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- EMDB-71772: Cryo-EM structure of K001-A1 Fab in complex with HIV-1 459C-OPT R... -

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Basic information

Entry
Database: EMDB / ID: EMD-71772
TitleCryo-EM structure of K001-A1 Fab in complex with HIV-1 459C-OPT RnS DS-SOSIP Env trimer
Map data
Sample
  • Complex: HIV-1 Env 459C-OPT RnS DS-SOSIP in complex with antibody Fab
    • Protein or peptide: K001-A1 Fab heavy chain
    • Protein or peptide: K001-A1 Fab light chain
    • Protein or peptide: 459C-OPT probe RnS DS-SOSIP gp41
    • Protein or peptide: 459C-OPT probe RnS DS-SOSIP gp120
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsantibody-antigen complex / fusion peptide directed / viral surface glycoprotein / V2-directed antibody / ANTIVIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesHuman immunodeficiency virus 1 / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.01 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 21, 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_71772.png

Downloads & links

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Map

FileDownload / File: emd_71772.map.gz / Format: CCP4 / Size: 282.6 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 420 pix.
= 346.5 Å		0.83 Å/pix.
x 420 pix.
= 346.5 Å		0.83 Å/pix.
x 420 pix.
= 346.5 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: 0.029
Minimum - Maximum-0.30066913 - 0.5584142
Average (Standard dev.)-0.000102803715 (±0.011466683)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 346.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_71772_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_71772_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-OPT RnS DS-SOSIP in complex with antibody Fab

EntireName: HIV-1 Env 459C-OPT RnS DS-SOSIP in complex with antibody Fab
Components
  • Complex: HIV-1 Env 459C-OPT RnS DS-SOSIP in complex with antibody Fab
    • Protein or peptide: K001-A1 Fab heavy chain
    • Protein or peptide: K001-A1 Fab light chain
    • Protein or peptide: 459C-OPT probe RnS DS-SOSIP gp41
    • Protein or peptide: 459C-OPT probe RnS DS-SOSIP gp120
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: HIV-1 Env 459C-OPT RnS DS-SOSIP in complex with antibody Fab

SupramoleculeName: HIV-1 Env 459C-OPT RnS DS-SOSIP in complex with antibody Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: K001-A1 Fab heavy chain

MacromoleculeName: K001-A1 Fab heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 26.498471 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQQWGEG LVKPSETLSL TCAVYGGSIS GDYYWTWIRQ PPGMGLEWIG YIYGDTASTN YNPSLKNRVT ISKDTSKNQF SLKLDSVTA ADTAVYYCAR ECGGQQVLHD DD(TYS)DFYDPTI GLDSWGQGVV VTVSSASTKG PSVFPLAPSS KSTSGGT AA LGCLVKDYFP ...String:
QVQLQQWGEG LVKPSETLSL TCAVYGGSIS GDYYWTWIRQ PPGMGLEWIG YIYGDTASTN YNPSLKNRVT ISKDTSKNQF SLKLDSVTA ADTAVYYCAR ECGGQQVLHD DD(TYS)DFYDPTI GLDSWGQGVV VTVSSASTKG PSVFPLAPSS KSTSGGT AA LGCLVKDYFP EPVTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DKKVEPKS C DKGLEVLFQ

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Macromolecule #2: K001-A1 Fab light chain

MacromoleculeName: K001-A1 Fab light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 24.248904 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVMTQTPLS LPVTPGEPAS ISCRSSQSLL DSGDGNTYLD WYLQKPGQSP QPLIYEVSNR ASGVPDRFSG SGSDTDFTLR IRKVEAEDV GVYYCMQYTH IPWTFGQGTK VEIKRTVAAP SVFIFPPSDE QLKSGTASVV CLLNNFYPRE AKVQWKVDNA L QSGNSQES ...String:
DIVMTQTPLS LPVTPGEPAS ISCRSSQSLL DSGDGNTYLD WYLQKPGQSP QPLIYEVSNR ASGVPDRFSG SGSDTDFTLR IRKVEAEDV GVYYCMQYTH IPWTFGQGTK VEIKRTVAAP SVFIFPPSDE QLKSGTASVV CLLNNFYPRE AKVQWKVDNA L QSGNSQES VTEQDSKDST YSLSSTLTLS KADYEKHKVY ACEVTHQGLS SPVTKSFNRG EC

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Macromolecule #3: 459C-OPT probe RnS DS-SOSIP gp41

MacromoleculeName: 459C-OPT probe RnS DS-SOSIP gp41 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 19.924455 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASNTLTVQA RQLLSGIVQQ QSNLLKAPEA QQHLLQLGVW GFKQLQTRVL AIERYLEVQQ LLGLWGCSG KLICCTAVPW NSSWSNKSET EIWNNMTWMQ WDREISNYTN TIYRLLEESQ FQQEINEKDL LALDGGGLVP Q QSGGLNDI FEAQKIEWHE G

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Macromolecule #4: 459C-OPT probe RnS DS-SOSIP gp120

MacromoleculeName: 459C-OPT probe RnS DS-SOSIP gp120 / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 53.263703 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPNLWVTVYY GVPVWREAKT TLFCASDAKA YDREVHNVWA THACVPTDPN PQEIVLENVT ENFNMWKNDM VDQMHEDIIS LWDQSLKPC VKLTPLCVTL ECTAFNSSSH TNSSIAMQEM KNCSFNMTTE LRDKKKKVSA LFYKLDIVPL NKNGRQYRLI N CNTSTCTQ ...String:
GPNLWVTVYY GVPVWREAKT TLFCASDAKA YDREVHNVWA THACVPTDPN PQEIVLENVT ENFNMWKNDM VDQMHEDIIS LWDQSLKPC VKLTPLCVTL ECTAFNSSSH TNSSIAMQEM KNCSFNMTTE LRDKKKKVSA LFYKLDIVPL NKNGRQYRLI N CNTSTCTQ ICPKVSFDPI PIHYCTPAGY AILKCNNKTF NGTGPCNNVS TVQCTHGIKP VVSTQLLLNG SLAEEDIIIR SE NLTNNAK TIIVHLNESV EIVCIRPNNM TRKSIRIGPG QTFYALNDII GDIRQPHCNI SKEKWNNTLH RVWKKLVEHF PNK TIIFFD RHSGGDLEIT THSFNCGGEF FYCNTSGLFN ITYNSNYTYN DTKHNGTKVI TLPCRIKQII NMWQEVGRCM YAPP IAGNI TCTSNITGLL LTRDGGNNST ETETFRPGGG DMRDNWRSEL YKYKVVEIKP LGIAPTGCKR RVVER

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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: 24 / 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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.01 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 218288
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-9pnu:
Cryo-EM structure of K001-A1 Fab in complex with HIV-1 459C-OPT RnS DS-SOSIP Env trimer

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