[English] 日本語
- PDB-5mcy: The structure of the mature HIV-1 CA pentamer in intact virus par... -

Open data

ID or keywords:


no data

Basic information

Database: PDB / ID: 5mcy
TitleThe structure of the mature HIV-1 CA pentamer in intact virus particles
DescriptorCapsid protein p24
KeywordsVIRAL PROTEIN / retrovirus / HIV-1 / capsid / pentamer / viral protein
Specimen sourceHuman immunodeficiency virus 1 / virus / ヒト免疫不全ウイルス 1
MethodElectron microscopy (8.8 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 Yorodumi Papers
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
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 28, 2016Structure modelrepositoryInitial release
1.1Aug 30, 2017Structure modelAuthor supporting evidence / Data collection / Experimental preparation / Refinement descriptionem_3d_fitting / em_imaging_optics / em_sample_support / em_software / pdbx_audit_support_em_3d_fitting.target_criteria / _em_imaging_optics.energyfilter_name / _em_sample_support.grid_type / _em_software.name / _pdbx_audit_support.funding_organization

Structure visualization

  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-3466
  • Imaged by Jmol
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /

Downloads & links


Deposited unit
A: Capsid protein p24
B: Capsid protein p24
F: Capsid protein p24
R: Capsid protein p24
S: Capsid protein p24
T: Capsid protein p24
P: Capsid protein p24
Q: Capsid protein p24
M: Capsid protein p24
N: Capsid protein p24
O: Capsid protein p24
G: Capsid protein p24
d: Capsid protein p24
g: Capsid protein p24
b: Capsid protein p24
e: Capsid protein p24
h: Capsid protein p24
Z: Capsid protein p24
c: Capsid protein p24
f: Capsid protein p24

Theoretical massNumber of molelcules
Total (without water)493,08520

TypeNameSymmetry operationNumber
identity operation1_5551


#1: Polypeptide(L)
Capsid protein p24

Mass: 24654.268 Da / Num. of mol.: 20
Source: (natural) Human immunodeficiency virus 1 / virus / ヒト免疫不全ウイルス 1
References: UniProt: B6DRA0

Cellular component

Molecular function

Biological process

Experimental details


EM experimentAggregation state: PARTICLE / Reconstruction method: SUBTOMOGRAM AVERAGING

Sample preparation

ComponentName: Human immunodeficiency virus 1 / Type: VIRUS
Details: HIV-1 particles were produced by infection of MT-4 cells with HIV-1 strain NL43 by coculture.
Entity ID: 1 / Source: NATURAL
Source (natural)Organism: Human immunodeficiency virus 1
Details of virusEmpty: NO / Enveloped: YES / Virus isolate: STRAIN / Virus type: VIRION
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 % / Chamber temperature: 292 kelvins
Details: 10nm colloidal gold was added to the sample prior to plunge freezing

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: GIF Quantum LS / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV
Image scansDimension width: 3710 / Dimension height: 3838 / Movie frames/image: 5


EM software
IDNameCategoryImaging IDImage processing IDFitting ID
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.
SymmetryPoint symmetry: C5
3D reconstructionResolution: 8.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 2191 / Number of class averages: 1 / Symmetry type: POINT
EM volume selectionDetails: Subtomograms were extracted in the pentamerically-coordinated positions of the mature CA hexameric lattice.
Number of tomograms: 103 / Number of volumes extracted: 2191 / Reference model: reference free
Atomic model buildingRef protocol: FLEXIBLE FIT / Ref space: REAL / Target criteria: Cross-correlation coefficient
Atomic model building
IDPDB-IDPdb chain ID 3D fitting IDPdb chain residue range

About Yorodumi


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


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