[English] 日本語
Yorodumi
- EMDB-76863: HIV-1 Gag (CASP1NCSP2p6) assembled with core encapsidation signal... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-76863
TitleHIV-1 Gag (CASP1NCSP2p6) assembled with core encapsidation signal - tomography map
Map datamain map
Sample
  • Complex: Gag-RNA ribonucleoprotein complex
    • Protein or peptide: HIV-1 Gag CASP1NCSP2p6
    • RNA: HIV-1 core encapsidation signal
KeywordsHIV-1 / RNA packaging / Gag polyprotein / ribonucleoprotein complex (RNP) / viral assembly / viral genome selectivity / VIRUS LIKE PARTICLE
Biological speciesHuman immunodeficiency virus 1
Methodsubtomogram averaging / cryo EM / Resolution: 15.0 Å
AuthorsHollmann NM / Ganser-Pornillos BK / Pornillos O / Summers MF
Funding support United States, 5 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U54 AI70660 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI150498 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI179691 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)K99AI186598 United States
CitationJournal: To Be Published
Title: Structural Basis for Dimeric Genome Selection by HIV-1
Authors: Hollmann NM / Kharytonchyk S / Buchannan A / Phillips C / Ledbetter A / Ahmed F / Adelstein A / Barry K / Geleta SA / Telesnitsky A / Ganser-Pornillos BK / Pornillos O / Summers MF
History
DepositionApr 23, 2026-
Header (metadata) releaseJun 24, 2026-
Map releaseJun 24, 2026-
UpdateJun 24, 2026-
Current statusJun 24, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_76863.png

Downloads & links

-
Map

FileDownload / File: emd_76863.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.81 Å/pix.
x 64 pix.
= 180.096 Å		2.81 Å/pix.
x 64 pix.
= 180.096 Å		2.81 Å/pix.
x 64 pix.
= 180.096 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.814 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5
Minimum - Maximum-5.173129 - 5.2335052
Average (Standard dev.)-0.08569838 (±1.2510692)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 180.096 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: half map A

Fileemd_76863_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_76863_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Gag-RNA ribonucleoprotein complex

EntireName: Gag-RNA ribonucleoprotein complex
Components
  • Complex: Gag-RNA ribonucleoprotein complex
    • Protein or peptide: HIV-1 Gag CASP1NCSP2p6
    • RNA: HIV-1 core encapsidation signal

-
Supramolecule #1: Gag-RNA ribonucleoprotein complex

SupramoleculeName: Gag-RNA ribonucleoprotein complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: NL4-3

-
Macromolecule #1: HIV-1 Gag CASP1NCSP2p6

MacromoleculeName: HIV-1 Gag CASP1NCSP2p6 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Human immunodeficiency virus 1 / Strain: NL4-3
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: VSQNYPIVQN LQGQMVHQAI SPRTLNAWVK VVEEKAFSPE VIPMFSALSE GATPQDLNTM LNTVGGHQAA MQMLKETINE EAAEWDRLHP VHAGPIAPGQ MREPRGSDIA GTTSTLQEQI GWMTHNPPIP VGEIYKRWII LGLNKIVRMY SPTSILDIRQ GPKEPFRDYV ...String:
VSQNYPIVQN LQGQMVHQAI SPRTLNAWVK VVEEKAFSPE VIPMFSALSE GATPQDLNTM LNTVGGHQAA MQMLKETINE EAAEWDRLHP VHAGPIAPGQ MREPRGSDIA GTTSTLQEQI GWMTHNPPIP VGEIYKRWII LGLNKIVRMY SPTSILDIRQ GPKEPFRDYV DRFYKTLRAE QASQEVKNWM TETLLVQNAN PDCKTILKAL GPGATLEEMM TACQGVGGPG HKARVLAEAM SQVTNPATIM IQKGNFRNQR KTVKCFNCGK EGHIAKNCRA PRKKGCWKCG KEGHQMKDCT ERQANFLGKI WPSHKGRPGN FLQSRPEPTA PPEESFRFGE ETTTPSQKQE PIDKELYPLA SLRSLFGSDP SSQ

-
Macromolecule #2: HIV-1 core encapsidation signal

MacromoleculeName: HIV-1 core encapsidation signal / type: rna / ID: 2
Source (natural)Organism: Human immunodeficiency virus 1
SequenceString:
GGUGCCCGUC UGUUGUGUGA CUCUGGUGAG AGCCAGAGGA GAUCUCUCGA CGCAGGACUC GGCUUGCUGA AGCGCGCACG GCAAGAGGCG AGGGGCGGCG ACUGGUGAGU ACGCCAAAAA UUUUGACUAG CGGAGGCUAG AAGGAGAGAG AUGGGUGCC

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
Component:
ConcentrationName
20.0 mMMOPS
10.0 mMNaCl
140.0 mMKCl
1.0 mMIP6
5.0 mMTCEP
GridModel: C-flat-2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 2.46 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 4.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionNumber classes used: 767 / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Dynamo / Number subtomograms used: 3
ExtractionNumber tomograms: 3 / Number images used: 5313 / Software - Name: Dynamo
CTF correctionSoftware - Name: RELION (ver. 5) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: Dynamo

-
Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL

+
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