[English] 日本語
Yorodumi
- EMDB-26706: Cryo-EM structure of SHIV-elicited, FP-directed Rhesus Fab RM6561... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-26706
TitleCryo-EM structure of SHIV-elicited, FP-directed Rhesus Fab RM6561.DH1021.14 in complex with stabilized HIV-1 Env Ce1176 DS-SOSIP.664
Map datasharpened map
Sample
  • Complex: Fab RM6561.DH1021.14 with stabilized HIV-1 Env Ce1176
    • Protein or peptide: gp120Envelope glycoprotein GP120
    • Protein or peptide: gp41
    • Protein or peptide: Heavy Chain
    • Protein or peptide: Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


: / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / 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 ...: / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / 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 / plasma 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 / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1 / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsGorman J / Kwong PD
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
Other privateSimons Foundation (SF349247)
CitationJournal: To Be Published
Title: Cryo-EM structure of SHIV-elicited, FP-directed Rhesus Fab RM6561.DH1021.14 in complex with stabilized HIV-1 Env Ce1176 DS-SOSIP.664
Authors: Gorman J / Kwong PD
History
DepositionApr 21, 2022-
Header (metadata) releaseApr 26, 2023-
Map releaseApr 26, 2023-
UpdateApr 26, 2023-
Current statusApr 26, 2023Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_26706.png

Downloads & links

-
Map

FileDownload / File: emd_26706.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Voxel sizeX=Y=Z: 1.083 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.2629692 - 0.8430627
Average (Standard dev.)0.004016307 (±0.02506657)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 346.56 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_26706_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Density modified with resolve

Fileemd_26706_additional_1.map
AnnotationDensity modified with resolve
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: unsharpened map

Fileemd_26706_additional_2.map
Annotationunsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map A

Fileemd_26706_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_26706_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Fab RM6561.DH1021.14 with stabilized HIV-1 Env Ce1176

EntireName: Fab RM6561.DH1021.14 with stabilized HIV-1 Env Ce1176
Components
  • Complex: Fab RM6561.DH1021.14 with stabilized HIV-1 Env Ce1176
    • Protein or peptide: gp120Envelope glycoprotein GP120
    • Protein or peptide: gp41
    • Protein or peptide: Heavy Chain
    • Protein or peptide: Light Chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: Fab RM6561.DH1021.14 with stabilized HIV-1 Env Ce1176

SupramoleculeName: Fab RM6561.DH1021.14 with stabilized HIV-1 Env Ce1176 / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Human immunodeficiency virus 1

-
Macromolecule #1: gp120

MacromoleculeName: gp120 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 53.648887 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPAENLWVTV YYGVPVWKEA KTTLFCASDA KAYEKEVHNV WATHACVPTD PNPQEMVLEN VTENFNMWKN DMVDQMHEDV ISLWDQSLK PCVKLTPLCV TLNCTNTTVS NGSSNSNANF EEMKNCSFNA TTEIKDKKKN EYALFYKLDI VPLNNSSGKY R LINCNTSA ...String:
GPAENLWVTV YYGVPVWKEA KTTLFCASDA KAYEKEVHNV WATHACVPTD PNPQEMVLEN VTENFNMWKN DMVDQMHEDV ISLWDQSLK PCVKLTPLCV TLNCTNTTVS NGSSNSNANF EEMKNCSFNA TTEIKDKKKN EYALFYKLDI VPLNNSSGKY R LINCNTSA CTQICPKVTF EPIPIHYCAP AGYAILKCNN KTFNGTGPCN NVSTVQCTHG IKPVVSTQLL LNGSLAEKEI II RSENLTN NAKTIIVHLN ESVGIVCTRP SNMTRKSIRI GPGQTFYALG DIIGDIRQPH CNISKQNWNR TLQQVGRKLA EHF PNRNIT FNHSSGGDLE ITTHSFNCRG EFFYCNTSGL FNGTYHPNGT YNETAVNSSD TITLQCRIKQ IINMWQEVGR CMYA PPIAG NITCNSNITG LLLTRDGGIN QTGEEIFRPG GGDMRDNWRS ELYKYKVVEI KPLGIAPTKC KRRVVERRRR RR

-
Macromolecule #2: gp41

MacromoleculeName: gp41 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1
Molecular weightTheoretical: 17.24051 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AVGIGAVFLG FLGAAGSTMG AASNTLTVQA RQLLSGIVQQ QSNLLRAPEA QQHMLQLGVW GFKQLQARVL AIERYLEVQQ LLGIWGCSG KLICCTNVPW NSTWSNRTQE DIWNNMTWME WEREIGNYTH TIYSLLEESQ FQQEINEKDL LALD

-
Macromolecule #3: Heavy Chain

MacromoleculeName: Heavy Chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 14.505475 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVTLKESGPA LVKPTQTLTL TCTFSGFSMS NFGSGIYWIR QPPGKALEWL AGIYWTDSKY YNLSLKTRLT ISKDTSKSQV ILIMTNMDP VDTATYYCAD IRGRYYYSNG FLFDVVGVES WGQGVVVTVS S

-
Macromolecule #4: Light Chain

MacromoleculeName: Light Chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 11.679873 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSVLTQPPSA SEAARKTVTI SCSGSRSNIG SNSVSWYKQV PGTAPKLLIK YNDQRPSGVS DRFSGSKSGT SASLAISGLQ TEDEADYYC ATWDDSLNGY IFGVGTRLIV L

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

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 10 / Number of copies: 42 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2 mg/mL
BufferpH: 7.4 / Component - Concentration: 1.0 X / Component - Formula: PBS / Component - Name: PBS
GridModel: C-flat-1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average exposure time: 2.0 sec. / Average electron dose: 51.27 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Initial angle assignmentType: NOT APPLICABLE
Final 3D classificationSoftware - Name: cryoSPARC (ver. 2.12)
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15) / Number images used: 13272

-
Atomic model buiding 1

Initial modelPDB ID:

6vtt

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7ur6:
Cryo-EM structure of SHIV-elicited, FP-directed Rhesus Fab RM6561.DH1021.14 in complex with stabilized HIV-1 Env Ce1176 DS-SOSIP.664

+
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