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- EMDB-9166: Cryo-EM structure of BG505.SOSIP.664 in complex with BF520.1 anti... -

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Basic information

Entry
Database: EMDB / ID: EMD-9166
TitleCryo-EM structure of BG505.SOSIP.664 in complex with BF520.1 antigen binding fragment
Map dataCryo-EM of BG505.SOSIP.664 in complex with BF520.1-Fab
Sample
  • Complex: Cryo-EM structure of BF520.1 Fab in complex with BG505.SOSIP.664
    • Protein or peptide: Envelope Glycoprotein gp120
    • Protein or peptide: Envelope Glycoprotein gp41
    • Protein or peptide: BF520.1 Fab variable region
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


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 / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope ...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 / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / identical protein binding / 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
Similarity search - Domain/homology
Envelope glycoprotein gp160 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsWilliams JA / Lee KK / Overbaugh J
CitationJournal: Nat Commun / Year: 2019
Title: Kappa chain maturation helps drive rapid development of an infant HIV-1 broadly neutralizing antibody lineage.
Authors: Cassandra A Simonich / Laura Doepker / Duncan Ralph / James A Williams / Amrit Dhar / Zak Yaffe / Lauren Gentles / Christopher T Small / Brian Oliver / Vladimir Vigdorovich / Vidya Mangala ...Authors: Cassandra A Simonich / Laura Doepker / Duncan Ralph / James A Williams / Amrit Dhar / Zak Yaffe / Lauren Gentles / Christopher T Small / Brian Oliver / Vladimir Vigdorovich / Vidya Mangala Prasad / Ruth Nduati / D Noah Sather / Kelly K Lee / Frederick A Matsen Iv / Julie Overbaugh /
Abstract: HIV-infected infants develop broadly neutralizing plasma responses with more rapid kinetics than adults, suggesting the ontogeny of infant responses could better inform a path to achievable vaccine ...HIV-infected infants develop broadly neutralizing plasma responses with more rapid kinetics than adults, suggesting the ontogeny of infant responses could better inform a path to achievable vaccine targets. Here we reconstruct the developmental lineage of BF520.1, an infant-derived HIV-specific broadly neutralizing antibody (bnAb), using computational methods developed specifically for this purpose. We find that the BF520.1 inferred naive precursor binds HIV Env. We also show that heterologous cross-clade neutralizing activity evolved in the infant within six months of infection and that, ultimately, only 2% SHM is needed to achieve the full breadth of the mature antibody. Mutagenesis and structural analyses reveal that, for this infant bnAb, substitutions in the kappa chain were critical for activity, particularly in CDRL1. Overall, the developmental pathway of this infant antibody includes features distinct from adult antibodies, including several that may be amenable to better vaccine responses.
History
DepositionOct 1, 2018-
Header (metadata) releaseJan 9, 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: 0.102
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.102
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6mn7
  • Surface level: 0.102
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9166.png

Downloads & links

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Map

FileDownload / File: emd_9166.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM of BG505.SOSIP.664 in complex with BF520.1-Fab
Voxel sizeX=Y=Z: 2.2 Å
Density
Contour LevelBy AUTHOR: 0.102 / Movie #1: 0.102
Minimum - Maximum-0.20188709 - 0.33509022
Average (Standard dev.)0.0013772685 (±0.011176277)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 352.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.22.22.2
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z352.000352.000352.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.2020.3350.001

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Supplemental data

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Sample components

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Entire : Cryo-EM structure of BF520.1 Fab in complex with BG505.SOSIP.664

EntireName: Cryo-EM structure of BF520.1 Fab in complex with BG505.SOSIP.664
Components
  • Complex: Cryo-EM structure of BF520.1 Fab in complex with BG505.SOSIP.664
    • Protein or peptide: Envelope Glycoprotein gp120
    • Protein or peptide: Envelope Glycoprotein gp41
    • Protein or peptide: BF520.1 Fab variable region
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Cryo-EM structure of BF520.1 Fab in complex with BG505.SOSIP.664

SupramoleculeName: Cryo-EM structure of BF520.1 Fab in complex with BG505.SOSIP.664
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: Envelope Glycoprotein gp120

MacromoleculeName: Envelope Glycoprotein gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 53.278301 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNMTTELRD KKQKVYSLFY RLDVVQINEN QGNRSNNSNK E YRLINCNT ...String:
AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNNIT DDMRGELKNC SFNMTTELRD KKQKVYSLFY RLDVVQINEN QGNRSNNSNK E YRLINCNT SAITQACPKV SFEPIPIHYC APAGFAILKC KDKKFNGTGP CPSVSTVQCT HGIKPVVSTQ LLLNGSLAEE EV MIRSENI TNNAKNILVQ FNTPVQINCT RPNNNTRKSI RIGPGQAFYA TGDIIGDIRQ AHCNVSKATW NETLGKVVKQ LRK HFGNNT IIRFANSSGG DLEVTTHSFN CGGEFFYCNT SGLFNSTWIS NTSVQGSNST GSNDSITLPC RIKQIINMWQ RIGQ AMYAP PIQGVIRCVS NITGLILTRD GGSTNSTTET FRPGGGDMRD NWRSELYKYK VVKIEPLGVA PTRCKRRVVG R

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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: 17.146482 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEA QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD

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Macromolecule #3: BF520.1 Fab variable region

MacromoleculeName: BF520.1 Fab variable region / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.974941 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAE MKMPGASVKV SCKASGYTFT GNYIHWVRQA PGQGLEWMGW IAPHSGDTSY AQRFQGRVTM TGDTSLSTAY MELSRLRSD DTAVYYCARG PFPNYYGPGS YWGGLDFWGQ GTLVSVSSEI VMTQSPATLS VSLGERATLS CRTSQNVAYN F AWYQQKPG ...String:
QVQLVQSGAE MKMPGASVKV SCKASGYTFT GNYIHWVRQA PGQGLEWMGW IAPHSGDTSY AQRFQGRVTM TGDTSLSTAY MELSRLRSD DTAVYYCARG PFPNYYGPGS YWGGLDFWGQ GTLVSVSSEI VMTQSPATLS VSLGERATLS CRTSQNVAYN F AWYQQKPG QAPRLLIYEA SSRATGTPAR FSGSGFGTEF TLTISSMQSE DFAVYYCQQY NNWPSPFTFG PGTKVHIK

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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: 9 / 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: 7.4
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: 66.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 67174
FSC plot (resolution estimation)

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