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Crystal structure of the ectodomain of human transferrin receptor fitted into a cryo-EM reconstruction of canine parvovirus and feline transferrin receptor complex

by single particle reconstruction, at 27 A resolution

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#1: Depositted structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1288, Image by Jmol

#3: Superimposing with EM 3D map: EMDB-1288, Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 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
AuthorsHafenstein, S., Kostyuchenko, V.A., Rossmann, M.G.
DateDeposition: 2006-11-06, Release: 2007-03-27
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
MoviesMovie Page

#1: Depositted structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-1288, Image by Jmol

#3: Superimposing with EM 3D map: EMDB-1288, Image by UCSF CHIMERA

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EMDB-1288

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Article
Citation - primary
ArticleProc. Natl. Acad. Sci. U.S.A., Vol. 104, Issue 16, Page 6585-9, Year 2007
TitleAsymmetric binding of transferrin receptor to parvovirus capsids.
AuthorsSusan 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
Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054, USA.
KeywordsAnimals, Binding Sites, Capsid (chemistry), Cats, Cryoelectron Microscopy, Crystallography, X-Ray, Dogs, Feline panleukopenia virus (chemistry), Humans, Parvovirus, Canine (chemistry), Protein Binding, Receptors, Transferrin (chemistry), Spodoptera, Virion (chemistry)
LinksDOI: 10.1073/pnas.0701574104, PubMed: 17420467, PMC: PMC1871829
Components
ID 1 : TfR1, TR, TfR, Trfr, CD71 antigen, T9, p90
Image
DescriptionTransferrin receptor protein 1
Typepolypeptide(L)
FragmentTHE ECTODOMAIN OF HUMAN TRANSFERRIN RECEPTOR
Formula weight71623.695 Da
Number of molecules2
ID1
SourceMethod: Isolated from a genetically manipulated source
Gene: human, Homo, TFRC, ID:9606, Homo sapiens
Host: Chinese hamster, Cricetulus, ID:10029, OVARY CELLS, Cricetulus griseus, Plasmid
Plasmid name: PCMVTFR
LinksUniProt: P02786, Sequence view
Sample
Assembly
Aggregation statePARTICLE
DetailsNOT AVAILABLE
NameMIXTURE OF EMPTY CANINE PARVOVIRUS CAPSIDS AND ECTODOMAINS OF FELINE TRANSFERRIN RECEPTORS
Entity assembly
Assembly-ID1
DetailsBased on PDB entry 1CX8
Buffer
Name0.02M TRIS-HCL
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Sample preparation
pH7.5
Sample support
DetailsQUANTIFOIL 200
Vitrification
DetailsPLUNGED IN LIQUID ETHANE
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: FEI/PHILIPS CM200 FEG
Date2003-01-22
Electron gun
Electron sourceFEG
Accelerating voltage200 kV
Electron dose25.96 e/A**2
Lens
ModeBRIGHTFIELD
MagnificationCalibrated: 54000 X, Nominal: 50000 X
CsNominal: 2 mm
Nominal defocusMax: 3900 nm, Min: 1700 nm
Detector
TypeKODAK SO163 FILM
Image scans
Number digital images115
Processing
2D projection selection
Number of particles8566
Software nameXMIPP, SPIDER, EMAN
Single particle entity
Symmetry typeMIXED SYMMETRY
3D reconstruction
Actual pixel size2.6 A/pix
CTF correction methodCTF correction of each particle
Detailsa modified version of XMIPP software was used
Methodprojection matching
Nominal pixel size2.6 A/pix
Resolution27.0 A
3D fitting
MethodMANUAL FITTING USING THE PROGRAM O
Refinement ProtocolRIGID BODY
Refinement SpaceREAL
Target criteriaBEST VISUAL FIT USING THE PROGRAM O
3D fitting list
3D Fitting ID1
Refine
Refine idELECTRON MICROSCOPY
Ls d res high27.0 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
D res high27.0
Total atoms10112
Protein atoms10112
Download
PDB format
Allpdb2nsu.ent.gz
pdb2nsu.ent (uncompressed file)
Header onlypdb2nsu.ent.gz
mmCIF format
mmCIF2nsu.cif.gz
XML format
All2nsu.xml.gz
No-atom2nsu-noatom.xml.gz
Ext-atom2nsu-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 2.8 MB
.webm (WebM/VP8 format), 3.6 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 4.6 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3 MB
.webm (WebM/VP8 format), 3.9 MB