[English] 日本語
Yorodumi
- EMDB-74656: Cryo-EM structure of SHIV-elicited CI93-1365 Fab in complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-74656
TitleCryo-EM structure of SHIV-elicited CI93-1365 Fab in complex with HIV Env trimer Q23-SCT27
Map data
Sample
  • Complex: CI93-1365 Fab in complex with HIV envelope trimer
    • Protein or peptide: CI93-1365 heavy chain
    • Protein or peptide: CI93-1365 light chain
    • Protein or peptide: Envelope gp120
    • Protein or peptide: Envelope gp41 ectodomain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsimmune complex / neutralization / SHIV / HIV V2 apex / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated perturbation of host defense response / 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 ...symbiont-mediated perturbation of host defense response / 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 speciesMacaca mulatta (Rhesus monkey) / Human immunodeficiency virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 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: Enhanced Priming Leads to Rapid Induction of Broadly Neutralizing HIV-1 Apex Antibodies
Authors: Roark RS / Shapiro L / Kwong PD
History
DepositionDec 21, 2025-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_74656.png

Downloads & links

-
Map

FileDownload / File: emd_74656.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.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å		0.83 Å/pix.
x 384 pix.
= 318.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.26177076 - 0.57787776
Average (Standard dev.)0.00017129489 (±0.014709306)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 318.72 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_74656_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_74656_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : CI93-1365 Fab in complex with HIV envelope trimer

EntireName: CI93-1365 Fab in complex with HIV envelope trimer
Components
  • Complex: CI93-1365 Fab in complex with HIV envelope trimer
    • Protein or peptide: CI93-1365 heavy chain
    • Protein or peptide: CI93-1365 light chain
    • Protein or peptide: Envelope gp120
    • Protein or peptide: Envelope gp41 ectodomain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: CI93-1365 Fab in complex with HIV envelope trimer

SupramoleculeName: CI93-1365 Fab in complex with HIV envelope trimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

-
Macromolecule #1: CI93-1365 heavy chain

MacromoleculeName: CI93-1365 heavy chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 26.700262 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGGG LVQPGGSLRL SCAASGFTFS NYGIYWVRQA SGKGLEWIGR VRSKANSYET GYAASLGGRF TISREDSRDT SYLQMNSLK TDDTAVYYCA TGPQEDYYAD D(TYS)GDYYTENY GLDSWGQGVV VTVSSASTKG PSVFPLAPSS RSTSEST AA LGCLVKDYFP ...String:
EVQLVESGGG LVQPGGSLRL SCAASGFTFS NYGIYWVRQA SGKGLEWIGR VRSKANSYET GYAASLGGRF TISREDSRDT SYLQMNSLK TDDTAVYYCA TGPQEDYYAD D(TYS)GDYYTENY GLDSWGQGVV VTVSSASTKG PSVFPLAPSS RSTSEST AA LGCLVKDYFP EPVTVSWNSG SLTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYVCN VNHKPSNTKV DKRVEIKT C GGHHHHHHHH

-
Macromolecule #2: CI93-1365 light chain

MacromoleculeName: CI93-1365 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 23.142561 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LSASVGDRVT VTCRASQGIG DSVNWYQQKP GKAPKRLIHA ASNLETGVPS RFSGSGSGTD FTLTISSLQP EDFATYHCL QYNSDPLTFG QGTKVEIKRT VAAPSVFIFP PSEDQVKSGT VSVVCLLNNF YPREASVKWK VDGALKTGNS Q ESVTEQDS ...String:
DIQMTQSPSS LSASVGDRVT VTCRASQGIG DSVNWYQQKP GKAPKRLIHA ASNLETGVPS RFSGSGSGTD FTLTISSLQP EDFATYHCL QYNSDPLTFG QGTKVEIKRT VAAPSVFIFP PSEDQVKSGT VSVVCLLNNF YPREASVKWK VDGALKTGNS Q ESVTEQDS KDNTYSLSST LTLSSTEYQS HKVYACEVTH QGLSSPVTKS FNRGEC

-
Macromolecule #3: Envelope gp120

MacromoleculeName: Envelope gp120 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus
Molecular weightTheoretical: 56.731629 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 VPINENQGSE 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

UniProtKB: Envelope glycoprotein gp160

-
Macromolecule #4: Envelope gp41 ectodomain

MacromoleculeName: Envelope gp41 ectodomain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus
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

UniProtKB: Envelope glycoprotein gp160

-
Macromolecule #9: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 9 / Number of copies: 32 / 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: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9nvv

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 132734
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

-
Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-9zrz:
Cryo-EM structure of SHIV-elicited CI93-1365 Fab in complex with HIV Env trimer Q23-SCT27

+
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