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- EMDB-27628: Cryo-EM structure of HIV-1 Env(BG505.T332N SOSIP) in complex with... -

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Basic information

Entry
Database: EMDB / ID: EMD-27628
TitleCryo-EM structure of HIV-1 Env(BG505.T332N SOSIP) in complex with DH1030.1 Fab
Map datacryosparc generated full map
Sample
  • Complex: HIV-1 Env(BG505.T332N SOSIP) in complex with DH1030.1 Fab
    • Protein or peptide: DH1030.1 Fab light chain
    • Protein or peptide: DH1030.1 Fab Heavy chain
    • Protein or peptide: Envelope glycoprotein gp41
    • Protein or peptide: Envelope glycoprotein gp120
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV-1 Env / VIRAL PROTEIN / 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 / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / 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 / fusion of virus membrane with host plasma membrane / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / 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
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsGobeil S / Acharya P
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Shared recognition mechanism for HIV-1 envelope-reactive V3 glycan broadly neutralizing B cell lineage maturation in humans and macaques
Authors: Gobeil SM / Janowska K / Stalls V / Mansouri K / Edwards RJ / Henderson RC / Wiehe K / Saunders K / Acharya P / Williams W / Haynes BF
History
DepositionJul 14, 2022-
Header (metadata) releaseJul 19, 2023-
Map releaseJul 19, 2023-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27628.png

Downloads & links

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Map

FileDownload / File: emd_27628.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryosparc generated full map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å		1.08 Å/pix.
x 320 pix.
= 345.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.9
Minimum - Maximum-1.2660557 - 4.111181
Average (Standard dev.)0.0028603664 (±0.13623506)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: cryosparc generated half map A

Fileemd_27628_half_map_1.map
Annotationcryosparc generated half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: cryosparc generated half map B

Fileemd_27628_half_map_2.map
Annotationcryosparc generated half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HIV-1 Env(BG505.T332N SOSIP) in complex with DH1030.1 Fab

EntireName: HIV-1 Env(BG505.T332N SOSIP) in complex with DH1030.1 Fab
Components
  • Complex: HIV-1 Env(BG505.T332N SOSIP) in complex with DH1030.1 Fab
    • Protein or peptide: DH1030.1 Fab light chain
    • Protein or peptide: DH1030.1 Fab Heavy chain
    • Protein or peptide: Envelope glycoprotein gp41
    • Protein or peptide: Envelope glycoprotein gp120
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HIV-1 Env(BG505.T332N SOSIP) in complex with DH1030.1 Fab

SupramoleculeName: HIV-1 Env(BG505.T332N SOSIP) in complex with DH1030.1 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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Macromolecule #1: DH1030.1 Fab light chain

MacromoleculeName: DH1030.1 Fab light chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 24.050713 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: YVVMTQSPLS LPITPGQPAS ISCRSSQRLL HSDGNTYLAW YQQRPGQPPR RLIYEVSKLD SGVPDRFSGS GAGTDFTLKI SRVEAEDVG VYYCGQNTYL PYSFGQGSKV EIKRAVAAPS VFIFPPSEDQ VKSGTVSVVC LLNNFYPREA SVKWKVDGVL K TGNSQESV ...String:
YVVMTQSPLS LPITPGQPAS ISCRSSQRLL HSDGNTYLAW YQQRPGQPPR RLIYEVSKLD SGVPDRFSGS GAGTDFTLKI SRVEAEDVG VYYCGQNTYL PYSFGQGSKV EIKRAVAAPS VFIFPPSEDQ VKSGTVSVVC LLNNFYPREA SVKWKVDGVL K TGNSQESV TEQDSKDNTY SLSSTLTLSN TDYQSHNVYA CEVTHQGLSS PVTKSFNRGE C

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Macromolecule #2: DH1030.1 Fab Heavy chain

MacromoleculeName: DH1030.1 Fab Heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 24.947818 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLAESGGG LTKPGGSLRL SCAASGFTFS DFYMDWVRQT PGKGLEWVSR INNDGRNKWY ADSVRGRFTV SRENAKNTLY LQMDSLRAE DTAVYYCARD RPVYRYWSGG YHLDPWGQGV VVTVSSASTK GPSVFPLAPS SRSTSESTAA LGCLVKDYFP E PVTVSWNS ...String:
EVQLAESGGG LTKPGGSLRL SCAASGFTFS DFYMDWVRQT PGKGLEWVSR INNDGRNKWY ADSVRGRFTV SRENAKNTLY LQMDSLRAE DTAVYYCARD RPVYRYWSGG YHLDPWGQGV VVTVSSASTK GPSVFPLAPS SRSTSESTAA LGCLVKDYFP E PVTVSWNS GSLTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYVC NVNHKPSNTK VDKRVEIKTC GG

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Macromolecule #3: Envelope glycoprotein gp41

MacromoleculeName: Envelope glycoprotein gp41 / type: protein_or_peptide / ID: 3 / 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

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #4: Envelope glycoprotein gp120

MacromoleculeName: Envelope glycoprotein gp120 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 54.02125 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNAIT DDMRGELKNC SFNMTTELRD KKQKVYSLFY RLDVVQINEN QGNRSNNSNK E YRLINCNT ...String:
AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPC VKLTPLCVTL QCTNVTNAIT 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 RRRRR R

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #9: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 9 / Number of copies: 33 / 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

Concentration1 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.75 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6mtj


Details: 6MTJ for Env 8DKF for DH1030.1 Fab
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 441080
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

Initial model
PDB IDChain

6mtj

source_name: PDB, initial_model_type: experimental model

8dkf

source_name: PDB, initial_model_type: experimental model
RefinementProtocol: AB INITIO MODEL
Output model

PDB-8dp1:
Cryo-EM structure of HIV-1 Env(BG505.T332N SOSIP) in complex with DH1030.1 Fab

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