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- EMDB-28555: Glycan-trimmed BG505 UFO trimer complex with VRC01 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-28555
TitleGlycan-trimmed BG505 UFO trimer complex with VRC01 Fab
Map dataMRC volume file of Glycan-trimmed BG505 UFO trimer complex with VRC01 Fab
Sample
  • Complex: Glycan-trimmed BG505 UFO trimer complex with VRC01
    • Protein or peptide: Glycan-trimmed BG505 UFO trimer
    • Protein or peptide: heavy chain of VRC01 Fab
    • Protein or peptide: light chain of VRC01 Fab
KeywordsHIV / VRC01 / BG505 UFO / VIRAL PROTEIN
Biological speciesHuman immunodeficiency virus 1 / Homo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 12.16 Å
AuthorsLee YZ / Zhu J
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI129698 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI140844 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI124337 United States
CitationJournal: To Be Published
Title: Glycan-trimmed BG505 UFO trimer complex with VRC01 Fab
Authors: Lee YZ / Zhu J
History
DepositionOct 12, 2022-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateNov 1, 2023-
Current statusNov 1, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28555.png

Downloads & links

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Map

FileDownload / File: emd_28555.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMRC volume file of Glycan-trimmed BG505 UFO trimer complex with VRC01 Fab
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.93 Å/pix.
x 150 pix.
= 289.5 Å		1.93 Å/pix.
x 150 pix.
= 289.5 Å		1.93 Å/pix.
x 150 pix.
= 289.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.72
Minimum - Maximum-2.2156935 - 2.9382436
Average (Standard dev.)-0.042686816 (±0.2818486)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 289.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A file of Glycan-trimmed BG505 UFO...

Fileemd_28555_half_map_1.map
Annotationhalf map A file of Glycan-trimmed BG505 UFO trimer complex with VRC01 Fab
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B file of Glycan-trimmed BG505 UFO...

Fileemd_28555_half_map_2.map
Annotationhalf map B file of Glycan-trimmed BG505 UFO trimer complex with VRC01 Fab
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Glycan-trimmed BG505 UFO trimer complex with VRC01

EntireName: Glycan-trimmed BG505 UFO trimer complex with VRC01
Components
  • Complex: Glycan-trimmed BG505 UFO trimer complex with VRC01
    • Protein or peptide: Glycan-trimmed BG505 UFO trimer
    • Protein or peptide: heavy chain of VRC01 Fab
    • Protein or peptide: light chain of VRC01 Fab

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Supramolecule #1: Glycan-trimmed BG505 UFO trimer complex with VRC01

SupramoleculeName: Glycan-trimmed BG505 UFO trimer complex with VRC01 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Glycan-trimmed BG505 UFO trimer complex with 3 copies of VRC01 Fab Fragment
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: Glycan-trimmed BG505 UFO trimer

MacromoleculeName: Glycan-trimmed BG505 UFO trimer / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: AENLWVTVYY GVPVWKDAET TLFCASDAKA YDTEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPCV KLTPLCVTLQ CTNVTNNITD DMRGELKNCS FNMTTELRDK KQKVYSLFYR LDVVQINENQ GNRSNNSNKE YRLINCNTSA ...String:
AENLWVTVYY GVPVWKDAET TLFCASDAKA YDTEKHNVWA THACVPTDPN PQEIHLENVT EEFNMWKNNM VEQMHTDIIS LWDQSLKPCV KLTPLCVTLQ CTNVTNNITD DMRGELKNCS FNMTTELRDK KQKVYSLFYR LDVVQINENQ GNRSNNSNKE YRLINCNTSA ITQACPKVSF EPIPIHYCAP AGFAILKCKD KKFNGTGPCP SVSTVQCTHG IKPVVSTQLL LNGSLAEEEV MIRSENITNN AKNILVQFNT PVQINCTRPN NNTRKSIRIG PGQAFYATGD IIGDIRQAHC NVSKATWNET LGKVVKQLRK HFGNNTIIRF ANSSGGDLEV TTHSFNCGGE FFYCNTSGLF NSTWISNTSV QGSNSTGSND SITLPCRIKQ IINMWQRIGQ AMYAPPIQGV IRCVSNITGL ILTRDGGSTN STTETFRPGG GDMRDNWRSE LYKYKVVKIE PLGVAPTRCK RRVVGGGGGS GGGGSAVGIG AVFLGFLGAA GSTMGAASMT LTVQARNLLS GNPDWLPDMT VWGIKQLQAR VLAVERYLRD QQLLGIWGCS GKLICCTNVP WNSSWSNRNL SEIWDNMTWL QWDKEISNYT QIIYGLLEES QNQQEKNEQD LLALD

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Macromolecule #2: heavy chain of VRC01 Fab

MacromoleculeName: heavy chain of VRC01 Fab / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: QVQLVQSGGQ MKKPGESMRI SCRASGYEFI DCTLNWIRLA PGKRPEWMGW LKPRGGAVNY ARPLQGRVTM TRDVYSDTAF LELRSLTVDD TAVYFCTRGK NCDYNWDFEH WGRGTPVIVS SPSTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV SWNSGALTSG ...String:
QVQLVQSGGQ MKKPGESMRI SCRASGYEFI DCTLNWIRLA PGKRPEWMGW LKPRGGAVNY ARPLQGRVTM TRDVYSDTAF LELRSLTVDD TAVYFCTRGK NCDYNWDFEH WGRGTPVIVS SPSTKGPSVF PLAPSSKSTS GGTAALGCLV KDYFPEPVTV SWNSGALTSG VHTFPAVLQS SGLYSLSSVV TVPSSSLGTQ TYICNVNHKP SNTKVDKKAE PKSC

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Macromolecule #3: light chain of VRC01 Fab

MacromoleculeName: light chain of VRC01 Fab / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString: EIVLTQSPGT LSLSPGETAI ISCRTSQYGS LAWYQQRPGQ APRLVIYSGS TRAAGIPDRF SGSRWGPDYN LTISNLESGD FGVYYCQQYE FFGQGTKVQV DIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL QSGNSQESVT EQDSKDSTYS ...String:
EIVLTQSPGT LSLSPGETAI ISCRTSQYGS LAWYQQRPGQ APRLVIYSGS TRAAGIPDRF SGSRWGPDYN LTISNLESGD FGVYYCQQYE FFGQGTKVQV DIKRTVAAPS VFIFPPSDEQ LKSGTASVVC LLNNFYPREA KVQWKVDNAL QSGNSQESVT EQDSKDSTYS LSSTLTLSKA DYEKHKVYAC EVTHQGLRSP VTKSFNRGEC

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.008 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
0.2 g/LKCLPotassium chloride
0.24 g/LKH2PO4Potassium dihydrogen phosphate
8.0 g/LNaClSodium chloride
1.44 g/LNa2HPODisodium phosphate

Details: PBS
StainingType: NEGATIVE / Material: Uranyl Formate
Details: Sample diluted to 0.008 mg/mL. 8 uL was applied onto the grid, blotted off, and then stained with 2% uranyl formate for 120 seconds.
GridModel: Homemade / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE

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Electron microscopy

MicroscopeTFS TALOS L120C
Image recordingFilm or detector model: FEI CETA (4k x 4k) / Number real images: 55 / Average exposure time: 2.0 sec. / Average electron dose: 466.38 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 10.644 µm / Nominal defocus min: 12.455 µm / Nominal magnification: 73000
Experimental equipment
Model: Talos L120C / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 12.16 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 14636
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3)

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