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- EMDB-21383: Cryo-EM Structure of CAP256-VRC26.25 Fab bound to HIV-1 Env trime... -

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Entry
Database: EMDB / ID: EMD-21383
TitleCryo-EM Structure of CAP256-VRC26.25 Fab bound to HIV-1 Env trimer CAP256.wk34.c80 SOSIP.RnS2
Map dataSharpened map
Sample
  • Complex: Cryo-EM Structure of CAP256-VRC26.25 Fab bound to HIV-1 Env trimer CAP256.wk34.c80 SOSIP.RnS2
    • Complex: HIV-1 Env trimer CAP256.wk34.c80 SOSIP.RnS2
      • Protein or peptide: Envelope glycoprotein gp120
      • Protein or peptide: Envelope glycoprotein gp41
    • Complex: CAP256-VRC26.25 Fab
      • Protein or peptide: VRC26.25 Heavy Chain
      • Protein or peptide: VRC26.25 Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsV1V2 / VRC26 / CAP256 / HIV-1 / SOSIP / Vaccine / Superinfecting / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / extracellular region / 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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain ...: / Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Envelope glycoprotein gp160 / Lambda-chain (AA -20 to 215)
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsGorman J / Kwong PD
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
CitationJournal: Cell Rep / Year: 2020
Title: Structure of Super-Potent Antibody CAP256-VRC26.25 in Complex with HIV-1 Envelope Reveals a Combined Mode of Trimer-Apex Recognition.
Authors: Jason Gorman / Gwo-Yu Chuang / Yen-Ting Lai / Chen-Hsiang Shen / Jeffrey C Boyington / Aliaksandr Druz / Hui Geng / Mark K Louder / Krisha McKee / Reda Rawi / Raffaello Verardi / Yongping ...Authors: Jason Gorman / Gwo-Yu Chuang / Yen-Ting Lai / Chen-Hsiang Shen / Jeffrey C Boyington / Aliaksandr Druz / Hui Geng / Mark K Louder / Krisha McKee / Reda Rawi / Raffaello Verardi / Yongping Yang / Baoshan Zhang / Nicole A Doria-Rose / Bob Lin / Penny L Moore / Lynn Morris / Lawrence Shapiro / John R Mascola / Peter D Kwong /
Abstract: Antibodies targeting the V1V2 apex of the HIV-1 envelope (Env) trimer comprise one of the most commonly elicited categories of broadly neutralizing antibodies. Structures of these antibodies indicate ...Antibodies targeting the V1V2 apex of the HIV-1 envelope (Env) trimer comprise one of the most commonly elicited categories of broadly neutralizing antibodies. Structures of these antibodies indicate diverse modes of Env recognition typified by antibodies of the PG9 class and the PGT145 class. The mode of recognition, however, has been unclear for the most potent of the V1V2 apex-targeting antibodies, CAP256-VRC26.25 (named for donor-lineage.clone and referred to hereafter as VRC26.25). Here, we determine the cryoelectron microscopy structure at 3.7 Å resolution of the antigen-binding fragment of VRC26.25 in complex with the Env trimer thought to have initiated the lineage. The 36-residue protruding loop of VRC26.25 displays recognition incorporating both strand-C interactions similar to the PG9 class and V1V2 apex insertion similar to the PGT145 class. Structural elements of separate antibody classes can thus intermingle to form a "combined" class, which in this case yields an antibody of extraordinary potency.
History
DepositionFeb 13, 2020-
Header (metadata) releaseApr 8, 2020-
Map releaseApr 8, 2020-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6vtt
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21383.png

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Map

FileDownload / File: emd_21383.map.gz / Format: CCP4 / Size: 115.9 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 312 pix.
= 341.983 Å		1.1 Å/pix.
x 312 pix.
= 341.983 Å		1.1 Å/pix.
x 312 pix.
= 341.983 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: 0.4 / Movie #1: 0.4
Minimum - Maximum-1.1956356 - 2.849231
Average (Standard dev.)0.009486767 (±0.070868015)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions312312312
Spacing312312312
CellA=B=C: 341.9832 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.09609935897441.09609935897441.0960993589744
M x/y/z312312312
origin x/y/z0.0000.0000.000
length x/y/z341.983341.983341.983
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS312312312
D min/max/mean-1.1962.8490.009

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Supplemental data

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Mask #1

Fileemd_21383_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Additional map: Unsharpened map

Fileemd_21383_additional.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_21383_half_map_1.map
AnnotationHalf map A
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AxesZYX

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Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_21383_half_map_2.map
AnnotationHalf map B
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Sample components

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Entire : Cryo-EM Structure of CAP256-VRC26.25 Fab bound to HIV-1 Env trime...

EntireName: Cryo-EM Structure of CAP256-VRC26.25 Fab bound to HIV-1 Env trimer CAP256.wk34.c80 SOSIP.RnS2
Components
  • Complex: Cryo-EM Structure of CAP256-VRC26.25 Fab bound to HIV-1 Env trimer CAP256.wk34.c80 SOSIP.RnS2
    • Complex: HIV-1 Env trimer CAP256.wk34.c80 SOSIP.RnS2
      • Protein or peptide: Envelope glycoprotein gp120
      • Protein or peptide: Envelope glycoprotein gp41
    • Complex: CAP256-VRC26.25 Fab
      • Protein or peptide: VRC26.25 Heavy Chain
      • Protein or peptide: VRC26.25 Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Cryo-EM Structure of CAP256-VRC26.25 Fab bound to HIV-1 Env trime...

SupramoleculeName: Cryo-EM Structure of CAP256-VRC26.25 Fab bound to HIV-1 Env trimer CAP256.wk34.c80 SOSIP.RnS2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

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Supramolecule #2: HIV-1 Env trimer CAP256.wk34.c80 SOSIP.RnS2

SupramoleculeName: HIV-1 Env trimer CAP256.wk34.c80 SOSIP.RnS2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #4
Source (natural)Organism: Human immunodeficiency virus 1

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Supramolecule #3: CAP256-VRC26.25 Fab

SupramoleculeName: CAP256-VRC26.25 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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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: 53.322434 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GLWVTVYYGV PVWREAKTTL FCASDAKSYE KEVHNVWATH ACVPTDPNPQ ELVLENVTEN FNMWKNDMVD QMHEDIISLW DQSLKPCVK LTPLCVTLNC SDAKVNATYK GTREEIKNCS FNATTELRDK KRREYALFYR LDIVPLSGEG NNNSEYRLIN C NTSVITQI ...String:
GLWVTVYYGV PVWREAKTTL FCASDAKSYE KEVHNVWATH ACVPTDPNPQ ELVLENVTEN FNMWKNDMVD QMHEDIISLW DQSLKPCVK LTPLCVTLNC SDAKVNATYK GTREEIKNCS FNATTELRDK KRREYALFYR LDIVPLSGEG NNNSEYRLIN C NTSVITQI CPKVTFDPIP IHYCAPAGYA ILKCNNKTFN GTGPCNNVST VQCTHGIKPV VSTQLLLNGS LAEEEIIIRS EN LTDNVKT IIVHLNESVE ITCTRPNNMT RKSVRIGPGQ TFYALGDIIG DIRQPHCNIS EIKWEKTLQR VSEKLREHFN KTI IFNQSS GGDLEITTHS FNCGGEFFYC NTSDLFFNKT FNETYSTGSN STNSTITLPC RIKQIINMWQ EVGRAMYAPP IAGN ITCKS NITGLLLTRD GGGNNSTKET FRPGGGNMRD NWRSELYKYK VVEVKPLGIA PTECNRTVVQ RRRRRR

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Macromolecule #2: VRC26.25 Heavy Chain

MacromoleculeName: VRC26.25 Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.083482 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVESGGG VVQPGTSLRL SCAASQFRFD GYGMHWVRQA PGKGLEWVAS ISHDGIKKYH AEKVWGRFTI SRDNSKNTLY LQMNSLRPE DTALYYCAKD LREDECEEWW SD(TYS)(TYS)DFGKQL PCAKSRGGLV GIADNWGQGT MVTVSSASTK GPS VFPLAP ...String:
QVQLVESGGG VVQPGTSLRL SCAASQFRFD GYGMHWVRQA PGKGLEWVAS ISHDGIKKYH AEKVWGRFTI SRDNSKNTLY LQMNSLRPE DTALYYCAKD LREDECEEWW SD(TYS)(TYS)DFGKQL PCAKSRGGLV GIADNWGQGT MVTVSSASTK GPS VFPLAP SSKSTSGGTA ALGCLVKDYF PEPVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNH KPSNT KVDKRVEPKS CDKGLEVLFQ

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Macromolecule #3: VRC26.25 Light Chain

MacromoleculeName: VRC26.25 Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.052611 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSVLTQPPSV SAAPGQKVTI SCSGNTSNIG NNFVSWYQQR PGRAPQLLIY ETDKRPSGIP DRFSASKSGT SGTLAITGLQ TGDEADYYC ATWAASLSSA RVFGTGTKVI VLVQPKANPT VTLFPPSSEE LQANKATLVC LISDFYPGAV TVAWKADSSP V KAGVETTT ...String:
QSVLTQPPSV SAAPGQKVTI SCSGNTSNIG NNFVSWYQQR PGRAPQLLIY ETDKRPSGIP DRFSASKSGT SGTLAITGLQ TGDEADYYC ATWAASLSSA RVFGTGTKVI VLVQPKANPT VTLFPPSSEE LQANKATLVC LISDFYPGAV TVAWKADSSP V KAGVETTT PSKQSNNKYA ASSYLSLTPE QWKSHRSYSC QVTHEGSTVE KTVAPTECS

UniProtKB: Lambda-chain (AA -20 to 215)

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Macromolecule #4: Envelope glycoprotein gp41

MacromoleculeName: Envelope glycoprotein gp41 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.355703 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVVGLGAVFL GFLGAAGSTM GAASNTLTVQ ARQLLSGIVQ QQSNLLRAPE AQQHMLQLGV WGFKQLQARV LAIERYLEVQ QLLGMWGCS GKLICCTNVP WNSSWSNKTY NEIWDNMTWM QWDREIGNYT DTIYKLLEVS QFQQEINEKD NLTLD

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Macromolecule #11: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 11 / Number of copies: 41 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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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 / Component - Formula: PBS
GridModel: C-flat-1.2/1.3 4C / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV
DetailsCryo-EM Structure of Fab CAP256-VRC26.25 bound to HIV-1 Env trimer CAP256 SU.wk34.80 SOSIP.RnS2

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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 / Number real images: 1777 / Average exposure time: 10.0 sec. / Average electron dose: 64.48 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
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.12) / Number images used: 108977
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationSoftware - Name: cryoSPARC (ver. 2.12)

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Atomic model buiding 1

Initial model
PDB IDChain

5dt1

source_name: PDB, initial_model_type: experimental model

6vrw

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6vtt:
Cryo-EM Structure of CAP256-VRC26.25 Fab bound to HIV-1 Env trimer CAP256.wk34.c80 SOSIP.RnS2

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