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- EMDB-71781: Cryo-EM structure of HIV-1 459C-WT DS-SOSIP RnS Env trimer -

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Basic information

Entry
Database: EMDB / ID: EMD-71781
TitleCryo-EM structure of HIV-1 459C-WT DS-SOSIP RnS Env trimer
Map data
Sample
  • Complex: HIV-1 Env 459C-WT RnS DS-SOSIP
    • Protein or peptide: 459C-WT RnS DS-SOSIP gp120
    • Protein or peptide: 459C-WT RnS DS-SOSIP gp41
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsEnvelope trimer / 459C-WT / RnS DS-SOSIP immunogen / VIRAL PROTEIN
Biological speciesHuman immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.33 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_71781.png

Downloads & links

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Map

FileDownload / File: emd_71781.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: 0.0259
Minimum - Maximum-0.145197 - 0.36928993
Average (Standard dev.)0.00013951071 (±0.008590148)
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: #2

Fileemd_71781_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_71781_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-WT RnS DS-SOSIP

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

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

SupramoleculeName: HIV-1 Env 459C-WT 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: 459C-WT RnS DS-SOSIP gp120

MacromoleculeName: 459C-WT RnS DS-SOSIP gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 54.848867 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GNLWVTVYYG VPVWREAKTT LFCASDAKAY DREVHNVWAT HACVPTDPNP QEIVLENVTE NFNMWKNDMV DQMHEDIISL WDQSLKPCV KLTPLCVTLN CTNVTSSAAN VTSNVTNDAN NASNANGRNV INEDMKNCSF NATTEIRDRK KEMYALFYKL D IVPLDGEK ...String:
GNLWVTVYYG VPVWREAKTT LFCASDAKAY DREVHNVWAT HACVPTDPNP QEIVLENVTE NFNMWKNDMV DQMHEDIISL WDQSLKPCV KLTPLCVTLN CTNVTSSAAN VTSNVTNDAN NASNANGRNV INEDMKNCSF NATTEIRDRK KEMYALFYKL D IVPLDGEK SDNRYRLINC NTSTITQACP KVSFDPIPIH YCTPAGFAIL KCNNKTFNGT GPCNNVSTVQ CTHGIKPVVS TQ LLLNGSL AEEDIIIRSE NLTNNAKTII VHLNESVEIV CTRPNNMTRK SIRIGPGQTF YALNDIIGDI RQAHCNISEE KWN NTLHRV WKKLVEHFPN KTTIRFDRHS GGDLEITTHS FNCGGEFFYC NTSGLFNITY NSNYTYNDTK HNGTKVITLP CRIK QIINM WQEVGRAMYA PPIAGNITCT SNITGLLLTR DGGNNSTETE TFRPGGGDMR DNWRSELYKY KVVEIKPLGI APTGC KRRV VER

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Macromolecule #2: 459C-WT RnS DS-SOSIP gp41

MacromoleculeName: 459C-WT RnS DS-SOSIP gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.164449 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASNTLTVQA RQLLSGIVQQ QSNLPKAPEA QQHLLQLTVW GIKQLQTRVL AIERYLEVQQ LLGLWGCSG KLICCTAVPW NSSWSNKSET EIWNNMTWMQ WDREINNYTN TIYRLLEESQ FQQEINEVDL LALD

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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: 9 / 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
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: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 207797
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-9pq2:
Cryo-EM structure of HIV-1 459C-WT DS-SOSIP RnS Env trimer

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