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- EMDB-71782: Cryo-EM structure of HIV-1 459C-ALT DS-SOSIP RnS Env trimer -

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Basic information

Entry
Database: EMDB / ID: EMD-71782
TitleCryo-EM structure of HIV-1 459C-ALT DS-SOSIP RnS Env trimer
Map data
Sample
  • Complex: HIV-1 Env 459C-ALT RnS DS-SOSIP
    • Protein or peptide: HIV-1 459C-ALT RnS DS-SOSIP gp41
    • Protein or peptide: HIV-1 459C-ALT RnS DS-SOSIP gp120
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsEnvelope trimer / 459C-ALT / RnS DS-SOSIP immunogen / VIRAL PROTEIN
Biological speciesHuman immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.94 Å
AuthorsWang S / Zhou T / Kwong PD / Morano NC / Shapiro L
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: Dual Vaccine Elicitation of HIV-1 Neutralizing Antibodies against V2 Apex and Fusion Peptide
Authors: Duan H / Nkolola JP / Wang S / Kwong PD / Barouch DH / Zhou T
History
DepositionJul 22, 2025-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71782.png

Downloads & links

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Map

FileDownload / File: emd_71782.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 432 pix.
= 356.4 Å		0.83 Å/pix.
x 432 pix.
= 356.4 Å		0.83 Å/pix.
x 432 pix.
= 356.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0275
Minimum - Maximum-0.105617076 - 0.24857686
Average (Standard dev.)0.00019075423 (±0.0075267553)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 356.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_71782_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_71782_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 : HIV-1 Env 459C-ALT RnS DS-SOSIP

EntireName: HIV-1 Env 459C-ALT RnS DS-SOSIP
Components
  • Complex: HIV-1 Env 459C-ALT RnS DS-SOSIP
    • Protein or peptide: HIV-1 459C-ALT RnS DS-SOSIP gp41
    • Protein or peptide: HIV-1 459C-ALT RnS DS-SOSIP gp120
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HIV-1 Env 459C-ALT RnS DS-SOSIP

SupramoleculeName: HIV-1 Env 459C-ALT RnS DS-SOSIP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: HIV-1 459C-ALT RnS DS-SOSIP gp41

MacromoleculeName: HIV-1 459C-ALT RnS DS-SOSIP gp41 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.137424 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASNTLTVQA RQLLSGIVQQ QSNLPKAPEA QQHLLQLTVW GIKQLQTRVL AIERYLEVQQ LLGLWGCSG KLICCTAVPW NSSWSNKSET EIWNNMTWMQ WDREISNYTN TIYRLLEESQ FQQEINEVDL LALD

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Macromolecule #2: HIV-1 459C-ALT RnS DS-SOSIP gp120

MacromoleculeName: HIV-1 459C-ALT RnS DS-SOSIP gp120 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 53.049219 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GNLWVTVYYG VPVWREAETT LFCASDAKAY DREVHNVWAT HACVPTDPNP QEIVLENVTE NFNMWKNDMV DQMHEDIISL WDQSLKPCV KLTPLCVTLD CKAFNSSSHT NSSIAMQEMK NCTFNITTSV KGKRQQEHAL FYKLDIVPLN KNGRQYRLIN C NTSTITQA ...String:
GNLWVTVYYG VPVWREAETT LFCASDAKAY DREVHNVWAT HACVPTDPNP QEIVLENVTE NFNMWKNDMV DQMHEDIISL WDQSLKPCV KLTPLCVTLD CKAFNSSSHT NSSIAMQEMK NCTFNITTSV KGKRQQEHAL FYKLDIVPLN KNGRQYRLIN C NTSTITQA CPKVSFDPIP IHYCTPAGYA ILKCNNKTFN GTGPCNNVST VQCTHGIKPV VSTQLLLNGS LAEEDIIIRS EN LTNNAKT IIVHLNESVE IVCVRPNNMT RKSIRIGPGQ TFYALNEIIG DIRQAHCNIS KEKWNNTLHR VWKKLVEHFP NKT TIRFDR HSGGDLEITT HSFNCGGEFF YCNTSGLFNI TYNSNYTYND TKHNGTKVIT LPCRIKQIIN MWQEVGRAMY APPI AGNIT CTSNITGLLL TRDGGNNSTE TETFRPGGGD MRDNWRSELY KYKVVEIKPL GIAPTGCKRR VVER

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 15 / 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

BufferpH: 7.4 / Details: PBS + 0.005% (w/v) DDM
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8fr6

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.94 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 158204
Initial angle assignmentType: NOT APPLICABLE / Software - Name: UCSF ChimeraX (ver. 1.9)
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.4.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-9pq3:
Cryo-EM structure of HIV-1 459C-ALT DS-SOSIP RnS Env trimer

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