[English] 日本語
Yorodumi
- EMDB-5639: Cryo-electron tomography reconstruction of native HIV-1 core -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-5639
TitleCryo-electron tomography reconstruction of native HIV-1 core
Map dataThe figure shows the simulated density of all-atom HIV-1 capsid model (3J3Y) overlaid with a slice of HIV-1 core tomogram.
Sample
  • Sample: HIV-1 core with A14C/E45C cross-linked capsid protein
  • Virus: Human immunodeficiency virus 1
Keywordscryo-electron tomography / HIV-1 core
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral nucleocapsid / host cell cytoplasm / viral translational frameshifting / host cell nucleus / structural molecule activity / virion membrane / RNA binding / zinc ion binding / identical protein binding / cytoplasm
Similarity search - Function
Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retroviral matrix protein ...Gag protein p6 / Gag protein p6 / : / gag protein p24 N-terminal domain / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retroviral matrix protein / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
Methodelectron tomography / cryo EM
AuthorsZhao G / Perilla JR / Yufenyuy E / Meng X / Chen B / Ning J / Ahn J / Gronenborn AM / Schulten K / Aiken C / Zhang P
CitationJournal: Nature / Year: 2013
Title: Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics.
Authors: Gongpu Zhao / Juan R Perilla / Ernest L Yufenyuy / Xin Meng / Bo Chen / Jiying Ning / Jinwoo Ahn / Angela M Gronenborn / Klaus Schulten / Christopher Aiken / Peijun Zhang /
Abstract: Retroviral capsid proteins are conserved structurally but assemble into different morphologies. The mature human immunodeficiency virus-1 (HIV-1) capsid is best described by a 'fullerene cone' model, ...Retroviral capsid proteins are conserved structurally but assemble into different morphologies. The mature human immunodeficiency virus-1 (HIV-1) capsid is best described by a 'fullerene cone' model, in which hexamers of the capsid protein are linked to form a hexagonal surface lattice that is closed by incorporating 12 capsid-protein pentamers. HIV-1 capsid protein contains an amino-terminal domain (NTD) comprising seven α-helices and a β-hairpin, a carboxy-terminal domain (CTD) comprising four α-helices, and a flexible linker with a 310-helix connecting the two structural domains. Structures of the capsid-protein assembly units have been determined by X-ray crystallography; however, structural information regarding the assembled capsid and the contacts between the assembly units is incomplete. Here we report the cryo-electron microscopy structure of a tubular HIV-1 capsid-protein assembly at 8 Å resolution and the three-dimensional structure of a native HIV-1 core by cryo-electron tomography. The structure of the tubular assembly shows, at the three-fold interface, a three-helix bundle with critical hydrophobic interactions. Mutagenesis studies confirm that hydrophobic residues in the centre of the three-helix bundle are crucial for capsid assembly and stability, and for viral infectivity. The cryo-electron-microscopy structures enable modelling by large-scale molecular dynamics simulation, resulting in all-atom models for the hexamer-of-hexamer and pentamer-of-hexamer elements as well as for the entire capsid. Incorporation of pentamers results in closer trimer contacts and induces acute surface curvature. The complete atomic HIV-1 capsid model provides a platform for further studies of capsid function and for targeted pharmacological intervention.
History
DepositionApr 12, 2013-
Header (metadata) releaseMay 29, 2013-
Map releaseMay 29, 2013-
UpdateJun 12, 2013-
Current statusJun 12, 2013Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.355
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.355
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3j3y
  • Surface level: 0.355
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3j3q
  • Surface level: 0.355
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j3q
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_5639.map.gz / Format: CCP4 / Size: 17.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe figure shows the simulated density of all-atom HIV-1 capsid model (3J3Y) overlaid with a slice of HIV-1 core tomogram.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.25 Å/pix.
x 161 pix.
= 1006.25 Å
6.25 Å/pix.
x 175 pix.
= 1093.75 Å
6.25 Å/pix.
x 163 pix.
= 1018.75 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 6.25 Å
Density
Contour LevelBy AUTHOR: 0.355 / Movie #1: 0.355
Minimum - Maximum0.0 - 0.62596595
Average (Standard dev.)0.06133261 (±0.12504502)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions175163161
Spacing175163161
CellA: 1018.75 Å / B: 1093.75 Å / C: 1006.25 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.256.256.25
M x/y/z163175161
origin x/y/z0.0000.0000.000
length x/y/z1018.7501093.7501006.250
α/β/γ90.00090.00090.000
start NX/NY/NZ-132-122-147
NX/NY/NZ250274261
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS163175161
D min/max/mean0.0000.6260.061

-
Supplemental data

-
Sample components

-
Entire : HIV-1 core with A14C/E45C cross-linked capsid protein

EntireName: HIV-1 core with A14C/E45C cross-linked capsid protein
Components
  • Sample: HIV-1 core with A14C/E45C cross-linked capsid protein
  • Virus: Human immunodeficiency virus 1

-
Supramolecule #1000: HIV-1 core with A14C/E45C cross-linked capsid protein

SupramoleculeName: HIV-1 core with A14C/E45C cross-linked capsid protein / type: sample / ID: 1000 / Details: The sample was purified from HIV-1 virions / Number unique components: 1

-
Supramolecule #1: Human immunodeficiency virus 1

SupramoleculeName: Human immunodeficiency virus 1 / type: virus / ID: 1 / Name.synonym: HIV-1
Details: HIV-1 core was isolated from virions carrying A14C/E45C mutation in capsid protein.
NCBI-ID: 11676 / Sci species name: Human immunodeficiency virus 1 / Sci species strain: R9 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: HIV-1
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

-
Sample preparation

Concentration0.011 mg/mL
BufferpH: 8 / Details: 10 mM Tris-HCl, 100 mM NaCl, 1 mM EDTA
GridDetails: Quantifoil R2/2 200 mesh holey carbon copper grids
VitrificationCryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER
Method: Purified HIV-1 A14C/E45C cores (3 uL) were applied to the carbon side of glow-discharged, perforated R2/2 Quantifoil grids and quickly mixed with 3 uL of a 15 nM fiducial gold bead solution ...Method: Purified HIV-1 A14C/E45C cores (3 uL) were applied to the carbon side of glow-discharged, perforated R2/2 Quantifoil grids and quickly mixed with 3 uL of a 15 nM fiducial gold bead solution before plunge-freezing.

-
Electron microscopy

MicroscopeFEI POLARA 300
TemperatureMin: 80 K / Max: 85 K / Average: 82 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 115,000 times magnification
DateSep 11, 2010
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 53 / Average electron dose: 120 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 8.0 µm / Nominal defocus min: 8.0 µm / Nominal magnification: 39000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC / Tilt series - Axis1 - Min angle: -70 ° / Tilt series - Axis1 - Max angle: 66 ° / Tilt series - Axis1 - Angle increment: 2 °
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

-
Image processing

Final reconstructionAlgorithm: OTHER / Software - Name: tomo3d
Details: The raw tomogram was denoised using the nonlinear anisotropic diffusion edge-enhancing algorithm available in IMOD. The core density was segmented out using Volume Tracer in UCSF Chimera.
Number images used: 53

-
Atomic model buiding 1

Initial modelPDB ID:
SoftwareName: MD
DetailsThe model was built using hexamer of hexamers (PDB entry 3J34) and pentamer of hexamers (computer-based MD model available upon request).
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-3j3q:
Atomic-level structure of the entire HIV-1 capsid

PDB-3j3y:
Atomic-level structure of the entire HIV-1 capsid (186 hexamers + 12 pentamers)

+
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