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- EMDB-29783: Cryo-EM structure of T/F100 SOSIP.664 HIV-1 Env trimer with LMHS ... -

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Basic information

Entry
Database: EMDB / ID: EMD-29783
TitleCryo-EM structure of T/F100 SOSIP.664 HIV-1 Env trimer with LMHS mutations in complex with 8ANC195 and 10-1074
Map data
Sample
  • Complex: Cryo-EM structure of T/F100 SOSIP.664 HIV-1 Env trimer with LMHS mutations in complex with 8ANC195 and 10-1074
    • Protein or peptide: CRF01_AE T/F100 HIV-1 gp120
    • Protein or peptide: CRF-1_AE T/F100 HIV-1 gp41
    • Protein or peptide: Heavy chain of 8ANC195
    • Protein or peptide: Light chain of 8ANC195
    • Protein or peptide: Heavy chain of 10-1074
    • Protein or peptide: Light chain of 10-1074
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsT/F100 SOSIP / Clade A/E HIV-1 / 8ANC195 / 10-1074 / LMHS mutant. / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / viral protein processing / virus-mediated perturbation of host defense response / 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 / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / virus-mediated perturbation of host defense response / 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 speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsChen Y / Zhou F / Huang R / Tolbert W / Pazgier M
Funding support United States, 1 items
OrganizationGrant numberCountry
Other governmentStart-up funds United States
CitationJournal: Nat Commun / Year: 2023
Title: Structure-function analyses reveal key molecular determinants of HIV-1 CRF01_AE resistance to the entry inhibitor temsavir.
Authors: Jérémie Prévost / Yaozong Chen / Fei Zhou / William D Tolbert / Romain Gasser / Halima Medjahed / Manon Nayrac / Dung N Nguyen / Suneetha Gottumukkala / Ann J Hessell / Venigalla B Rao / ...Authors: Jérémie Prévost / Yaozong Chen / Fei Zhou / William D Tolbert / Romain Gasser / Halima Medjahed / Manon Nayrac / Dung N Nguyen / Suneetha Gottumukkala / Ann J Hessell / Venigalla B Rao / Edwin Pozharski / Rick K Huang / Doreen Matthies / Andrés Finzi / Marzena Pazgier /
Abstract: The HIV-1 entry inhibitor temsavir prevents the viral receptor CD4 (cluster of differentiation 4) from interacting with the envelope glycoprotein (Env) and blocks its conformational changes. To do ...The HIV-1 entry inhibitor temsavir prevents the viral receptor CD4 (cluster of differentiation 4) from interacting with the envelope glycoprotein (Env) and blocks its conformational changes. To do this, temsavir relies on the presence of a residue with small side chain at position 375 in Env and is unable to neutralize viral strains like CRF01_AE carrying His375. Here we investigate the mechanism of temsavir resistance and show that residue 375 is not the sole determinant of resistance. At least six additional residues within the gp120 inner domain layers, including five distant from the drug-binding pocket, contribute to resistance. A detailed structure-function analysis using engineered viruses and soluble trimer variants reveals that the molecular basis of resistance is mediated by crosstalk between His375 and the inner domain layers. Furthermore, our data confirm that temsavir can adjust its binding mode to accommodate changes in Env conformation, a property that likely contributes to its broad antiviral activity.
History
DepositionFeb 16, 2023-
Header (metadata) releaseNov 8, 2023-
Map releaseNov 8, 2023-
UpdateNov 8, 2023-
Current statusNov 8, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29783.png

Downloads & links

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Map

FileDownload / File: emd_29783.map.gz / Format: CCP4 / Size: 437.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 1.4
Minimum - Maximum-13.204788000000001 - 25.187595000000002
Average (Standard dev.)-0.014482076 (±0.60200167)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions486486486
Spacing486486486
CellA=B=C: 403.38 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_29783_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_29783_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 : Cryo-EM structure of T/F100 SOSIP.664 HIV-1 Env trimer with LMHS ...

EntireName: Cryo-EM structure of T/F100 SOSIP.664 HIV-1 Env trimer with LMHS mutations in complex with 8ANC195 and 10-1074
Components
  • Complex: Cryo-EM structure of T/F100 SOSIP.664 HIV-1 Env trimer with LMHS mutations in complex with 8ANC195 and 10-1074
    • Protein or peptide: CRF01_AE T/F100 HIV-1 gp120
    • Protein or peptide: CRF-1_AE T/F100 HIV-1 gp41
    • Protein or peptide: Heavy chain of 8ANC195
    • Protein or peptide: Light chain of 8ANC195
    • Protein or peptide: Heavy chain of 10-1074
    • Protein or peptide: Light chain of 10-1074
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Cryo-EM structure of T/F100 SOSIP.664 HIV-1 Env trimer with LMHS ...

SupramoleculeName: Cryo-EM structure of T/F100 SOSIP.664 HIV-1 Env trimer with LMHS mutations in complex with 8ANC195 and 10-1074
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Details: LM mutations refer to layer mutants (H61Y/Q105H/V108I/N474D/I475M/K476R) and HS mutation refer to H375S.
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 6.3 MDa

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Macromolecule #1: CRF01_AE T/F100 HIV-1 gp120

MacromoleculeName: CRF01_AE T/F100 HIV-1 gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 54.697098 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ATNNLWVTVY YGVPVWRDAD TTLFCASDAK AYETEVHNVW ATHACVPTDP NPQEMHLKNV TENFNMWKNN MVEQMHEDII SLWDQSLKP CVKLTPLCVT LNCTSATVTN YTKVNDTSDI IGNITDDVRN CSFNMTTELR DKQQKVYALF YKLDIVPIDD S SNNGSSNF ...String:
ATNNLWVTVY YGVPVWRDAD TTLFCASDAK AYETEVHNVW ATHACVPTDP NPQEMHLKNV TENFNMWKNN MVEQMHEDII SLWDQSLKP CVKLTPLCVT LNCTSATVTN YTKVNDTSDI IGNITDDVRN CSFNMTTELR DKQQKVYALF YKLDIVPIDD S SNNGSSNF SEYRLINCNT SVIKQACPKV SFDPIPIHYC TPAGYAILRC NDKKFNGTGP CKNVSSVQCT HGIKPVVSTQ LL LNGSLAE EGIIIRSENL TNNAKTIIVH FNESVKINCT RPSNNTRTGI HIGPGQVFYK TGDIIGDIRK AYCNISGAQW HKV LGRVAN KLKEHFNNKT IVFKPSSGGD PEITMHSFNC RGEFFYCNTT KLFNSTWGGN KNETRDNGTI TIPCRIKQII NMWQ GVGQA MYAPPIKGVI KCLSNITGIL LTRDGGNDTE NNETFRPGGG DMRDNWRNEL YKYKVVQIEP LGIAPTKCKR RVVER RRRR R

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #2: CRF-1_AE T/F100 HIV-1 gp41

MacromoleculeName: CRF-1_AE T/F100 HIV-1 gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.389781 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGLGAMIFG FLGAAGSTMG AASITLTVQA RQLLSGIVQQ QSNLLRAPEA QQHLLQLTVW GIKQLQARVL AVERYLQDQK FLGLWGCSG KIICCTAVPW NSSWSNKTFE EIWNNMTWIE WEREISNYTS QIYDILTISQ TQQEKNEKDL LELDAA

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #3: Heavy chain of 8ANC195

MacromoleculeName: Heavy chain of 8ANC195 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.324402 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QIHLVQSGTE VKKPGSSVTV SCKAYGVNTF GLYAVNWVRQ APGQSLEYIG QIWRWKSSAS HHFRGRVLIS AVDLTGSSPP ISSLEIKNL TSDDTAVYFC TTTSTYDRWS GLHHDGVMAF SSWGQGTLIS VSAASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP ...String:
QIHLVQSGTE VKKPGSSVTV SCKAYGVNTF GLYAVNWVRQ APGQSLEYIG QIWRWKSSAS HHFRGRVLIS AVDLTGSSPP ISSLEIKNL TSDDTAVYFC TTTSTYDRWS GLHHDGVMAF SSWGQGTLIS VSAASTKGPS VFPLAPSSKS TSGGTAALGC L VKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK RVEPKSCDKT

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Macromolecule #4: Light chain of 8ANC195

MacromoleculeName: Light chain of 8ANC195 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.460047 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPST LSASTGDTVR ISCRASQSIT GNWVAWYQQR PGKAPRLLIY RGAALLGGVP SRFRGSAAGT DFTLTIGNLQ AEDFGTFYC QQYDTYPGTF GQGTKVEVKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
DIQMTQSPST LSASTGDTVR ISCRASQSIT GNWVAWYQQR PGKAPRLLIY RGAALLGGVP SRFRGSAAGT DFTLTIGNLQ AEDFGTFYC QQYDTYPGTF GQGTKVEVKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #5: Heavy chain of 10-1074

MacromoleculeName: Heavy chain of 10-1074 / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.661688 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 RVEPKSCDKT

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Macromolecule #6: Light chain of 10-1074

MacromoleculeName: Light chain of 10-1074 / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.18076 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: SYVRPLSVAL GETARISCGR QALGSRAVQW YQHRPGQAPI LLIYNNQDRP SGIPERFSGT PDINFGTRAT LTISGVEAGD EADYYCHMW DSRSGFSWSF GGATRLTVLG QPKAAPSVTL FPPSSEELQA NKATLVCLIS DFYPGAVTVA WKADSSPVKA G VETTTPSK ...String:
SYVRPLSVAL GETARISCGR QALGSRAVQW YQHRPGQAPI LLIYNNQDRP SGIPERFSGT PDINFGTRAT LTISGVEAGD EADYYCHMW DSRSGFSWSF GGATRLTVLG QPKAAPSVTL FPPSSEELQA NKATLVCLIS DFYPGAVTVA WKADSSPVKA G VETTTPSK QSNNKYAASS YLSLTPEQWK SHRSYSCQVT HEGSTVEKTV APTECS

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Macromolecule #12: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 12 / Number of copies: 36 / 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

Concentration0.928 mg/mL
BufferpH: 7.4 / Details: 1x PBS saline, pH 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS / Support film - #1 - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsCRF01_AE T/F100 SOSIP (GnT1- produced) was incubated with 15-fold excess of ANC195 Fab and 10-1074 Fab overnight at 4 degrees Celsius before purification on a Superose 6 300/10 GL column (GE Healthcare). The complex peak was harvested, concentrated to 0.8-1.0 mg/mL in PBS buffer, and immediately used for CryoEM grid preparation.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.7 µm / Calibrated defocus min: 0.5 µm / Calibrated magnification: 60241 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1044853
Startup modelType of model: OTHER / Details: ab initio
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 2
Details: 2 good classes were picked from 4 classes. One class reconstructed to higher resolution than the other.
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 549061
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

8dok

chain_id: A, residue_range: 26-511, source_name: PDB, initial_model_type: experimental model

8dok

chain_id: B, residue_range: 512-666, source_name: PDB, initial_model_type: experimental model

8dok

chain_id: C, source_name: PDB, initial_model_type: experimental model

8dok

chain_id: D, source_name: PDB, initial_model_type: experimental model

8dok

chain_id: H, source_name: PDB, initial_model_type: experimental model

8dok

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

PDB-8g6u:
Cryo-EM structure of T/F100 SOSIP.664 HIV-1 Env trimer with LMHS mutations in complex with 8ANC195 and 10-1074

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