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- EMDB-26443: Structure of the DU422 SOSIP.664 trimer in complex with neutraliz... -

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Basic information

Entry
Database: EMDB / ID: EMD-26443
TitleStructure of the DU422 SOSIP.664 trimer in complex with neutralizing antibody Fab fragments 10-1074 and BG24
Map dataSharpened map
Sample
  • Complex: Complex of DU422 SOSIP trimer bound to 10-1074 and BG24 Fab fragments
    • Protein or peptide: Envelope glycoprotein gp41
    • Protein or peptide: BG24 CDRH2-v2 Fab heavy chain
    • Protein or peptide: BG24 light chain
    • Protein or peptide: Envelope glycoprotein gp160
    • Protein or peptide: 10-1074 Fab heavy chain
    • Protein or peptide: 10-1074 light chain
  • 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 / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane ...: / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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 / 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
Similarity search - Component
Biological speciesHomo sapiens (human) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsBarnes CO / Bjorkman PJ
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI100148 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P50 AI150464 United States
Bill & Melinda Gates FoundationOPP1124068 United States
CitationJournal: Sci Adv / Year: 2022
Title: A naturally arising broad and potent CD4-binding site antibody with low somatic mutation.
Authors: Christopher O Barnes / Till Schoofs / Priyanthi N P Gnanapragasam / Jovana Golijanin / Kathryn E Huey-Tubman / Henning Gruell / Philipp Schommers / Nina Suh-Toma / Yu Erica Lee / Julio C ...Authors: Christopher O Barnes / Till Schoofs / Priyanthi N P Gnanapragasam / Jovana Golijanin / Kathryn E Huey-Tubman / Henning Gruell / Philipp Schommers / Nina Suh-Toma / Yu Erica Lee / Julio C Cetrulo Lorenzi / Alicja Piechocka-Trocha / Johannes F Scheid / Anthony P West / Bruce D Walker / Michael S Seaman / Florian Klein / Michel C Nussenzweig / Pamela J Bjorkman /
Abstract: The induction of broadly neutralizing antibodies (bNAbs) is a potential strategy for a vaccine against HIV-1. However, most bNAbs exhibit features such as unusually high somatic hypermutation, ...The induction of broadly neutralizing antibodies (bNAbs) is a potential strategy for a vaccine against HIV-1. However, most bNAbs exhibit features such as unusually high somatic hypermutation, including insertions and deletions, which make their induction challenging. VRC01-class bNAbs not only exhibit extraordinary breadth and potency but also rank among the most highly somatically mutated bNAbs. Here, we describe a VRC01-class antibody isolated from a viremic controller, BG24, that is much less mutated than most relatives of its class while achieving comparable breadth and potency. A 3.8-Å x-ray crystal structure of a BG24-BG505 Env trimer complex revealed conserved contacts at the gp120 interface characteristic of the VRC01-class Abs, despite lacking common CDR3 sequence motifs. The existence of moderately mutated CD4-binding site (CD4bs) bNAbs such as BG24 provides a simpler blueprint for CD4bs antibody induction by a vaccine, raising the prospect that such an induction might be feasible with a germline-targeting approach.
History
DepositionMar 16, 2022-
Header (metadata) releaseAug 17, 2022-
Map releaseAug 17, 2022-
UpdateSep 7, 2022-
Current statusSep 7, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26443.png

Downloads & links

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Map

FileDownload / File: emd_26443.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Voxel sizeX=Y=Z: 0.869 Å
Density
Contour LevelBy AUTHOR: 0.013
Minimum - Maximum-0.07334901 - 0.101043016
Average (Standard dev.)0.00018126819 (±0.0024751876)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 291.984 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_26443_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_26443_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of DU422 SOSIP trimer bound to 10-1074 and BG24 Fab fragments

EntireName: Complex of DU422 SOSIP trimer bound to 10-1074 and BG24 Fab fragments
Components
  • Complex: Complex of DU422 SOSIP trimer bound to 10-1074 and BG24 Fab fragments
    • Protein or peptide: Envelope glycoprotein gp41
    • Protein or peptide: BG24 CDRH2-v2 Fab heavy chain
    • Protein or peptide: BG24 light chain
    • Protein or peptide: Envelope glycoprotein gp160
    • Protein or peptide: 10-1074 Fab heavy chain
    • Protein or peptide: 10-1074 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Complex of DU422 SOSIP trimer bound to 10-1074 and BG24 Fab fragments

SupramoleculeName: Complex of DU422 SOSIP trimer bound to 10-1074 and BG24 Fab fragments
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)
Molecular weightExperimental: 650 KDa

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Macromolecule #1: Envelope glycoprotein gp41

MacromoleculeName: Envelope glycoprotein gp41 / type: protein_or_peptide / ID: 1 / Details: Env mimic DU422 SOSIP.664 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.104527 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGLGAVLLG FLGAAGSTMG AASMTLTVQA RQLLSGIVQQ QSNLLRAPEA QQHLLQLTVW GIKQLQTRVL AIERYLKDQQ LLGLWGCSG KLICCTAVPW NSSWSNKSLG DIWDNMTWMQ WDREISNYTN TIFRLLEESQ NQQEKNEKDL LALD

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Macromolecule #2: BG24 CDRH2-v2 Fab heavy chain

MacromoleculeName: BG24 CDRH2-v2 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.49859 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSRAE VKKPGASVKV SCEASGYNFV DHYIHWVRQA PGQRPQWVGW MNPQWGQVNY ARTFQGRVTM TRDTSIDTAY MQLNRLTSG DTAVYYCATQ VKLDSSAGYP FDIWGQGTMV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String:
QVQLVQSRAE VKKPGASVKV SCEASGYNFV DHYIHWVRQA PGQRPQWVGW MNPQWGQVNY ARTFQGRVTM TRDTSIDTAY MQLNRLTSG DTAVYYCATQ VKLDSSAGYP FDIWGQGTMV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KKVEPKSCDK HHHHHH

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Macromolecule #3: BG24 light chain

MacromoleculeName: BG24 light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.925209 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSALTQPRSV SGSPGQSVNI SCTGAYSGLG WYQQHPGRAP KLIIYEVNRR PSGVSDRFSG SKSGNTASLT ISGLRTEDEA DYFCSAFEY FGEGTKLTVL SQPKAAPSVT LFPPSSEELQ ANKATLVCLI SDFYPGAVTV AWKADSSPVK AGVETTTPSK Q SNNKYAAS ...String:
QSALTQPRSV SGSPGQSVNI SCTGAYSGLG WYQQHPGRAP KLIIYEVNRR PSGVSDRFSG SKSGNTASLT ISGLRTEDEA DYFCSAFEY FGEGTKLTVL SQPKAAPSVT LFPPSSEELQ ANKATLVCLI SDFYPGAVTV AWKADSSPVK AGVETTTPSK Q SNNKYAAS SYLSLTPEQW KSHRSYSCQV THEGSTVEKT VAPTECS

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Macromolecule #4: Envelope glycoprotein gp160

MacromoleculeName: Envelope glycoprotein gp160 / type: protein_or_peptide / ID: 4 / Details: Env mimic DU422 SOSIP.664 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 56.99998 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGAENLDLW VTVYYGVPVW KEAKTTLFCA SDAKAYDKEV RNVWATHACV PTDPNPQEI VLENVTENFN MWKNDMVDQM HEDIISLWDQ SLKPCVKLTP LCVTLNCKNV NISANANATA TLNSSMNGEI K NCSFNTTT ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGAENLDLW VTVYYGVPVW KEAKTTLFCA SDAKAYDKEV RNVWATHACV PTDPNPQEI VLENVTENFN MWKNDMVDQM HEDIISLWDQ SLKPCVKLTP LCVTLNCKNV NISANANATA TLNSSMNGEI K NCSFNTTT ELRDKKQKVY ALFYKPDVVP LNGGEHNETG EYILINCNSS TITQACPKVS FDPIPIHYCA PAGYAILKCN NK TFNGTGP CNNVSTVQCT HGIKPVVSTQ LLLNGSLAEE EIIVRSENLT NNIKTIIVHL NKSVEINCTR PNNNTRKSVR IGP GQWFYA TGEIIGDIRE AHCNISRETW NSTLIQVKEK LREHYNKTIK FEPSSGGDLE VTTHSFNCRG EFFYCNTTKL FNET KLFNE SEYVDNKTII LPCRIKQIIN MWQEVGRAMY APPIEGNITC KSNITGLLLT WDGGENSTEG VFRPGGGNMK DNWRS ELYK YKVVEIKPLG VAPTKCKRKV VGR

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Macromolecule #5: 10-1074 Fab heavy chain

MacromoleculeName: 10-1074 Fab heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.389465 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQESGPG LVKPSETLSV TCSVSGDSMN NYYWTWIRQS PGKGLEWIGY ISDRESATYN PSLNSRVVIS RDTSKNQLSL KLNSVTPAD TAVYYCATAR RGQRIYGVVS FGEFFYYYSM DVWGKGTTVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP ...String:
QVQLQESGPG LVKPSETLSV TCSVSGDSMN NYYWTWIRQS PGKGLEWIGY ISDRESATYN PSLNSRVVIS RDTSKNQLSL KLNSVTPAD TAVYYCATAR RGQRIYGVVS FGEFFYYYSM DVWGKGTTVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK RVEPKSCDKH HH HHH

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Macromolecule #6: 10-1074 light chain

MacromoleculeName: 10-1074 light chain / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.708293 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SYVRPLSVAL GETARISCGR QALGSRAVQW YQHRPGQAPI LLIYNNQDRP SGIPERFSGT PDINFGTRAT LTISGVEAGD EADYYCHMW DSRSGFSWSF GGATRLTVLG QPKAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ ...String:
SYVRPLSVAL GETARISCGR QALGSRAVQW YQHRPGQAPI LLIYNNQDRP SGIPERFSGT PDINFGTRAT LTISGVEAGD EADYYCHMW DSRSGFSWSF GGATRLTVLG QPKAAPSVFI FPPSDEQLKS GTASVVCLLN NFYPREAKVQ WKVDNALQSG N SQESVTEQ DSKDSTYSLS STLTLSKADY EKHKVYACEV THQGLSSPVT KSFNRGEC

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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: 21 / 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

Concentration1.5 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 1989 / Average exposure time: 3.5 sec. / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 455671
CTF correctionSoftware - Name: CTFFIND
Startup modelType of model: OTHER / Details: ab initio
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2.12)
Final 3D classificationNumber classes: 6 / Avg.num./class: 50000 / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 204220
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5cez

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient
Output model

PDB-7ucg:
Structure of the DU422 SOSIP.664 trimer in complex with neutralizing antibody Fab fragments 10-1074 and BG24

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