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- EMDB-26706: Cryo-EM structure of SHIV-elicited, FP-directed Rhesus Fab RM6561... -

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Basic information

Entry
Database: EMDB / ID: EMD-26706
TitleCryo-EM structure of SHIV-elicited, FP-directed Rhesus Fab RM6561.DH1021.14 in complex with stabilized HIV-1 Env Ce1176 DS-SOSIP.664
Map datasharpened map
Sample
  • Complex: Fab RM6561.DH1021.14 with stabilized HIV-1 Env Ce1176
    • Protein or peptide: gp120
    • Protein or peptide: gp41
    • Protein or peptide: Heavy Chain
    • Protein or peptide: Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsFP / HIV-1 / SOSIP / Vaccine / IMMUNE SYSTEM / Rhesus / SHIV / VIRAL PROTEIN / VIRAL PROTEIN-Immune System complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host defense response / 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 ...symbiont-mediated perturbation of host defense response / 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 / 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 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1 / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsGorman J / Kwong PD
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
Other privateSimons Foundation (SF349247)
CitationJournal: To Be Published
Title: Cryo-EM structure of SHIV-elicited, FP-directed Rhesus Fab RM6561.DH1021.14 in complex with stabilized HIV-1 Env Ce1176 DS-SOSIP.664
Authors: Gorman J / Kwong PD
History
DepositionApr 21, 2022-
Header (metadata) releaseApr 26, 2023-
Map releaseApr 26, 2023-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26706.png

Downloads & links

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Map

FileDownload / File: emd_26706.map.gz / Format: CCP4 / Size: 125 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.)
1.08 Å/pix.
x 320 pix.
= 346.56 Å		1.08 Å/pix.
x 320 pix.
= 346.56 Å		1.08 Å/pix.
x 320 pix.
= 346.56 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.083 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.2629692 - 0.8430627
Average (Standard dev.)0.004016307 (±0.02506657)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 346.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_26706_msk_1.map
Projections & Slices
AxesZYX

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Additional map: Density modified with resolve

Fileemd_26706_additional_1.map
AnnotationDensity modified with resolve
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: unsharpened map

Fileemd_26706_additional_2.map
Annotationunsharpened map
Projections & Slices
AxesZYX

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Histogram

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Half map: half map A

Fileemd_26706_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_26706_half_map_2.map
Annotationhalf map B
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Sample components

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Entire : Fab RM6561.DH1021.14 with stabilized HIV-1 Env Ce1176

EntireName: Fab RM6561.DH1021.14 with stabilized HIV-1 Env Ce1176
Components
  • Complex: Fab RM6561.DH1021.14 with stabilized HIV-1 Env Ce1176
    • Protein or peptide: gp120
    • Protein or peptide: gp41
    • Protein or peptide: Heavy Chain
    • Protein or peptide: Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Fab RM6561.DH1021.14 with stabilized HIV-1 Env Ce1176

SupramoleculeName: Fab RM6561.DH1021.14 with stabilized HIV-1 Env Ce1176 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: gp120

MacromoleculeName: gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 53.648887 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPAENLWVTV YYGVPVWKEA KTTLFCASDA KAYEKEVHNV WATHACVPTD PNPQEMVLEN VTENFNMWKN DMVDQMHEDV ISLWDQSLK PCVKLTPLCV TLNCTNTTVS NGSSNSNANF EEMKNCSFNA TTEIKDKKKN EYALFYKLDI VPLNNSSGKY R LINCNTSA ...String:
GPAENLWVTV YYGVPVWKEA KTTLFCASDA KAYEKEVHNV WATHACVPTD PNPQEMVLEN VTENFNMWKN DMVDQMHEDV ISLWDQSLK PCVKLTPLCV TLNCTNTTVS NGSSNSNANF EEMKNCSFNA TTEIKDKKKN EYALFYKLDI VPLNNSSGKY R LINCNTSA CTQICPKVTF EPIPIHYCAP AGYAILKCNN KTFNGTGPCN NVSTVQCTHG IKPVVSTQLL LNGSLAEKEI II RSENLTN NAKTIIVHLN ESVGIVCTRP SNMTRKSIRI GPGQTFYALG DIIGDIRQPH CNISKQNWNR TLQQVGRKLA EHF PNRNIT FNHSSGGDLE ITTHSFNCRG EFFYCNTSGL FNGTYHPNGT YNETAVNSSD TITLQCRIKQ IINMWQEVGR CMYA PPIAG NITCNSNITG LLLTRDGGIN QTGEEIFRPG GGDMRDNWRS ELYKYKVVEI KPLGIAPTKC KRRVVERRRR RR

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #2: gp41

MacromoleculeName: gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.24051 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASNTLTVQA RQLLSGIVQQ QSNLLRAPEA QQHMLQLGVW GFKQLQARVL AIERYLEVQQ LLGIWGCSG KLICCTNVPW NSTWSNRTQE DIWNNMTWME WEREIGNYTH TIYSLLEESQ FQQEINEKDL LALD

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #3: Heavy Chain

MacromoleculeName: Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 14.505475 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVTLKESGPA LVKPTQTLTL TCTFSGFSMS NFGSGIYWIR QPPGKALEWL AGIYWTDSKY YNLSLKTRLT ISKDTSKSQV ILIMTNMDP VDTATYYCAD IRGRYYYSNG FLFDVVGVES WGQGVVVTVS S

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Macromolecule #4: Light Chain

MacromoleculeName: Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 11.679873 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSVLTQPPSA SEAARKTVTI SCSGSRSNIG SNSVSWYKQV PGTAPKLLIK YNDQRPSGVS DRFSGSKSGT SASLAISGLQ TEDEADYYC ATWDDSLNGY IFGVGTRLIV L

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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: 42 / 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 - Concentration: 1.0 X / Component - Formula: PBS / Component - Name: PBS
GridModel: C-flat-1.2/1.3 / 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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average exposure time: 2.0 sec. / Average electron dose: 51.27 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 / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15) / Number images used: 13272
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 modelPDB ID:

6vtt


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7ur6:
Cryo-EM structure of SHIV-elicited, FP-directed Rhesus Fab RM6561.DH1021.14 in complex with stabilized HIV-1 Env Ce1176 DS-SOSIP.664

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