[English] 日本語
Yorodumi
- PDB-2nsu: Crystal structure of the ectodomain of human transferrin receptor... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 2nsu
TitleCrystal structure of the ectodomain of human transferrin receptor fitted into a cryo-EM reconstruction of canine parvovirus and feline transferrin receptor complex
DescriptorTransferrin receptor protein 1
KeywordsMETAL TRANSPORT / transferrin receptor / virus-receptor complex
Specimen sourceHomo sapiens / human
MethodElectron microscopy (27 A resolution / Single particle / Vitreous ice (cryo EM))
AuthorsHafenstein, S. / Kostyuchenko, V.A. / Rossmann, M.G.
CitationProc. Natl. Acad. Sci. U.S.A., 2007, 104, 6585-6589

Proc. Natl. Acad. Sci. U.S.A., 2007, 104, 6585-6589 StrPapers
Asymmetric binding of transferrin receptor to parvovirus capsids.
Susan Hafenstein / Laura M Palermo / Victor A Kostyuchenko / Chuan Xiao / Marc C Morais / Christian D S Nelson / Valorie D Bowman / Anthony J Battisti / Paul R Chipman / Colin R Parrish / Michael G Rossmann

DateDeposition: Nov 6, 2006 / Release: Mar 27, 2007 / Last modification: Feb 24, 2009
Remark 999 SEQUENCE AUTHORS STATE THAT PDB ENTRY 1CX8 WAS USED FOR FITTING IN THIS ENTRY. THE SEQUENCE DIFFERENCES EXIST IN THE STRUCTURE 1CX8. THE UNIPROT ENTRY P02786 IS A RESULT OF DNA SEQUENCING, WHILE 1CX8 SEQUENCE IS APPARENTLY BASED ON MRNA SEQUENCE.

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Simplified surface model + fitted atomic model
  • EMDB-1288
  • 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: Transferrin receptor protein 1
B: Transferrin receptor protein 1


Theoretical massNumber of molelcules
Total (without water)143,2472
Polyers143,2472
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Polypeptide(L)Transferrin receptor protein 1 / TfR1 / TR / TfR / Trfr / CD71 antigen / T9 / p90


Mass: 71623.695 Da / Num. of mol.: 2 / Fragment: THE ECTODOMAIN OF HUMAN TRANSFERRIN RECEPTOR / Source: (gene. exp.) Homo sapiens / human / References: UniProt: P02786

Cellular component

Molecular function

Biological process

+
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SINGLE PARTICLE / Specimen type: VITREOUS ICE (CRYO EM)

-
Sample preparation

Assembly of specimenName: MIXTURE OF EMPTY CANINE PARVOVIRUS CAPSIDS AND ECTODOMAINS OF FELINE TRANSFERRIN RECEPTORS
Aggregation state: PARTICLE / Details: NOT AVAILABLE
ComponentDetails: Based on PDB entry 1CX8
Buffer solutionName: 0.02M TRIS-HCL
Sample preparationpH: 7.5
Specimen supportDetails: QUANTIFOIL 200
VitrificationDetails: PLUNGED IN LIQUID ETHANE

-
Electron microscopy imaging

MicroscopyMicroscope model: FEI/PHILIPS CM200 FEG / Date: Jan 22, 2003
Electron gunElectron source: FEG / Accelerating voltage: 200 kV / Electron dose: 25.96 e/A2
Electron lensMode: BRIGHTFIELD / Nominal magnification: 50000 X / Calibrated magnification: 54000 X / Nominal defocus max: 3900 nm / Nominal defocus min: 1700 nm / Cs: 2 mm
CameraType: KODAK SO163 FILM
EM image scansNumber digital images: 115
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

Image selectionSoftware name: XMIPP, SPIDER, EMAN / Number of particles: 8566
EM single particle entitySymmetry type: MIXED SYMMETRY
3D reconstructionMethod: projection matching / Resolution: 27 A / Nominal pixel size: 2.6 A/pix / Actual pixel size: 2.6 A/pix / CTF correction method: CTF correction of each particle / Details: a modified version of XMIPP software was used
Atomic model buildingMethod: MANUAL FITTING USING THE PROGRAM O / Ref protocol: RIGID BODY / Ref space: REAL / Target criteria: BEST VISUAL FIT USING THE PROGRAM O
Atomic model buildingPDB-ID: 2NSU
Least-squares processHighest resolution: 27 A
Refine hist #LASTHighest resolution: 27 A
Number of atoms included #LASTProtein: 10112 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 10112

+
About Yorodumi

-
News

-
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

+
Mar 3, 2016. Presentation (PDF format) at IPR seminar on Feb 19.

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