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- PDB-2nsu: Crystal structure of the ectodomain of human transferrin receptor... -

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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 Å resolution / Particle / Single particle)
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

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 6, 2006 / Release: Mar 27, 2007
RevisionDateData content typeGroupProviderType
1.0Mar 27, 2007Structure modelrepositoryInitial release
1.1May 1, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
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.

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Assembly

Deposited unit
A: Transferrin receptor protein 1
B: Transferrin receptor protein 1


Theoretical massNumber of molelcules
Total (without water)143,2462
Polyers143,2462
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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


Mass: 71622.961 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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: MIXTURE OF EMPTY CANINE PARVOVIRUS CAPSIDS AND ECTODOMAINS OF FELINE TRANSFERRIN RECEPTORS
Type: VIRUS / Details: Based on PDB entry 1CX8
Buffer solutionName: 0.02M TRIS-HCL / Details: 0.02M TRIS-HCL / pH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: QUANTIFOIL 200
VitrificationCryogen name: ETHANE / Details: PLUNGED IN LIQUID ETHANE

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Electron microscopy imaging

MicroscopyMicroscope model: FEI/PHILIPS CM200FEG / Date: Jan 22, 2003
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 / Calibrated magnification: 54000 / Nominal defocus max: 3900 nm / Nominal defocus min: 1700 nm / Cs: 2 mm
Image recordingElectron dose: 25.96 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNumber digital images: 115
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1EMANRECONSTRUCTION
2SPIDERRECONSTRUCTION
3XMIPPRECONSTRUCTION
CTF correctionDetails: CTF correction of each particle
SymmetryPoint symmetry: C2
3D reconstructionMethod: 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 buildingDetails: 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 buildingPDB-ID: 1CX8
Least-squares processHighest resolution: 27 Å
Refine hist #LASTHighest resolution: 27 Å
Number of atoms included #LASTProtein: 10112 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 10112

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