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

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 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
Authors	Hafenstein, S., Kostyuchenko, V.A., Rossmann, M.G.
Date	Deposition: 2006-11-06, Release: 2007-03-27
PDBj Mine pages	Summary, Structural Details, Experimental Details, Functional Details
Other databases	RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
Movies	Movie Page #1: Depositted structure unit, Made by Jmol #2: Superimposing with simplified surface model of EM map, EMDB-1288, Made by Jmol #3: Superimposing with EM 3D map: EMDB-1288, Made by UCSF CHIMERA
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	EMDB-1288 CiteFit EMDB-1287 Cite PDB-1cx8 Cite: data citing same article Fit: target map of fitting
Similar strucutres (beta)	Diagram PDB-3iym PDB-3dkn PDB-2xkx EMDB-1649 List of similar structure data about Omokage system

Article
Citation - primary
Article	Proc. Natl. Acad. Sci. U.S.A., Vol. 104, Issue 16, Page 6585-9, Year 2007
Title	Asymmetric binding of transferrin receptor to parvovirus capsids.
Authors	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 Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054, USA.
Keywords	Animals, 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)
Links	DOI: 10.1073/pnas.0701574104, PubMed: 17420467, PMC: PMC1871829

Components
ID 1 : TfR1, TR, TfR, Trfr, CD71 antigen, T9, p90
Image
Description	Transferrin receptor protein 1
Type	polymer
Fragment	THE ECTODOMAIN OF HUMAN TRANSFERRIN RECEPTOR
Formula weight	71623.695 Da
Number of molecules	2
Source	Method: 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
Links	UniProt: P02786, Sequence view

Sample
Assembly
Aggregation state	PARTICLE
Details	NOT AVAILABLE
Name	MIXTURE OF EMPTY CANINE PARVOVIRUS CAPSIDS AND ECTODOMAINS OF FELINE TRANSFERRIN RECEPTORS
Entity assembly
Details	Based on PDB entry 1CX8
Buffer
Name	0.02M TRIS-HCL
Experiment
Reconstruction method	SINGLE PARTICLE
Specimen type	VITREOUS ICE (CRYO EM)
Sample preparation
pH	7.5
Sample support
Details	QUANTIFOIL 200
Vitrification
Details	PLUNGED IN LIQUID ETHANE

Processing
2D projection selection
Number of particles	8566
Software name	XMIPP, SPIDER, EMAN
Single particle entity
Symmetry type	MIXED SYMMETRY
3D reconstruction
Actual pixel size	2.6 A/pix
CTF correction method	CTF correction of each particle
Details	a modified version of XMIPP software was used
Method	projection matching
Nominal pixel size	2.6 A/pix
Resolution	27.0 A
3D fitting
Method	MANUAL FITTING USING THE PROGRAM O
Refinement Protocol	RIGID BODY
Refinement Space	REAL
Target criteria	BEST VISUAL FIT USING THE PROGRAM O
Refine
Ls d res high	27.0 A
ID	1
Refine hist
D res high	27.0
Total atoms	10112
Protein atoms	10112