[English] 日本語
Yorodumi
- EMDB-70663: Cryo-EM structure of vaccine-elicited antibody T3_NB_G05 in compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-70663
TitleCryo-EM structure of vaccine-elicited antibody T3_NB_G05 in complex with HIV Env trimer Q23-APEX-GT1.N187S
Map data
Sample
  • Complex: T3_NB_G05 Fab in complex with HIV Env trimer Q23-APEX-GT1.N187S
    • Protein or peptide: T3_NB_G05 heavy chain
    • Protein or peptide: T3_NB_G05 light chain
    • Protein or peptide: HIV Env gp120
    • Protein or peptide: HIV Env gp41 ectodomain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsimmune complex / neutralizing antibody / V2 apex / mouse model / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Biological speciesMacaca mulatta (Rhesus monkey) / Mus musculus (house mouse) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsRoark RS / Shapiro LS / 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: Rapid acquisition of HIV-1 neutralization breadth in a rhesus V2 apex germline antibody mouse model with a single bolus priming immunization
Authors: Amrit G / Roark RS / Kwong PD / Batista FD
History
DepositionMay 15, 2025-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_70663.png

Downloads & links

-
Map

FileDownload / File: emd_70663.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 316.8 Å		0.83 Å/pix.
x 384 pix.
= 316.8 Å		0.83 Å/pix.
x 384 pix.
= 316.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.16531563 - 0.45991024
Average (Standard dev.)0.0007489879 (±0.014843834)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 316.8 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_70663_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_70663_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : T3_NB_G05 Fab in complex with HIV Env trimer Q23-APEX-GT1.N187S

EntireName: T3_NB_G05 Fab in complex with HIV Env trimer Q23-APEX-GT1.N187S
Components
  • Complex: T3_NB_G05 Fab in complex with HIV Env trimer Q23-APEX-GT1.N187S
    • Protein or peptide: T3_NB_G05 heavy chain
    • Protein or peptide: T3_NB_G05 light chain
    • Protein or peptide: HIV Env gp120
    • Protein or peptide: HIV Env gp41 ectodomain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: T3_NB_G05 Fab in complex with HIV Env trimer Q23-APEX-GT1.N187S

SupramoleculeName: T3_NB_G05 Fab in complex with HIV Env trimer Q23-APEX-GT1.N187S
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

-
Macromolecule #1: T3_NB_G05 heavy chain

MacromoleculeName: T3_NB_G05 heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 25.198158 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVHLVESGGG LATPGGSLRL SCAASGFTFS NYWMNWVRQT PGKGLEWIAS INSAGGARDY ADSVMGRFTI SRDNSKNTLS LKMNSLRTE DTAVYYCAKV DEDDYGYFSI VPGDLKKYYF KYWGQGVQVT VSSASTTPPS VYPLAPGSAA QTNSMVTLGC L VKGYFPEP ...String:
EVHLVESGGG LATPGGSLRL SCAASGFTFS NYWMNWVRQT PGKGLEWIAS INSAGGARDY ADSVMGRFTI SRDNSKNTLS LKMNSLRTE DTAVYYCAKV DEDDYGYFSI VPGDLKKYYF KYWGQGVQVT VSSASTTPPS VYPLAPGSAA QTNSMVTLGC L VKGYFPEP VTVTWNSGSL SSGVHTFPAV LQSDLYTLSS SVTVPSSTWP SETVTCNVAH PASSTKVDKK IVPRDCG

-
Macromolecule #2: T3_NB_G05 light chain

MacromoleculeName: T3_NB_G05 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.470697 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LSASVGDRVT ITCQASQGIS SWLAWYQQKP GKAPKSLIYK ASSLESGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QYDSAPFSFG QGTEVEIKRT DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS ...String:
DIQMTQSPSS LSASVGDRVT ITCQASQGIS SWLAWYQQKP GKAPKSLIYK ASSLESGVPS RFSGSGSGTD FTLTISSLQP EDFATYYCQ QYDSAPFSFG QGTEVEIKRT DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS KDSTYSMSST LTLTKDEYER HNSYTCEATH KTSTSPIVKS FNRNEC

-
Macromolecule #3: HIV Env gp120

MacromoleculeName: HIV Env gp120 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.704605 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAENLW VTVYYGVPVW RDAETTLFCA SDAKAYETEK HNVWATHACV PTDPNPQEI HLDNVTEKFN MWKNNMVEQM HTDIISLWDQ SLKPCVKLTP LCVTLHCTNV TSVNTTGDRE ELKNCSFNMT T ELRDKRQK ...String:
MDAMKRGLCC VLLLCGAVFV SPSQEIHARF RRGARAENLW VTVYYGVPVW RDAETTLFCA SDAKAYETEK HNVWATHACV PTDPNPQEI HLDNVTEKFN MWKNNMVEQM HTDIISLWDQ SLKPCVKLTP LCVTLHCTNV TSVNTTGDRE ELKNCSFNMT T ELRDKRQK VYSLFYRLDI VPINESQGSE YRLINCNTSA CTQACPKVSF EPIPIHYCAP AGFAILKCKD EGFNGTGLCK NV STVQCTH GIKPVVSTQL LLNGSLAEKN ITIRSENITN NAKIIIVQLV QPVTIKCIRP NNYTRKSIRI GPGQAFYAMG DII GDIRQA HCNVSRSRWN KTLQEVAEKL RTYFGNKTII FANSSGGDLE ITTHSFNCGG EFFYCNTSGL FNSTWYVNST WNDT DSTQE SNDTITLPCR IKQIINMWQR AGQCMYAPPI PGVIKCESNI TGLLLTRDGG KDNNVNETFR PGGGDMRDNW RSELY KYKV VEIEPLGVAP TRCKRRVVE

-
Macromolecule #4: HIV Env gp41 ectodomain

MacromoleculeName: HIV Env gp41 ectodomain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.205666 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVRRG FLGAAGSTMG AASITLTVQA RQLLSGIVQP QNNLLRAPEA QQHLLKLGVW GIKQLQARVL AVERYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNKSLD EIWNNMTWLQ WDKEIGNYTQ LIYRLIEESQ NQQEKNEKEL LALD

-
Macromolecule #10: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 10 / Number of copies: 31 / 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

BufferpH: 7.5 / Details: PBS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

-
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: OTHER / 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

+
Image processing

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

9bnp

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 211700
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

+
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