIIS LWDQSLKPCV KLTPLCVTLN CSNATVDSSK VYDTRSNVNV TSINNTIMGE MKNCSFNTTT EIRDKEKKEY ALFYRPDVVP LDETSNTSEY RLINCNTSAV TQACPKVTFE PIPIHYCAPA GYAILKCNNK TFNGTGPCSN VSTVQCTHGI RPVVSTQLLL NGSLAEKEIV IRSENLTNNA KIIIVHLNTS VEIVCTRPGN NTRKSVRIGP GQTFYATGDI IGDIRQAHCN ISERQWNKTL QEVGKELQKH FPNKTIKYER SAGGDMEIAT HSFNCGGEFF YCNTSNLFNG TYNGTYISTN STSNITLQCR IKQIINMWQG VGRAMYAPPI AGNITCKSNI TGLLLTRDGG TKNNSNETEE TFRPAGGDMR DNWRSELYKY KVVEIQPLGI APTGCKRRVV GRRRRRRAAG LGALFLGFLG AAGSTMGAAS ITLTVQARQL LSGIVQQQSN LLRAPEAQQH MLQLTVWGIK QLQARVLALE RYLKDQQLLG MWGCSGKLIC CTAVPWNTSW SNKSEKDIWD NMTWMQWERE ISNYTETIYM LLEDSQHQQE RNEKDLLALD

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Macromolecule #2: DH576 Fab Light Chain

MacromoleculeName: DH576 Fab Light Chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LSASVGDRVT ITCQASQDID NYLNWYQQKP GKAPKLLIYD ASNLETGVPS RFSGSGSGT SFTLTISSLQ PEDIGTYYCQ KYGSVPFPFG QGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS QESVTEQDSK ...String:
DIQMTQSPSS LSASVGDRVT ITCQASQDID NYLNWYQQKP GKAPKLLIYD ASNLETGVPS RFSGSGSGT SFTLTISSLQ PEDIGTYYCQ KYGSVPFPFG QGTKLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS QESVTEQDSK DSTYSLSSTL TLSKADYEKH KVYACEVTHQ GLSSPVTKSF NRGEC

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Macromolecule #3: DH576 Fab Heavy Chain

MacromoleculeName: DH576 Fab Heavy Chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGGG VVQPGRSLRL SCGVSGFTFS NYAIHWVRQA PGKRLEWVAL ISYDGKKQYY LDSVKGRFTI SRDNSKDMVY LQMNSLKAED TAIYYCARDR ARSTGYFGGI YYYYYGMDVW GQGTTVTVS GASTKGPSVF PLAPSSKSTS GG TAALGCL VKDYFPEPVT ...String:
EVQLVESGGG VVQPGRSLRL SCGVSGFTFS NYAIHWVRQA PGKRLEWVAL ISYDGKKQYY LDSVKGRFTI SRDNSKDMVY LQMNSLKAED TAIYYCARDR ARSTGYFGGI YYYYYGMDVW GQGTTVTVS GASTKGPSVF PLAPSSKSTS GG TAALGCL VKDYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTY ICNVNH KPSNTKVDKR VEPKSCDKHH HHHH

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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
0.02 %NaN3sodium azide
StainingType: NEGATIVE / Material: Uranyl Formate / Details: 2% uranyl formate used to stain sample for 20 s
GridModel: EMS / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
DetailsHIV-1 CH505 Transmitted Founder SOSIP.664 Env trimer in Complex with the DH576 Fab from the RV305 Trial

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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
Sample stageCooling holder cryogen: NITROGEN
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 reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 28.1 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN2 (ver. 2.1) / Number images used: 22929

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