[English] 日本語
Yorodumi
- PDB-5md5: The structure of the mature HIV-1 CA hexameric lattice with curva... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 5md5
TitleThe structure of the mature HIV-1 CA hexameric lattice with curvature parameters: tilt=11, twist=0
DescriptorCapsid protein p24
KeywordsVIRAL PROTEIN / retrovirus / HIV-1 / capsid / lattice curvature / viral protein
Specimen sourceHuman immunodeficiency virus 1 / virus / ヒト免疫不全ウイルス 1
MethodElectron microscopy (8.2 Å resolution / Particle / Subtomogram averaging)
AuthorsMattei, S. / Glass, B. / Hagen, W.J.H. / Kraeusslich, H.-G. / Briggs, J.A.G.
CitationScience, 2016, 354, 1434-1437

Science, 2016, 354, 1434-1437 StrPapers
The structure and flexibility of conical HIV-1 capsids determined within intact virions.
Simone Mattei / Bärbel Glass / Wim J H Hagen / Hans-Georg Kräusslich / John A G Briggs

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 10, 2016 / Release: Dec 28, 2016

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
3D viewer


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

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

Downloads & links

-
Assembly

Deposited unit
A: Capsid protein p24
B: Capsid protein p24
F: Capsid protein p24
W: Capsid protein p24
a: Capsid protein p24
b: Capsid protein p24
f: Capsid protein p24
C: Capsid protein p24
D: Capsid protein p24
E: Capsid protein p24
G: Capsid protein p24
H: Capsid protein p24
I: Capsid protein p24
J: Capsid protein p24


Theoretical massNumber of molelcules
Total (without water)164,77514
Polyers164,77514
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA

-
Components

#1: Polypeptide(L)
Capsid protein p24


Mass: 8370.568 Da / Num. of mol.: 8 / Fragment: C-terminal domain, UNP residues 141-214
Source: (natural) Human immunodeficiency virus 1 / virus / ヒト免疫不全ウイルス 1
References: UniProt: A0A0K0V8J8

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)
Capsid protein p24


Mass: 16301.689 Da / Num. of mol.: 6 / Fragment: N-terminal domain, UNP residues 123-269
Source: (natural) Human immunodeficiency virus 1 / virus / ヒト免疫不全ウイルス 1
References: UniProt: E9MJT0

Cellular component

Molecular function

Biological process

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SUBTOMOGRAM AVERAGING

-
Sample preparation

ComponentName: Human immunodeficiency virus 1
Details: HIV-1 particles were produced by infection of MT-4 cells with HIV-1 strain NL43 by coculture.
Type: VIRUS / Entity ID: 1, 2 / Source: NATURAL
Source (natural)Organism: Human immunodeficiency virus 1
Details of the virusEmpty: NO / Enveloped: YES / Virus isolate: STRAIN / Virus type: VIRION
EM virus natural hostOrganism: Homo sapiens
Buffer solutionpH: 7.4
Buffer componentName: PBS
SpecimenDetails: Viral particles were purified from cell culture supernatant by iodixanol gradient centrifugation.
Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 / Grid type: C-Flat
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 %
Details: 10nm colloidal gold was added to the sample prior to plunge freezing
Chamber temperature: 292 kelvins

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS / Details: Nanoprobe
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 / Nominal defocus max: 6500 nm / Nominal defocus min: 2000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 mm / Alignment procedure: ZEMLIN TABLEAU
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 2.2 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Number of grids imaged: 1
EM imaging opticsEnergyfilter name: GATAN Quantum LS / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV
Image scansDimension width: 3710 / Dimension height: 3838 / Movie frames/image: 5

-
Processing

EM software
IDNameCategoryImaging IDImage processing IDFitting ID
2SerialEMIMAGE ACQUISITION1
4IMODCTF CORRECTION1
7ChimeraMODEL FITTING1
12AV3FINAL EULER ASSIGNMENT1
13TOMFINAL EULER ASSIGNMENT1
15AV3RECONSTRUCTION1
16TOMRECONSTRUCTION1
Image processingDetails: Frames were aligned using MotionCorr. Tilts in a tilt series were exposure filtered for cumulative electron dose. Tomograms were reconstructed using IMOD.
CTF correctionDetails: CTF correction was performed using the ctfphaseflip program in IMOD prior to backprojection.
Type: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C1
3D reconstructionResolution: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 17239
Details: The final reconstruction is obtained by averaging, without further alignment, subtomograms that were selected based on the local curvature of the hexameric lattice. This reconstruction has hexamer-hexamer curvature parameters: tilt=11, twist=0.
Number of class averages: 1 / Symmetry type: POINT
EM volume selectionDetails: Subtomograms were extracted along the manually rendered core surface of each viral particle.
Number of tomograms: 103 / Number of volumes extracted: 652618 / Reference model: reference free
Atomic model buildingRef protocol: RIGID BODY FIT / Ref space: REAL / Target criteria: Correlation coefficient

+
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