3D Electron Microscopy (3D-EM) Data Navigator [English / [日本語]]
Top Gallery List Statistics Shape search Viewer
Movie pageYodrodumi (structure viewer)
PDBj>EM Navigator>Detail page - PDB-5njg

This page is a legacy version and will be discarded in future. The new page is here.

Structure of an ABC transporter: part of the structure that could be built de novo

by single particle reconstruction, at 3.78 A resolution

Movie

Orientation:

#1: Deposited structure unit, Imaged by Jmol

#2: Superimposition on EM map, EMDB-3654, Imaged by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 5njg
TitleStructure of an ABC transporter: part of the structure that could be built de novo
DescriptorATP-binding cassette sub-family G member 2
5D3-Fab heavy chain
5D3-Fab light chain
KeywordsTRANSPORT PROTEIN, ABC transporter, transport protein
AuthorsTaylor, N.M.I., Manolaridis, I., Jackson, S.M., Kowal, J., Stahlberg, H., Locher, K.P.
DateDeposition: 2017-03-28, Release: 2017-06-07
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, FSSP, SCOP
Structure Visualization
MoviesMovie Page

#1: Deposited structure unit, Imaged by Jmol

#2: Superimposition on EM map, EMDB-3654, Imaged by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries

EMDB-3654

CiteFit

Cite: data citing same article

Fit: target map of fitting

Similar-shape strucutres
Search for similar-shape assemblies throgh:
EMDB + EM entries in PDB
all of EMDB & PDB (Omokage search)
Article
Citation - primary
ArticleNature, Vol. 546, Issue 7659, Page 504-509, Year 2017
TitleStructure of the human multidrug transporter ABCG2.
AuthorsNicholas M I Taylor, Ioannis Manolaridis, Scott M Jackson, Julia Kowal, Henning Stahlberg, Kaspar P Locher
Center for Cellular Imaging and NanoAnalytics (C-CINA), Biozentrum, University of Basel, Mattenstrasse 26, 4058 Basel, Switzerland.
Institute of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093 Zürich, Switzerland.
KeywordsABCG2 protein, human, ATP Binding Cassette Transporter, Sub-Family G, Member 2 (antagonists & inhibitors), Adenosine Triphosphatases (chemistry, 3.6.1.-), Amino Acid Sequence, Antibodies (chemistry), Binding Sites, Biological Transport, Cholesterol (chemistry), Cryoelectron Microscopy, Humans, Immunoglobulin Fab Fragments (chemistry), Models, Molecular, Neoplasm Proteins (antagonists & inhibitors), Polymorphism, Single Nucleotide (genetics), Protein Domains
LinksPubMed: 28554189, DOI: 10.1038/nature22345
Components
ID 1 : Breast cancer resistance protein,CDw338,Mitoxantrone resistance-associated protein,Placenta-specific ATP-binding cassette transporter,Urate exporter
DescriptionATP-binding cassette sub-family G member 2
Typepolypeptide(L)
MutationHas an N-terminal Flag-tag
Formula weight73395.742 Da
Number of molecules2
ID1
SourceMethod: Isolated from a genetically manipulated source
Src id: 1
Gene: Human, ABCG2, ABCP, BCRP, BCRP1, MXR, ID:9606, Homo sapiens
Host: Human, HEK293-EBNA, ID:9606, Homo sapiens
Alt source flag: sample
Beg seq num: 1
End seq num: 664
Seq type: Biological sequence
LinksUniProt: Q9UNQ0, Sequence view
ID 2 : 5D3-Fab heavy chain
Description5D3-Fab heavy chain
Typepolypeptide(L)
Formula weight23843.633 Da
Number of molecules2
ID2
SourceMethod: Isolated from a genetically manipulated source
Src id: 1
Gene: House Mouse, ID:10090, Mus musculus
Host: House Mouse, Hybridoma, ID:10090, Mus musculus


Alt source flag: sample
Beg seq num: 1
End seq num: 221
Seq type: Biological sequence
LinksSequence view
ID 3 : 5D3-Fab light chain
Description5D3-Fab light chain
Typepolypeptide(L)
Formula weight23594.016 Da
Number of molecules2
ID3
SourceMethod: Isolated from a genetically manipulated source
Src id: 1
Gene: House Mouse, ID:10090, Mus musculus
Host: House Mouse, Hybridoma, ID:10090, Mus musculus
Alt source flag: sample
Beg seq num: 1
End seq num: 214
Seq type: Biological sequence
LinksSequence view
ID 4 : N-ACETYL-D-GLUCOSAMINE
DescriptionN-ACETYL-D-GLUCOSAMINE
Typenon-polymer
Formula weight221.208 Da
Number of molecules4
ID4
SourceMethod: Isolated from a genetically manipulated source
Sample
Entity assembly
Entity id list1, 2, 3
NameNanodisc-reconstituted ABCG2 in complex with 5D3-Fab
SourceMULTIPLE SOURCES
TypeCOMPLEX
Entity assembly
Entity id list1
NameNanodisc-reconstituted ABCG2
Parent id1
SourceRECOMBINANT
TypeCOMPLEX
Entity assembly
Entity id list2, 3
Name5D3-Fab
Parent id1
SourceRECOMBINANT
TypeCOMPLEX
Buffer
Specimen id1
PH7.5
Experiment
Aggregation statePARTICLE
Reconstruction methodSINGLE PARTICLE
Vitrification
Specimen id1
Cryogen nameETHANE-PROPANE
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: FEI TITAN KRIOS
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage300 kV
Illumination modeFLOOD BEAM
Lens
ModeBRIGHT FIELD
Image scans
Image recording id1
Frames per image40
Used frames per image1-40
Processing
Single particle entity
Image processing id1
Point symmetryC2
3D reconstruction
Image processing id1
Number of particles97612
Resolution3.78 A
Resolution methodFSC 0.143 CUT-OFF
Symmetry typePOINT
3D fitting
Refinement SpaceREAL
Download
PDB format
Allpdb5njg.ent.gz
pdb5njg.ent (uncompressed file)
Header onlypdb5njg.ent.gz
mmCIF format
mmCIF5njg.cif.gz
XML format
All5njg.xml.gz
No-atom5njg-noatom.xml.gz
Ext-atom5njg-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 2.7 MB
.webm (WebM/VP8 format), 5.3 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 6.1 MB