[English] 日本語
Yorodumi
- EMDB-44897: Cryo-EM structure of rhesus antibody T646-a.01 in complex with HI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-44897
TitleCryo-EM structure of rhesus antibody T646-a.01 in complex with HIV-1 Env trimer Q23.17 MD39
Map data
Sample
  • Complex: Complex of T646-a.01 with HIV-1 Q23.17 envelope trimer
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: Q23.MD39 Transmembrane protein gp41
    • Protein or peptide: T646-a.01 heavy chain
    • Protein or peptide: T646-a.01 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsNeutralizing antibody / HIV-1 V2 apex / SHIV-elicited / Viral protein / IMMUNE SYSTEM / 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 speciesMacaca mulatta (Rhesus monkey) / Human immunodeficiency virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.48 Å
AuthorsRoark RS / Shapiro L / 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: HIV-1 neutralizing antibodies in SHIV-infected macaques recapitulate structurally divergent modes of human V2 apex recognition with a single D gene
Authors: Roark RS / Shapiro L / Kwong PD
History
DepositionMay 15, 2024-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_44897.png

Downloads & links

-
Map

FileDownload / File: emd_44897.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: 0.11
Minimum - Maximum-0.18837744 - 0.4636509
Average (Standard dev.)0.0007973448 (±0.015083276)
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_44897_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_44897_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex of T646-a.01 with HIV-1 Q23.17 envelope trimer

EntireName: Complex of T646-a.01 with HIV-1 Q23.17 envelope trimer
Components
  • Complex: Complex of T646-a.01 with HIV-1 Q23.17 envelope trimer
    • Protein or peptide: Envelope glycoprotein gp120
    • Protein or peptide: Q23.MD39 Transmembrane protein gp41
    • Protein or peptide: T646-a.01 heavy chain
    • Protein or peptide: T646-a.01 light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: Complex of T646-a.01 with HIV-1 Q23.17 envelope trimer

SupramoleculeName: Complex of T646-a.01 with HIV-1 Q23.17 envelope trimer
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

-
Macromolecule #1: Envelope glycoprotein gp120

MacromoleculeName: Envelope glycoprotein gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 52.996059 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VENLWVTVYY GVPVWRDADT TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLDNVT EKFNMWKNNM VEQMHEDIIS LWDQSLKPC VKLTPLCVTL HCTNVTSVNT TGDREGLKNC SFNMTTELRD KRQKVYSLFY RLDIVPINEN QGSEYRLINC N TSAITQAC ...String:
VENLWVTVYY GVPVWRDADT TLFCASDAKA YETEKHNVWA THACVPTDPN PQEIHLDNVT EKFNMWKNNM VEQMHEDIIS LWDQSLKPC VKLTPLCVTL HCTNVTSVNT TGDREGLKNC SFNMTTELRD KRQKVYSLFY RLDIVPINEN QGSEYRLINC N TSAITQAC PKVSFEPIPI HYCTPAGFAI LKCKDEGFNG TGLCKNVSTV QCTHGIKPVV STQLLLNGSL AEKNIIIRSE NI TNNAKII IVQLVQPVTI KCIRPNNNTV KSIRIGPGQA FYYTGDIIGD IRQAHCNVTR SRWNKTLQEV AEKLRTYFGN KTI IFANSS GGDLEITTHS FNCGGEFFYC NTSGLFNSTW YVNSTWNDTD STQESNDTIT LPCRIKQIIN MWQRAGQAMY APPI PGVIK CESNITGLLL TRDGGKDNNV NETFRPGGSD MRDNWRSELY KYKVVEIEPL GVAPTRCKRR VVER

UniProtKB: Envelope glycoprotein gp160

-
Macromolecule #2: Q23.MD39 Transmembrane protein gp41

MacromoleculeName: Q23.MD39 Transmembrane protein gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.313646 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVSLG FLGAAGSTMG AASITLTVQA RNLLSGIVQQ QNNLLRAPEP QQHLLKLTHW GIKQLQARVL AVEHYLRDQQ LLGIWGCSG KLICCTNVPW NSSWSNKSLD EIWNNMTWLQ WDKEINNYTQ LIYRLIEESQ NQQEKNEKEL LELD

UniProtKB: Envelope glycoprotein gp160

-
Macromolecule #3: T646-a.01 heavy chain

MacromoleculeName: T646-a.01 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 26.645637 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLRESGPG LVKPSETLSL TCAVSGASIS DEYYWTWIRQ PPGRGLEWIG YFSGRDGYPH YNRFLESRVT ISVDTSKKQI SLRLTSVTA ADTAVYFCAK APRSFLYGDD (TYS)GDFYTESDY FDSWGQGVLV TVSSASTKGP SVFPLAPSSR STSESTA AL GCLVKDYFPE ...String:
QVQLRESGPG LVKPSETLSL TCAVSGASIS DEYYWTWIRQ PPGRGLEWIG YFSGRDGYPH YNRFLESRVT ISVDTSKKQI SLRLTSVTA ADTAVYFCAK APRSFLYGDD (TYS)GDFYTESDY FDSWGQGVLV TVSSASTKGP SVFPLAPSSR STSESTA AL GCLVKDYFPE PVTVSWNSGS LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYVCNV NHKPSNTKVD KRVEIKTC G GGLEVLFQ

-
Macromolecule #4: T646-a.01 light chain

MacromoleculeName: T646-a.01 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 22.689908 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSVLTQPPSA SEAARKSVTI SCSGSSSNIG SNSVSWYQQL PETAPKLLIY NNNQRPSGVP DRFSGSKSGT SASLAISGLQ TEDEADYYC GAWDGSLRGN VFGSGTKLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVE VAWKADGSAV N AGVETTKP ...String:
QSVLTQPPSA SEAARKSVTI SCSGSSSNIG SNSVSWYQQL PETAPKLLIY NNNQRPSGVP DRFSGSKSGT SASLAISGLQ TEDEADYYC GAWDGSLRGN VFGSGTKLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVE VAWKADGSAV N AGVETTKP SKQSNNKYAA SSYLSLTSDQ WKSHKSYSCQ VTHEGSTVEK TVAPAECS

-
Macromolecule #11: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 11 / Number of copies: 19 / 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: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / 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:

7llk

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 39411
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