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- EMDB-44342: RM018 Fab in complex with Apex GT 6.2 trimer and RM20A3 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-44342
TitleRM018 Fab in complex with Apex GT 6.2 trimer and RM20A3 Fab
Map data
Sample
  • Complex: RM018 Fab in complex with Apex-GT6.2 trimer and RM20A3 Fab
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: Transmembrane protein gp41
    • Protein or peptide: RM20A3 fragment antigen binding light chain
    • Protein or peptide: RM018 fragment antigen binding heavy chain
    • Protein or peptide: RM20A3 fragment antigen binding heavy chain
    • Protein or peptide: RM018 fragment antigen binding light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV Env / immune complex / macaque antibody / VIRAL PROTEIN / V1V2 apex / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / identical protein binding / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsPratap PP / Ozorowski G / Ward AB
Funding support United States, 2 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-002916 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI144462 United States
CitationJournal: To Be Published
Title: Induction of HIV broadly neutralizing antibody precursors to the Apex epitope in rhesus macaques
Authors: Ma KM / Sutton H / Pratap PP / Ozorowski G / Ward AB / Crotty S / Schief WR
History
DepositionMar 29, 2024-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44342.png

Downloads & links

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Map

FileDownload / File: emd_44342.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 400 pix.
= 522. Å		1.31 Å/pix.
x 400 pix.
= 522. Å		1.31 Å/pix.
x 400 pix.
= 522. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.305 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.8071387 - 1.5298266
Average (Standard dev.)0.000294873 (±0.023918668)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 522.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_44342_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_44342_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_44342_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 : RM018 Fab in complex with Apex-GT6.2 trimer and RM20A3 Fab

EntireName: RM018 Fab in complex with Apex-GT6.2 trimer and RM20A3 Fab
Components
  • Complex: RM018 Fab in complex with Apex-GT6.2 trimer and RM20A3 Fab
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: Transmembrane protein gp41
    • Protein or peptide: RM20A3 fragment antigen binding light chain
    • Protein or peptide: RM018 fragment antigen binding heavy chain
    • Protein or peptide: RM20A3 fragment antigen binding heavy chain
    • Protein or peptide: RM018 fragment antigen binding light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: RM018 Fab in complex with Apex-GT6.2 trimer and RM20A3 Fab

SupramoleculeName: RM018 Fab in complex with Apex-GT6.2 trimer and RM20A3 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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Macromolecule #1: Envelope glycoprotein gp120

MacromoleculeName: Envelope glycoprotein gp120 / type: protein_or_peptide / ID: 1 / Details: HIV-1 Env Apex-GT6 gp120 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 52.220219 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVSTDPN PQEIHLENVT EEFNMWKNNM VEQMHEDIIS LWDQSLKPC VKLTPLCVGL QCTNVTNNIT DDMRGELKNC SFNATTELRN KRQKVYSLFY RLDIVPMVDL WTNYRLISCN T SAITQACP ...String:
AENLWVTVYY GVPVWKDAET TLFCASDAKA YETEKHNVWA THACVSTDPN PQEIHLENVT EEFNMWKNNM VEQMHEDIIS LWDQSLKPC VKLTPLCVGL QCTNVTNNIT DDMRGELKNC SFNATTELRN KRQKVYSLFY RLDIVPMVDL WTNYRLISCN T SAITQACP KVSFEPIPIH YCAPAGFAIL KCKDKKFNGT GPCQNVSTVQ CTHGIKPVVS TQLLLNGSLA EEEVIIRSEN IT NNAKNIL VQLNTSVQIN CTRPNNNTVK SIRIGPGQAF YYTGDIIGDI RQAHCNVSKA TWNETLGKVV KQLRKHFGNN TII RFAQSS GGDLEVTTHS FNCGGEFFYC NTSGLFNSTW ISNTSVQGSN STGSNDSITL PCRIKQIINM WQRIGQAMYA PPIQ GVIRC VSNITGLILT RDGGSTNSTT ETFRPGGGDM RDNWRSELYK YKVVKIEPLG VAPTRCKRRV VG

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #2: Transmembrane protein gp41

MacromoleculeName: Transmembrane protein gp41 / type: protein_or_peptide / ID: 2 / Details: HIV-1 Env Apex-GT6 gp41 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.134324 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVSLG FLGAAGSTMG AASMTLTVQA RNLLSGIVQQ QSNLLRAPEP QQHLLKDTHW GIKQLQARVL AVEHYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNRNLS EIWDNMTWLQ WDKEISNYTQ IIYGLLEESQ NQQEKNEQDL LALD

UniProtKB: Envelope glycoprotein gp160

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Macromolecule #3: RM20A3 fragment antigen binding light chain

MacromoleculeName: RM20A3 fragment antigen binding light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 13.5088 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
ALTQPPSVSG SPGQSVTISC TGTSSDIGSY NYVSWYQQHP GKAPKLMIYD VTQRPSGVSD RFSGSKSGNT ASLTISGLQA DDEADYYCS AYAGRQTFYI FGGGTRLTVL GQPKASPTVT LFPPSSEEL

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Macromolecule #4: RM018 fragment antigen binding heavy chain

MacromoleculeName: RM018 fragment antigen binding heavy chain / type: protein_or_peptide / ID: 4
Details: Sulfated tyrosine (post translational modification)
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 14.729432 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVQSGAE VKKPGASVKL SCKASGYTFS IYAITWVRQA PGQGLEWMGG IIPLVGITNY AQKFQGRVTI TADTSTTTAY MELSSLRSE DTAVYYCSRG LGPSIETEDD YD(TYS)SYTSEYN LLHVWGRGVL VTVSS

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Macromolecule #5: RM20A3 fragment antigen binding heavy chain

MacromoleculeName: RM20A3 fragment antigen binding heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 13.511111 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
EVQLVETGGG LVQPGGSLKL SCRASGYTFS SFAMSWVRQA PGKGLEWVSL INDRGGLTFY VDSVKGRFTI SRDNSKNTLS LQMHSLRDG DTAVYYCATG GMSSALQSSK YYFDFWGQGA LVTVSS

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Macromolecule #6: RM018 fragment antigen binding light chain

MacromoleculeName: RM018 fragment antigen binding light chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 22.984229 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QAALTQPRSV SESPGQSVTF SCTGTSSDIG GYNYVSWFQQ HPETAPKLMI YEVSKRPSGV SDRFSGSKSG NTASLTISGL QAEDEADYY CSSYADSNTL VFGGGTRLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP ...String:
QAALTQPRSV SESPGQSVTF SCTGTSSDIG GYNYVSWFQQ HPETAPKLMI YEVSKRPSGV SDRFSGSKSG NTASLTISGL QAEDEADYY CSSYADSNTL VFGGGTRLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP SKQSNNKYAA SSYLSLTPEQ WKSHRSYSCQ VTHEGSTVEK TVAPTECS

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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: 48 / 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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (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: 1.7 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 190000

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7t73

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 108789
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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