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- EMDB-44595: Structure of VRC44.01 Fab in complex with 3BNC117-purified C1080.... -

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Basic information

Entry
Database: EMDB / ID: EMD-44595
TitleStructure of VRC44.01 Fab in complex with 3BNC117-purified C1080.c3 RnS SOSIP.664 HIV-1 Env trimer
Map datasharpened map
Sample
  • Complex: VRC44 and 3BNC117 Fabs with Repaired C1080 Env trimer
    • Protein or peptide: Envelope glycoprotein gp41
    • Protein or peptide: Envelope glycoprotein gp160
    • Protein or peptide: 3BNC117 heavy chain
    • Protein or peptide: 3BNC117 light chain
    • Protein or peptide: VRC44.01 light chain
    • Protein or peptide: VRC44.01 heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: PHOSPHATE ION
KeywordsHIV-1 / SOSIP / Vaccine / therapeutic / VIRAL PROTEIN-IMMUNE SYSTEM complex / subunit / multi-donor
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / 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 / 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: 2.83 Å
AuthorsGorman J / Kwong PD
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
Simons FoundationSF349247 United States
CitationJournal: Cell Rep / Year: 2024
Title: A multidonor class of highly glycan-dependent HIV-1 gp120-gp41 interface-targeting broadly neutralizing antibodies.
Authors: Evan M Cale / Chen-Hsiang Shen / Adam S Olia / Nathan A Radakovich / Reda Rawi / Yongping Yang / David R Ambrozak / Anthony K Bennici / Gwo-Yu Chuang / Emma D Crooks / Jefferson I Driscoll / ...Authors: Evan M Cale / Chen-Hsiang Shen / Adam S Olia / Nathan A Radakovich / Reda Rawi / Yongping Yang / David R Ambrozak / Anthony K Bennici / Gwo-Yu Chuang / Emma D Crooks / Jefferson I Driscoll / Bob C Lin / Mark K Louder / Patrick J Madden / Michael A Messina / Keiko Osawa / Guillaume B E Stewart-Jones / Raffaello Verardi / Zoe Vrakas / Danielle Xie / Baoshan Zhang / James M Binley / Mark Connors / Richard A Koup / Theodore C Pierson / Nicole A Doria-Rose / Peter D Kwong / John R Mascola / Jason Gorman /
Abstract: Antibodies that target the gp120-gp41 interface of the HIV-1 envelope (Env) trimer comprise a commonly elicited category of broadly neutralizing antibodies (bNAbs). Here, we isolate and characterize ...Antibodies that target the gp120-gp41 interface of the HIV-1 envelope (Env) trimer comprise a commonly elicited category of broadly neutralizing antibodies (bNAbs). Here, we isolate and characterize VRC44, a bNAb lineage with up to 52% neutralization breadth. The cryoelectron microscopy (cryo-EM) structure of antibody VRC44.01 in complex with the Env trimer reveals binding to the same gp120-gp41 interface site of vulnerability as antibody 35O22 from a different HIV-1-infected donor. In addition to having similar angles of approach and extensive contacts with glycans N88 and N625, VRC44 and 35O22 derive from the same IGHV1-18 gene and share convergent mutations, indicating these two antibodies to be members of the only known highly glycan-dependent multidonor class. Strikingly, both lineages achieved almost 100% neutralization breadth against virus strains displaying high-mannose glycans. The high breadth and reproducible elicitation of VRC44 and 35O22 lineages validate germline-based methods of immunogen design for targeting the HIV-1 gp120-gp41 interface.
History
DepositionApr 23, 2024-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateJan 1, 2025-
Current statusJan 1, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44595.png

Downloads & links

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Map

FileDownload / File: emd_44595.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 400 pix.
= 438.44 Å		1.1 Å/pix.
x 400 pix.
= 438.44 Å		1.1 Å/pix.
x 400 pix.
= 438.44 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0961 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-2.8881297 - 5.4040527
Average (Standard dev.)0.0109048635 (±0.13078216)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 438.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_44595_msk_1.map
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Additional map: unsharpened map

Fileemd_44595_additional_1.map
Annotationunsharpened map
Projections & Slices
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Additional map: deepEMhancer map

Fileemd_44595_additional_2.map
AnnotationdeepEMhancer map
Projections & Slices
AxesZYX

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Half map: half map A

Fileemd_44595_half_map_1.map
Annotationhalf map A
Projections & Slices
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Histogram

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Half map: half map B

Fileemd_44595_half_map_2.map
Annotationhalf map B
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Sample components

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Entire : VRC44 and 3BNC117 Fabs with Repaired C1080 Env trimer

EntireName: VRC44 and 3BNC117 Fabs with Repaired C1080 Env trimer
Components
  • Complex: VRC44 and 3BNC117 Fabs with Repaired C1080 Env trimer
    • Protein or peptide: Envelope glycoprotein gp41
    • Protein or peptide: Envelope glycoprotein gp160
    • Protein or peptide: 3BNC117 heavy chain
    • Protein or peptide: 3BNC117 light chain
    • Protein or peptide: VRC44.01 light chain
    • Protein or peptide: VRC44.01 heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: PHOSPHATE ION

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Supramolecule #1: VRC44 and 3BNC117 Fabs with Repaired C1080 Env trimer

SupramoleculeName: VRC44 and 3BNC117 Fabs with Repaired C1080 Env trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: Envelope glycoprotein gp41

MacromoleculeName: Envelope glycoprotein gp41 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 19.174828 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAMIFG FLGAAGSTMG AASNTLTVQA RQLLSGIVQQ QSNLPRAPEA QQHLLQLTVW GIKQLQARVL AVERYLEVQK FLGLWGCSG KIICCTAVPW NSTWSNKSFE QIWNNMTWIE WEREISNYTS QIYDILTESQ FQQDINEVDL LELDGSAPTK A KRRVVQRE KR

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #2: Envelope glycoprotein gp160

MacromoleculeName: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 54.23475 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AENLWVTVYY GVPVWKDADT TLFCASDAKA HETEAHNIWA THACVPTDPN PQEIYMENVT ENFNMWKNNM VEQMQEDIIS LWDQSLKPC VKLTPLCVTL SCTNVTLTNV NYTNNFPNIG NITDEVRNCS FNVTTEIRDK KQKVYALFYK LDIVQMENKN S YRLINCNT ...String:
AENLWVTVYY GVPVWKDADT TLFCASDAKA HETEAHNIWA THACVPTDPN PQEIYMENVT ENFNMWKNNM VEQMQEDIIS LWDQSLKPC VKLTPLCVTL SCTNVTLTNV NYTNNFPNIG NITDEVRNCS FNVTTEIRDK KQKVYALFYK LDIVQMENKN S YRLINCNT SVCKQACPKI SFDPIPIHYC TPAGYAILKC NEKNFNGTGP CKNVSSVQCT HGIKPVVSTQ LLLNGSLAEG EI IIRSENL TNNAKTIIVH LNKSVEINCT RPSNNTRTSV TIGPGQVFYR TGDIIGDIRK AYCEINGTKW NETLKQVVGK LKE HFPNKT ISFQPPSGGD LEITMHHFNC RGEFFYCNTT QLFNSTWINS TTIKEYNDTI IYLPCKIKQI INMWQGVGQC MYAP PIRGK INCVSNITGI LLTRDGGDAN ATNDTETFRP GGGNIKDNWR SELYKYKVVQ IEPLGIAPTK CKRRVVERRR RRR

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #3: 3BNC117 heavy chain

MacromoleculeName: 3BNC117 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.656484 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLLQSGAA VTKPGASVRV SCEASGYNIR DYFIHWWRQA PGQGLQWVGW INPKTGQPNN PRQFQGRVSL TRHASWDFDT YSFYMDLKA LRSDDTAVYF CARQRSDYWD FDVWGSGTQV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String:
QVQLLQSGAA VTKPGASVRV SCEASGYNIR DYFIHWWRQA PGQGLQWVGW INPKTGQPNN PRQFQGRVSL TRHASWDFDT YSFYMDLKA LRSDDTAVYF CARQRSDYWD FDVWGSGTQV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSC

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Macromolecule #4: 3BNC117 light chain

MacromoleculeName: 3BNC117 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.022658 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LSASVGDTVT ITCQANGYLN WYQQRRGKAP KLLIYDGSKL ERGVPSRFSG RRWGQEYNLT INNLQPEDIA TYFCQVYEF VVPGTRLDLK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG NSQESVTEQD S KDSTYSLS ...String:
DIQMTQSPSS LSASVGDTVT ITCQANGYLN WYQQRRGKAP KLLIYDGSKL ERGVPSRFSG RRWGQEYNLT INNLQPEDIA TYFCQVYEF VVPGTRLDLK RTVAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG NSQESVTEQD S KDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGEC

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Macromolecule #5: VRC44.01 light chain

MacromoleculeName: VRC44.01 light chain / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.591962 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AIYLTQSPSS LSASVGERVT ITCRASQDIG DTLAWYQQQP GRPPFLVVYR ASTLNYGVPS RFSGGGSGTR FTLTISSLQP ADSGTYFCQ QFKTFPFTFG PGTKVEVK

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Macromolecule #6: VRC44.01 heavy chain

MacromoleculeName: VRC44.01 heavy chain / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.926507 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSYLVQSGPE VKKPGTAVKV SCQASRYPFT FFGISWVRQA PGKGPQWMGW ISPYNGHAIY LDELKDRLTL TTDTDTTTAY MELRNLRSA DTAVYFCARD HTRQDSRGYD FWGQGTLVTV SSAST

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Macromolecule #13: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 13 / Number of copies: 34 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #14: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 14 / Number of copies: 1 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

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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

Concentration2 mg/mL
BufferpH: 7.4 / Details: PBS
GridModel: C-flat-1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average exposure time: 10.0 sec. / Average electron dose: 64.09 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3) / Number images used: 90268
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3)

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Atomic model buiding 1

Initial modelPDB ID:

6vtt


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9bio:
Structure of VRC44.01 Fab in complex with 3BNC117-purified C1080.c3 RnS SOSIP.664 HIV-1 Env trimer

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