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- EMDB-73007: PC94-A.16 Fab in complex with P94_v18_c046 Chimera DS-SOSIP trime... -

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Basic information

Entry
Database: EMDB / ID: EMD-73007
TitlePC94-A.16 Fab in complex with P94_v18_c046 Chimera DS-SOSIP trimer and RM20A3 Fab
Map datasharpened map
Sample
  • Complex: PC94-A.16 Fab in complex with P94_v18_c046 Chimera DS-SOSIP trimer and RM20A3 Fab
    • Protein or peptide: RM20A3 Fab heavy chain
    • Protein or peptide: RM20A3 light chain
    • Protein or peptide: P94_v18_c046 Chimera DS-SOSIP gp120
    • Protein or peptide: PC94-A.16 Fab heavy chain
    • Protein or peptide: PC94-A.16 light chain
    • Protein or peptide: P94_v18_c046 Chimera DS-SOSIP gp41
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV / broadly neutralizing antibody / bnAb / V3-glycan / N332 / Env / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesHomo sapiens (human) / Macaca mulatta (Rhesus monkey) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsPhulera S / Omorodion O / Ward AB / Ozorowski G
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI144462 United States
CitationJournal: To Be Published
Title: Tolerance of multiple glycan conformations by an N332-directed HIV bnAb lineage provides a roadmap to broad neutralization
Authors: Nemoz B / Rouzeau R
History
DepositionOct 3, 2025-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73007.png

Downloads & links

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Map

FileDownload / File: emd_73007.map.gz / Format: CCP4 / Size: 729 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.)
0.72 Å/pix.
x 576 pix.
= 413.568 Å		0.72 Å/pix.
x 576 pix.
= 413.568 Å		0.72 Å/pix.
x 576 pix.
= 413.568 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.718 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.33366433 - 0.4617231
Average (Standard dev.)-0.000060016082 (±0.007062038)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions576576576
Spacing576576576
CellA=B=C: 413.568 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_73007_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_73007_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_73007_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PC94-A.16 Fab in complex with P94_v18_c046 Chimera DS-SOSIP trime...

EntireName: PC94-A.16 Fab in complex with P94_v18_c046 Chimera DS-SOSIP trimer and RM20A3 Fab
Components
  • Complex: PC94-A.16 Fab in complex with P94_v18_c046 Chimera DS-SOSIP trimer and RM20A3 Fab
    • Protein or peptide: RM20A3 Fab heavy chain
    • Protein or peptide: RM20A3 light chain
    • Protein or peptide: P94_v18_c046 Chimera DS-SOSIP gp120
    • Protein or peptide: PC94-A.16 Fab heavy chain
    • Protein or peptide: PC94-A.16 light chain
    • Protein or peptide: P94_v18_c046 Chimera DS-SOSIP gp41
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: PC94-A.16 Fab in complex with P94_v18_c046 Chimera DS-SOSIP trime...

SupramoleculeName: PC94-A.16 Fab in complex with P94_v18_c046 Chimera DS-SOSIP trimer and RM20A3 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: RM20A3 Fab heavy chain

MacromoleculeName: RM20A3 Fab heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 24.194145 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVETGGG LVQPGGSLKL SCRASGYTFS SFAMSWVRQA PGKGLEWVSL INDRGGLTFY VDSVKGRFTI SRDNSKNTLS LQMHSLRDG DTAVYYCATG GMSSALQSSK YYFDFWGQGA LVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS ...String:
EVQLVETGGG LVQPGGSLKL SCRASGYTFS SFAMSWVRQA PGKGLEWVSL INDRGGLTFY VDSVKGRFTI SRDNSKNTLS LQMHSLRDG DTAVYYCATG GMSSALQSSK YYFDFWGQGA LVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VDKKVEPKSC D

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Macromolecule #2: RM20A3 light chain

MacromoleculeName: RM20A3 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 22.82715 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ALTQPPSVSG SPGQSVTISC TGTSSDIGSY NYVSWYQQHP GKAPKLMIYD VTQRPSGVSD RFSGSKSGNT ASLTISGLQA DDEADYYCS AYAGRQTFYI FGGGTRLTVL GQPKAAPSVT LFPPSSEELQ ANKATLVCLI SDFYPGAVTV AWKADSSPVK A GVETTTPS ...String:
ALTQPPSVSG SPGQSVTISC TGTSSDIGSY NYVSWYQQHP GKAPKLMIYD VTQRPSGVSD RFSGSKSGNT ASLTISGLQA DDEADYYCS AYAGRQTFYI FGGGTRLTVL GQPKAAPSVT LFPPSSEELQ ANKATLVCLI SDFYPGAVTV AWKADSSPVK A GVETTTPS KQSNNKYAAS SYLSLTPEQW KSHRSYSCQV THEGSTVEKT VAPTECS

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Macromolecule #3: P94_v18_c046 Chimera DS-SOSIP gp120

MacromoleculeName: P94_v18_c046 Chimera DS-SOSIP gp120 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 56.276164 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MMPMGSLQPL ATLYLLGMLV ASVLAQQAEN LWVTVYYGVP VWREATTTLF CASDAKSYET EAHNIWATHA CVPTDPSPQE IELKNVTEN FNMWKNNMVE QMHEDVISLW AQSLKPCVRL TPLCVTLNCT ELKNKTVSNT TEEIEMRNCS FNITTELRDK K KQVYALFY ...String:
MMPMGSLQPL ATLYLLGMLV ASVLAQQAEN LWVTVYYGVP VWREATTTLF CASDAKSYET EAHNIWATHA CVPTDPSPQE IELKNVTEN FNMWKNNMVE QMHEDVISLW AQSLKPCVRL TPLCVTLNCT ELKNKTVSNT TEEIEMRNCS FNITTELRDK K KQVYALFY RPDVVSIDDD NTSYRLINCN TSVCTQACPK ISFEPIPIHY CAPAGFAILK CKDEEFNGTG PCRNVSTVQC TH GIKPVVS TQLLLNGSLA EKEIRIRSEN ISDNAKTIIV QLTKPVAINC TRPNNNTRKS IHIGPGQAFY ATGDIIGDIR QAH CNVSKS DWTNTLQQVA EQLKKLWNNK TIIFANHTGG DVEITTHSFN CGGEFFYCNT SGLFNSNWTD NSTTVNSTEI SNTS IILPC RIKQIVNMWQ EVGKCMYAPP IEGLIRCSSN ITGILLTRDG GINRTNNETF RPGGGNMKDN WRSELYKYKV VKIEP LGVA PTRCKRRVVG RRRRRR

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Macromolecule #4: PC94-A.16 Fab heavy chain

MacromoleculeName: PC94-A.16 Fab heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.153307 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGSE VKRPGASVKV SCKASGYTFT DHPISWVRQA PGAGLEWMGW LSFHNGVANY AQKFQGRVIM TTDTSTGTAY MELRSLKSD DTALYYCART PMRIYGLIVF NEYYYDAMDV WGQGTTVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV K DYFPEPVT ...String:
QVQLVQSGSE VKRPGASVKV SCKASGYTFT DHPISWVRQA PGAGLEWMGW LSFHNGVANY AQKFQGRVIM TTDTSTGTAY MELRSLKSD DTALYYCART PMRIYGLIVF NEYYYDAMDV WGQGTTVTVS SASTKGPSVF PLAPSSKSTS GGTAALGCLV K DYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV EPKSCD

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Macromolecule #5: PC94-A.16 light chain

MacromoleculeName: PC94-A.16 light chain / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.732234 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPST LSASVGDRVT ITCRTSQYVR NCLAWYQQKA GRAPTLLIHQ TSTLHSGVPS RFSGSGSGTE FTLTISSLQP DDFATYYCQ QCYYNGYWTF GQGTKVEVNR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
DIQMTQSPST LSASVGDRVT ITCRTSQYVR NCLAWYQQKA GRAPTLLIHQ TSTLHSGVPS RFSGSGSGTE FTLTISSLQP DDFATYYCQ QCYYNGYWTF GQGTKVEVNR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #6: P94_v18_c046 Chimera DS-SOSIP gp41

MacromoleculeName: P94_v18_c046 Chimera DS-SOSIP gp41 / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 20.88742 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEA QQHLLKLTVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALDGSGSGH H HHHHHHHH GSGGLNDIFE AQKIEWHE

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Macromolecule #11: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 11 / Number of copies: 30 / 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

Concentration5.0 mg/mL
BufferpH: 7.4
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: ab initio model from cryosparc
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 166412
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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