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- EMDB-70613: Cryo-EM structure of rhesus antibody V033-Int1 in complex with HI... -

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Basic information

Entry
Database: EMDB / ID: EMD-70613
TitleCryo-EM structure of rhesus antibody V033-Int1 in complex with HIV Env trimer Q23.17 MD39
Map data
Sample
  • Complex: V033-Int1 Fab in complex with Q23.17 MD39 envelope trimer
    • Protein or peptide: HIV Env gp120
    • Protein or peptide: HIV Env gp41 ectodomain
    • Protein or peptide: V033-Int1 heavy chain
    • Protein or peptide: V033-Int1 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsNeutralizing antibody / HIV-1 V2 apex / SHIV-elicited / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesMacaca mulatta (Rhesus monkey) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsRoark RS / Shapiro L / Kwong PD
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: Env-antibody coevolution identifies B cell priming as the principal bottleneck to HIV-1 V2 apex broadly neutralizing antibody development
Authors: Habib R / Roark RS / Kwong PD / Shaw GM
History
DepositionMay 13, 2025-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70613.png

Downloads & links

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Map

FileDownload / File: emd_70613.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 320 pix.
= 342.4 Å		1.07 Å/pix.
x 320 pix.
= 342.4 Å		1.07 Å/pix.
x 320 pix.
= 342.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.2518351 - 0.6150859
Average (Standard dev.)0.00017142811 (±0.017275983)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 342.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_70613_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_70613_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 : V033-Int1 Fab in complex with Q23.17 MD39 envelope trimer

EntireName: V033-Int1 Fab in complex with Q23.17 MD39 envelope trimer
Components
  • Complex: V033-Int1 Fab in complex with Q23.17 MD39 envelope trimer
    • Protein or peptide: HIV Env gp120
    • Protein or peptide: HIV Env gp41 ectodomain
    • Protein or peptide: V033-Int1 heavy chain
    • Protein or peptide: V033-Int1 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: V033-Int1 Fab in complex with Q23.17 MD39 envelope trimer

SupramoleculeName: V033-Int1 Fab in complex with Q23.17 MD39 envelope trimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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Macromolecule #1: HIV Env gp120

MacromoleculeName: HIV Env gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.996059 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VENLWVTVYY GVPVWRDADT TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLDNVT EKFNMWKNNM VEQMHEDIIS LWDQSLKPC VKLTPLCVTL HCTNVTSVNT TGDREGLKNC SFNMTTELRD KRQKVYSLFY RLDIVPINEN QGSEYRLINC N TSAITQAC ...String:
VENLWVTVYY GVPVWRDADT TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLDNVT EKFNMWKNNM VEQMHEDIIS LWDQSLKPC VKLTPLCVTL HCTNVTSVNT TGDREGLKNC SFNMTTELRD KRQKVYSLFY RLDIVPINEN QGSEYRLINC N TSAITQAC PKVSFEPIPI HYCTPAGFAI LKCKDEGFNG TGLCKNVSTV QCTHGIKPVV STQLLLNGSL AEKNIIIRSE NI TNNAKII IVQLVQPVTI KCIRPNNNTV KSIRIGPGQA FYYTGDIIGD IRQAHCNVTR SRWNKTLQEV AEKLRTYFGN KTI IFANSS GGDLEITTHS FNCGGEFFYC NTSGLFNSTW YVNSTWNDTD STQESNDTIT LPCRIKQIIN MWQRAGQAMY APPI PGVIK CESNITGLLL TRDGGKDNNV NETFRPGGSD MRDNWRSELY KYKVVEIEPL GVAPTRCKRR VVER

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Macromolecule #2: HIV Env gp41 ectodomain

MacromoleculeName: HIV Env gp41 ectodomain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.315576 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVSLG FLGAAGSTMG AASITLTVQA RNLLSGIVQQ QNNLLRAPEP QQHLLKDTHW GIKQLQARVL AVEHYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNKSLD EIWNNMTWLQ WDKEINNYTQ LIYRLIEESQ NQQEKNEKEL LELD

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Macromolecule #3: V033-Int1 heavy chain

MacromoleculeName: V033-Int1 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 26.214199 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGGG LAKPGGSLRL SCAASGFTFS SYWMNWVRQT PGKGLEWISA INSGGGSTYY ADSVKGRFTI SRDNSKNTLS LQMNSLRAE DTAVYYCAKV DEDDYGYYYT VPGDLKKYYF DYWGQGVLVT VSSASTKGPS VFPLAPSSRS TSESTAALGC L VKDYFPEP ...String:
EVQLVESGGG LAKPGGSLRL SCAASGFTFS SYWMNWVRQT PGKGLEWISA INSGGGSTYY ADSVKGRFTI SRDNSKNTLS LQMNSLRAE DTAVYYCAKV DEDDYGYYYT VPGDLKKYYF DYWGQGVLVT VSSASTKGPS VFPLAPSSRS TSESTAALGC L VKDYFPEP VTVSWNSGSL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYVCNVN HKPSNTKVDK RVEIKTCGGG LE VLFQ

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Macromolecule #4: V033-Int1 light chain

MacromoleculeName: V033-Int1 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 23.199662 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LSASVGDKVT ITCQASQSIS SWLAWYQQKP GKAPKPLIYK ASSLESGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QYNSAPFSFG QGTKVEIKRT VAAPSVFIFP PSEDQVKSGT VSVVCLLNNF YPREASVKWK VDGALKTGNS Q ESVTEQDS ...String:
DIQMTQSPSS LSASVGDKVT ITCQASQSIS SWLAWYQQKP GKAPKPLIYK ASSLESGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QYNSAPFSFG QGTKVEIKRT VAAPSVFIFP PSEDQVKSGT VSVVCLLNNF YPREASVKWK VDGALKTGNS Q ESVTEQDS KDNTYSLSST LTLSSTEYQS HKVYACEVTH QGLSSPVTKS FNRGEC

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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: 16 / 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: 7.5
VitrificationCryogen name: ETHANE

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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 / 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 correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9bnp

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 155379
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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