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- EMDB-48523: RM017 Fab in complex with Apex-GT6.2 trimer and RM20A3 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-48523
TitleRM017 Fab in complex with Apex-GT6.2 trimer and RM20A3 Fab
Map dataEM map
Sample
  • Complex: RM017 Fab in complex with Apex GT6.2 and RM20A3 Fab
    • Complex: RM017 Fab
      • Protein or peptide: RM017 Fab heavy chain
      • Protein or peptide: RM017 Fab light chain
    • Complex: RM20A3 Fab
      • Protein or peptide: RM20A3 Fab light chain
      • Protein or peptide: RM20A3 Fab heavy chain
    • Complex: Apex GT6.2
      • Protein or peptide: Envelope glycoprotein gp120
      • Protein or peptide: Transmembrane protein gp41
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsHIV Env / immune complex / VIRAL PROTEIN / macaque antibody / IMMUNE SYSTEM
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 HJ / Pratap PP / Ozorowski G / Ward AB / Crotty S / Schief WR
History
DepositionJan 3, 2025-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48523.png

Downloads & links

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Map

FileDownload / File: emd_48523.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 400 pix.
= 417.6 Å		1.04 Å/pix.
x 400 pix.
= 417.6 Å		1.04 Å/pix.
x 400 pix.
= 417.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.044 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.60219294 - 1.2580985
Average (Standard dev.)0.00007347231 (±0.021954682)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 417.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_48523_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: EM half map A

Fileemd_48523_half_map_1.map
AnnotationEM half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: EM half map B

Fileemd_48523_half_map_2.map
AnnotationEM half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RM017 Fab in complex with Apex GT6.2 and RM20A3 Fab

EntireName: RM017 Fab in complex with Apex GT6.2 and RM20A3 Fab
Components
  • Complex: RM017 Fab in complex with Apex GT6.2 and RM20A3 Fab
    • Complex: RM017 Fab
      • Protein or peptide: RM017 Fab heavy chain
      • Protein or peptide: RM017 Fab light chain
    • Complex: RM20A3 Fab
      • Protein or peptide: RM20A3 Fab light chain
      • Protein or peptide: RM20A3 Fab heavy chain
    • Complex: Apex GT6.2
      • Protein or peptide: Envelope glycoprotein gp120
      • Protein or peptide: Transmembrane protein gp41
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: RM017 Fab in complex with Apex GT6.2 and RM20A3 Fab

SupramoleculeName: RM017 Fab in complex with Apex GT6.2 and RM20A3 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6

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Supramolecule #2: RM017 Fab

SupramoleculeName: RM017 Fab / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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Supramolecule #3: RM20A3 Fab

SupramoleculeName: RM20A3 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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Supramolecule #4: Apex GT6.2

SupramoleculeName: Apex GT6.2 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: Human immunodeficiency virus 1

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Macromolecule #1: RM017 Fab heavy chain

MacromoleculeName: RM017 Fab heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 25.37332 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DVQLVESGGG LVKPGGSLRL SCVASGFTFS SYLMHWVRQA PGKGLEWVSV ISESGGNIYY SDSVKGRFTI SRDNAKNSLF LQMNSLRAE DTAVYYCTRG GLFHID(TYS)DDD (TYS)A(TYS)YYTGRGL DYWGQGVLVT VSAASTKGPS VFPLAPSSK STSGGTAALG ...String:
DVQLVESGGG LVKPGGSLRL SCVASGFTFS SYLMHWVRQA PGKGLEWVSV ISESGGNIYY SDSVKGRFTI SRDNAKNSLF LQMNSLRAE DTAVYYCTRG GLFHID(TYS)DDD (TYS)A(TYS)YYTGRGL DYWGQGVLVT VSAASTKGPS VFPLAPSSK STSGGTAALG CLVKDYFPEP VTVSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK KVEPKSC

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Macromolecule #2: RM017 Fab light chain

MacromoleculeName: RM017 Fab light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 24.141783 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVMTQTPLS LPVTPGEPAS ISCRSSQSLL NSEDGNTYLD WYLQKPGQSP QLLIYEVSNR ASGVPDRFSG SGSDTDFTLE ISRVEAEDV GVYYCMKALE FPFTFGPGTK LDIKRTVAAP SVFIFPPSDE QLKSGTASVV CLLNNFYPRE AKVQWKVDNA L QSGNSQES ...String:
DIVMTQTPLS LPVTPGEPAS ISCRSSQSLL NSEDGNTYLD WYLQKPGQSP QLLIYEVSNR ASGVPDRFSG SGSDTDFTLE ISRVEAEDV GVYYCMKALE FPFTFGPGTK LDIKRTVAAP SVFIFPPSDE QLKSGTASVV CLLNNFYPRE AKVQWKVDNA L QSGNSQES VTEQDSKDST YSLSSTLTLS KADYEKHKVY ACEVTHQGLS SPVTKSFNRG EC

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Macromolecule #3: RM20A3 Fab light chain

MacromoleculeName: RM20A3 Fab 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: RM20A3 Fab heavy chain

MacromoleculeName: RM20A3 Fab heavy chain / type: protein_or_peptide / ID: 4 / 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 #5: Envelope glycoprotein gp120

MacromoleculeName: Envelope glycoprotein gp120 / type: protein_or_peptide / ID: 5 / Details: engineered Apex-GT6.2 construct / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 53.163391 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 VGRRRRRR

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Macromolecule #6: Transmembrane protein gp41

MacromoleculeName: Transmembrane protein gp41 / type: protein_or_peptide / ID: 6 / Details: engineered Apex-GT6.2 construct / 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 #11: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 11 / Number of copies: 39 / 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 / 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: 1.0 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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 140520
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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