|Entry||Database: PDB / ID: 2nsu|
|Title||Crystal structure of the ectodomain of human transferrin receptor fitted into a cryo-EM reconstruction of canine parvovirus and feline transferrin receptor complex|
|Descriptor||Transferrin receptor protein 1|
|Keywords||METAL TRANSPORT / transferrin receptor / virus-receptor complex|
|Specimen source||Homo sapiens / human|
|Method||Electron microscopy (27 Å resolution / Particle / Single particle)|
|Authors||Hafenstein, S. / Kostyuchenko, V.A. / Rossmann, M.G.|
|Citation||Proc. Natl. Acad. Sci. U.S.A., 2007, 104, 6585-6589|
Proc. Natl. Acad. Sci. U.S.A., 2007, 104, 6585-6589 Yorodumi Papers
SummaryFull reportAbout validation report
|Date||Deposition: Nov 6, 2006 / Release: Mar 27, 2007|
|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.|
Downloads & links
A: Transferrin receptor protein 1
B: Transferrin receptor protein 1
Mass: 71622.961 Da / Num. of mol.: 2 / Fragment: THE ECTODOMAIN OF HUMAN TRANSFERRIN RECEPTOR / Source: (gene. exp.) Homo sapiens / human / References: UniProt: P02786
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE|
|Component||Name: MIXTURE OF EMPTY CANINE PARVOVIRUS CAPSIDS AND ECTODOMAINS OF FELINE TRANSFERRIN RECEPTORS|
Type: VIRUS / Details: Based on PDB entry 1CX8
|Buffer solution||Name: 0.02M TRIS-HCL / Details: 0.02M TRIS-HCL / pH: 7.5|
|Specimen||Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES|
|Specimen support||Details: QUANTIFOIL 200|
|Vitrification||Cryogen name: ETHANE / Details: PLUNGED IN LIQUID ETHANE|
-Electron microscopy imaging
|Microscopy||Microscope model: FEI/PHILIPS CM200FEG / Date: Jan 22, 2003|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELD / Nominal magnification: 50000 / Calibrated magnification: 54000 / Nominal defocus max: 3900 nm / Nominal defocus min: 1700 nm / Cs: 2 mm|
|Image recording||Electron dose: 25.96 e/Å2 / Film or detector model: KODAK SO-163 FILM|
|Image scans||Number digital images: 115|
|Radiation||Diffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M|
|Radiation wavelength||Relative weight: 1|
|CTF correction||Details: CTF correction of each particle|
|Symmetry||Point symmetry: C2|
|3D reconstruction||Method: projection matching / Resolution: 27 Å / Number of particles: 8566 / Nominal pixel size: 2.6 / Actual pixel size: 2.6 / Details: a modified version of XMIPP software was used / Symmetry type: POINT|
|Atomic model building||Details: METHOD--MANUAL FITTING USING THE PROGRAM O REFINEMENT PROTOCOL--RIGID BODY|
Ref protocol: RIGID BODY FIT / Ref space: REAL / Target criteria: BEST VISUAL FIT USING THE PROGRAM O
|Atomic model building||PDB-ID: 1CX8|
|Least-squares process||Highest resolution: 27 Å|
|Refine hist #LAST||Highest resolution: 27 Å|
|Number of atoms included #LAST||Protein: 10112 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 10112|
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