[English] 日本語
Yorodumi
- EMDB-48575: G002-293-0536 Fab in complex with 001428_T278M_L14 SOSIP and RM20... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-48575
TitleG002-293-0536 Fab in complex with 001428_T278M_L14 SOSIP and RM20A3 Fab
Map datasharpened map
Sample
  • Complex: G002-293-0536 Fab in complex with 001428_T278M_L14 SOSIP and RM20A3 Fab
    • Protein or peptide: 001428_T278M_L14 SOSIP gp140
    • Protein or peptide: RM20A3 Rab heavy chain
    • Protein or peptide: RM20A3 Fab light chain
    • Protein or peptide: G002-293-0536 Fab heavy chain
    • Protein or peptide: G002-293-0536 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsG002 / clinical trial / HIV-1 / VRC01 / human antibody / vaccine / Env / VIRAL PROTEIN / 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 / 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 speciesHuman immunodeficiency virus 1 / Homo sapiens (human) / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsPhulera S / Ozorowski G / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-002916 United States
CitationJournal: Science / Year: 2025
Title: Vaccination with mRNA-encoded nanoparticles drives early maturation of HIV bnAb precursors in humans.
Authors: Jordan R Willis / Madhu Prabhakaran / Michelle Muthui / Ansuya Naidoo / Troy Sincomb / Weiwei Wu / Christopher A Cottrell / Elise Landais / Allan C deCamp / Nahid R Keshavarzi / Oleksandr ...Authors: Jordan R Willis / Madhu Prabhakaran / Michelle Muthui / Ansuya Naidoo / Troy Sincomb / Weiwei Wu / Christopher A Cottrell / Elise Landais / Allan C deCamp / Nahid R Keshavarzi / Oleksandr Kalyuzhniy / Jeong Hyun Lee / Linda M Murungi / Wilfrida A Ogonda / Nicole L Yates / Martin M Corcoran / Swastik Phulera / Joel Musando / Amanda Tsai / Gabrielle Lemire / Yiakon Sein / Michael Muteti / Praveen Alamuri / Jennifer A Bohl / Drienna Holman / Sunny Himansu / Brett Leav / Caroline Reuter / Li-An Lin / Baoyu Ding / Chunla He / Walter L Straus / Kellie J MacPhee / Isabel Regadas / Diana V Nyabundi / Ruth Chirchir / Aggrey Anzala / John N Kimotho / Caleb Kibet / Kelli Greene / Hongmei Gao / Erica Beatman / Kiara Benson / Dominick Laddy / David M Brown / Rhianna Bronson / Jalen Baptiste / Suprabhath Gajjala / Zahra Rikhtegaran-Tehrani / Alison Benner / Mukundhan Ramaswami / Danny Lu / Nushin Alavi / Sonya Amirzehni / Michael Kubitz / Ryan Tingle / Erik Georgeson / Nicole Phelps / Yumiko Adachi / Alessia Liguori / Claudia Flynn / Katherine McKenney / Xiaoya Zhou / D Collins Owuor / Sharon Owuor / Soo-Young Kim / Michael Duff / Ju Yeong Kim / Grace Gibson / Sabyasachi Baboo / Jolene Diedrich / Torben Schiffner / Marisa Shields / Mabela Matsoso / Jennifer Santos / Kristen Syvertsen / Allison Kennedy / Melissa Schroeter / Johan Vekemans / John Yates / James C Paulson / Ollivier Hyrien / Adrian B McDermott / Pholo Maenetje / Julien Nyombayire / Etienne Karita / Rosine Ingabire / Vinodh Edward / Vincent Muturi-Kioi / Janine Maenza / Adrienne E Shapiro / M Juliana McElrath / Srilatha Edupuganti / Barbara S Taylor / David Diemert / Gabriel Ozorowski / Richard A Koup / David Montefiori / Andrew B Ward / Gunilla Karlsson Hedestam / Georgia Tomaras / Devin J Hunt / Daniel Muema / Devin Sok / Dagna S Laufer / Sarah F Andrews / Eunice W Nduati / William R Schief /
Abstract: A leading HIV vaccine strategy requires a priming immunogen to induce broadly neutralizing antibody (bnAb) precursors, followed by a series of heterologous boosters to elicit somatic hypermutation ...A leading HIV vaccine strategy requires a priming immunogen to induce broadly neutralizing antibody (bnAb) precursors, followed by a series of heterologous boosters to elicit somatic hypermutation (SHM) and produce bnAbs. In two randomized, open-label phase 1 human clinical trials, IAVI-G002 in the United States and IAVI-G003 in Rwanda and South Africa, we evaluated the safety and immunogenicity of mRNA-encoded nanoparticles as priming immunogens (both trials) and first-boosting immunogens (IAVI-G002). The vaccines were generally safe and well tolerated, except 18% of IAVI-G002 participants experienced skin reactions. Priming induced bnAb precursors with substantial frequencies and SHM, and heterologous boosting elicited increased SHM, affinity, and neutralization activity toward bnAb development. The results establish clinical proof of concept that heterologous boosting can advance bnAb-precursor maturation and demonstrate bnAb priming in Africa where the HIV burden is highest.
History
DepositionJan 9, 2025-
Header (metadata) releaseMay 28, 2025-
Map releaseMay 28, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_48575.png

Downloads & links

-
Map

FileDownload / File: emd_48575.map.gz / Format: CCP4 / Size: 244.1 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.)
1.01 Å/pix.
x 400 pix.
= 402.08 Å		1.01 Å/pix.
x 400 pix.
= 402.08 Å		1.01 Å/pix.
x 400 pix.
= 402.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0052 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.90376985 - 1.288565
Average (Standard dev.)-0.0001747449 (±0.024590008)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 402.08002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_48575_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map A

Fileemd_48575_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map B

Fileemd_48575_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : G002-293-0536 Fab in complex with 001428_T278M_L14 SOSIP and RM20...

EntireName: G002-293-0536 Fab in complex with 001428_T278M_L14 SOSIP and RM20A3 Fab
Components
  • Complex: G002-293-0536 Fab in complex with 001428_T278M_L14 SOSIP and RM20A3 Fab
    • Protein or peptide: 001428_T278M_L14 SOSIP gp140
    • Protein or peptide: RM20A3 Rab heavy chain
    • Protein or peptide: RM20A3 Fab light chain
    • Protein or peptide: G002-293-0536 Fab heavy chain
    • Protein or peptide: G002-293-0536 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: G002-293-0536 Fab in complex with 001428_T278M_L14 SOSIP and RM20...

SupramoleculeName: G002-293-0536 Fab in complex with 001428_T278M_L14 SOSIP and RM20A3 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1, #5, #4, #2-#3

-
Macromolecule #1: 001428_T278M_L14 SOSIP gp140

MacromoleculeName: 001428_T278M_L14 SOSIP gp140 / type: protein_or_peptide / ID: 1
Details: Envelope glycoprotein gp160 with 001428_T278M_L14 SOSIP gp140 engineered mutations
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 72.345602 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ETGVENLWVT VYYGVPVWKE ARTTLFCASD AKAYETEVHN VWATHACVPT DPNPQEMVLG NVTENFNMWK NDMVDQMHED VISLWAQSL KPCVKLTPLC VTLECTQVNA TQGNTTQVNV TQVNGDEMKN CSFNTTTEIR DKKQKAYALF YRLDLVPLER E NRGDSNSA ...String:
ETGVENLWVT VYYGVPVWKE ARTTLFCASD AKAYETEVHN VWATHACVPT DPNPQEMVLG NVTENFNMWK NDMVDQMHED VISLWAQSL KPCVKLTPLC VTLECTQVNA TQGNTTQVNV TQVNGDEMKN CSFNTTTEIR DKKQKAYALF YRLDLVPLER E NRGDSNSA SKYILINCNT SAITQACPKV NFDPIPIHYC TPAGYAILKC NNKTFNGTGS CNNVSTVQCT HGIKPVVSTQ LL LNGSLAE EEIIIRSENL MDNVKTIIVH LDQSVEIVCT RPNNNTVKSI RIGPGQTFYY TGDIIGNIRE AHCNISEKKW HEM LRRVSE KLAEHFPNKT IKFTSSSGGD LEITTHSFNC RGEFFYCNTS GLFNSTYMPN GTYMPNGTNN SNSTIILPCR IKQI INMWQ EVGRAMYAPP IAGNITCNSN ITGLLLVRDG GKNNNTEIFR PGGGDMRDNW RSELYKYKVV EIKPLGVAPT RCKRR VVGS HSGSGGSGSG GHAAVGLGAV SLGFLGAAGS TMGAASITLT VQARQLLSGI VQQQSNLLQA PEPQQHLLQD THWGIK QLQ TRVLAIEHYL KDQQLLGIWG CSGKLICCTA VPWNSSWSNK SLTDIWDNMT WMQWDREVSN YTGIIYRLLE DSQNQQE RN EQDLLALD

UniProtKB: Envelope glycoprotein gp160

-
Macromolecule #2: G002-293-0536 Fab heavy chain

MacromoleculeName: G002-293-0536 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.206357 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAE VKKPGASVKV SCKASGYSFT DYYIHWVRQA PGQGLEWMGW INPRFGGVNY AQKFQGRVTM TRDTSIRTAH MELSRLISD DTAFYYCARG RFADSVWNLL FWGQGTLVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT ...String:
QVQLVQSGAE VKKPGASVKV SCKASGYSFT DYYIHWVRQA PGQGLEWMGW INPRFGGVNY AQKFQGRVTM TRDTSIRTAH MELSRLISD DTAFYYCARG RFADSVWNLL FWGQGTLVTV SSASTKGPSV FPLAPSSKST SGGTAALGCL VKDYFPEPVT V SWNSGALT SGVHTFPAVL QSSGLYSLSS VVTVPSSSLG TQTYICNVNH KPSNTKVDKK VEPKSC

-
Macromolecule #3: G002-293-0536 Fab light chain

MacromoleculeName: G002-293-0536 Fab light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.943395 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LSASVGDRVT ITCQASQGIS NYLNWYQQKP GKAPKLLIYD ASNLETGVPS RFSGSGSGTD FTFTISGLQP EDIATYYCQ KYEFFGGGTK VEIKRTVAAP SVFIFPPSDE QLKSGTASVV CLLNNFYPRE AKVQWKVDNA LQSGNSQESV T EQDSKDST ...String:
DIQMTQSPSS LSASVGDRVT ITCQASQGIS NYLNWYQQKP GKAPKLLIYD ASNLETGVPS RFSGSGSGTD FTFTISGLQP EDIATYYCQ KYEFFGGGTK VEIKRTVAAP SVFIFPPSDE QLKSGTASVV CLLNNFYPRE AKVQWKVDNA LQSGNSQESV T EQDSKDST YSLSSTLTLS KADYEKHKVY ACEVTHQGLS SPVTKSFNRG EC

-
Macromolecule #4: RM20A3 Fab light chain

MacromoleculeName: RM20A3 Fab light chain / type: protein_or_peptide / ID: 4 / 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

-
Macromolecule #5: RM20A3 Rab heavy chain

MacromoleculeName: RM20A3 Rab heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 24.079055 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

-
Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 27 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration8.2 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

-
Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 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: 0.7000000000000001 µm / Nominal magnification: 190000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: ab initio model
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 47344
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more