[English] 日本語
Yorodumi
- EMDB-5294: 3D reconstruction of frozen hydrated HIV-1 integrase dimer in com... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 5294
Title3D reconstruction of frozen hydrated HIV-1 integrase dimer in complex with two Fabs.
KeywordsHIV-1 integrase dimer / Fab
SampleHIV-1 integrase - Fab complex
SourceHuman immunodeficiency virus 1 / virus / HIV-1 / ヒト免疫不全ウイルス 1
Map dataThis is 3D reconstruction of frozen hydrated HIV-1 integrase dimer in complex with 2 Fabs.
Methodsingle particle reconstruction, at 9.6 Å resolution
AuthorsWu S / Avila-Sakar A / Kim J / Booth DS / Greenberg CH / Rossi A / Liao M / Alian A / Griner SL / Juge N / Mergel CM / Chaparro-Riggers J / Strop P / Tampe R / Edwards RH / Stroud RM / Craik CS / Cheng Y
CitationStructure, 2012, 20, 582-592

Structure, 2012, 20, 582-592 Yorodumi Papers
Fabs enable single particle cryoEM studies of small proteins.
Shenping Wu / Agustin Avila-Sakar / JungMin Kim / David S Booth / Charles H Greenberg / Andrea Rossi / Maofu Liao / Xueming Li / Akram Alian / Sarah L Griner / Narinobu Juge / Yadong Yu / Claudia M Mergel / Javier Chaparro-Riggers / Pavel Strop / Robert Tampé / Robert H Edwards / Robert M Stroud / Charles S Craik / Yifan Cheng

DateDeposition: May 22, 2011 / Header (metadata) release: Oct 26, 2011 / Map release: May 29, 2012 / Last update: May 29, 2012

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 1
  • 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_5294.map.gz (map file in CCP4 format, 12665 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
148 pix
1.8 Å/pix.
= 266.4 Å
148 pix
1.8 Å/pix.
= 266.4 Å
148 pix
1.8 Å/pix.
= 266.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.8 Å
Density
Contour Level:1 (by author), 1 (movie #1):
Minimum - Maximum-1.03870511 - 3.12253904
Average (Standard dev.)-0.00818645 (0.18489794)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions148148148
Origin-74-54-74
Limit739373
Spacing148148148
CellA=B=C: 266.4 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.81.81.8
M x/y/z148148148
origin x/y/z0.0000.0000.000
length x/y/z266.400266.400266.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-54-74-74
NC/NR/NS148148148
D min/max/mean-1.0393.123-0.008

-
Supplemental data

-
Sample components

-
Entire HIV-1 integrase - Fab complex

EntireName: HIV-1 integrase - Fab complex / Number of components: 2 / Oligomeric State: 2 Fabs bind to one integrase dimer
MassTheoretical: 160 kDa / Experimental: 160 kDa

-
Component #1: protein, integrase

ProteinName: integrase / Oligomeric Details: dimer / Details: dimer, total molecular weight 65kDa / Recombinant expression: Yes / Number of Copies: 2
MassTheoretical: 32 kDa / Experimental: 32 kDa
SourceSpecies: Human immunodeficiency virus 1 / virus / HIV-1 / ヒト免疫不全ウイルス 1
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

-
Experimental details

-
Sample preparation

Specimen stateparticle
Support film200 mesh Quantifoil
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 100 K / Humidity: 100 % / Details: Vitrification instrument: Vitrobot

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20 / Date: Feb 1, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 30 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 80000 X (nominal) / Cs: 2.1 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000 - 5000 nm
Specimen HolderHolder: CT3500 / Model: GATAN LIQUID NITROGEN
CameraDetector: TVIPS TEMCAM-F816 (8k x 8k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 14000 / Applied symmetry: C2 (2 fold cyclic)
3D reconstructionAlgorithm: Fourier space / Software: Frealign / CTF correction: Each particle / Resolution: 9.6 Å / Resolution method: FSC 0.143

-
Atomic model buiding

Modeling #1Software: Chimera / Refinement protocol: rigid body / Refinement space: REAL / Details: Protocol: rigid body
Input PDB model: 1EXQ
Modeling #2Software: Chimera / Refinement protocol: rigid body / Refinement space: REAL / Details: Protocol: rigid body
Input PDB model: 1M71

+
About Yorodumi

-
News

-
Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

-
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)

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