[English] 日本語
Yorodumi
- EMDB-5136: CryoEM Structure of Tubular Assembly of HIV-1 CA and Evidence for... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 5136
TitleCryoEM Structure of Tubular Assembly of HIV-1 CA and Evidence for a Novel Interface
SampleHIV-1 CA A92E
SourceHuman immunodeficiency virus / virus
Map dataThis is a map of tubular assembly of HIV-1 CA
Methodhelical reconstruction, at 16 Å resolution
AuthorsByeon IL / Meng X / Jung J / Zhao G / Ahn J / Concel J / Aiken C / Gronenborn AM / Zhang P
CitationCell, 2009, 139, 780-790

Cell, 2009, 139, 780-790 StrPapers
Structural convergence between Cryo-EM and NMR reveals intersubunit interactions critical for HIV-1 capsid function.
In-Ja L Byeon / Xin Meng / Jinwon Jung / Gongpu Zhao / Ruifeng Yang / Jinwoo Ahn / Jiong Shi / Jason Concel / Christopher Aiken / Peijun Zhang / Angela M Gronenborn

DateDeposition: Oct 20, 2009 / Header (metadata) release: Nov 9, 2009 / Map release: May 5, 2010 / Last update: Sep 27, 2011

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0055
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0055
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide
Supplemental images

Downloads & links

-
Map

Fileemd_5136.map.gz (map file in CCP4 format, 27001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
120 pix
2.15 Å/pix.
= 258. Å
240 pix
2.15 Å/pix.
= 516. Å
240 pix
2.15 Å/pix.
= 516. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.15 Å
Density
Contour Level:0.01 (by emdb), 0.0055 (movie #1):
Minimum - Maximum-0.0263844 - 0.0278307
Average (Standard dev.)0.00019507 (0.00626063)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions240240120
Origin000
Limit239239119
Spacing240240120
CellA: 516 Å / B: 516 Å / C: 258 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.152.152.15
M x/y/z240240120
origin x/y/z0.0000.0000.000
length x/y/z516.000516.000258.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240120
D min/max/mean-0.0260.0280.000

-
Supplemental data

-
Sample components

-
Entire HIV-1 CA A92E

EntireName: HIV-1 CA A92E / Details: component name, HIV-1 CA protein / Number of components: 6

-
Component #1: protein, HIV-1 CA protein

ProteinName: HIV-1 CA protein / a.k.a: hexamer / Recombinant expression: Yes
SourceSpecies: Human immunodeficiency virus / virus

-
Experimental details

-
Sample preparation

Specimen statefilament
Helical parametersHand: RIGHT HANDED
VitrificationInstrument: NONE / Cryogen name: NITROGEN

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
LensImaging mode: BRIGHT FIELD
Specimen HolderHolder: liquid nitrogen-cooled cryo specimen holder / Model: GATAN LIQUID NITROGEN

-
Image processing

ProcessingMethod: helical reconstruction
3D reconstructionResolution: 16 Å / Resolution method: FSC 0.5

-
Atomic model buiding

Modeling #1Software: Chimera / Refinement space: REAL
Input PDB model: 3DIK

+
About Yorodumi

-
News

-
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. See below links for details.
  • 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

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more