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Yorodumi- PDB-4ayx: STRUCTURE OF THE HUMAN MITOCHONDRIAL ABC TRANSPORTER, ABCB10 (ROD... -
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-Basic information
Entry | Database: PDB / ID: 4ayx | ||||||
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Title | STRUCTURE OF THE HUMAN MITOCHONDRIAL ABC TRANSPORTER, ABCB10 (ROD FORM B) | ||||||
Components | ATP-BINDING CASSETTE SUB-FAMILY B MEMBER 10 | ||||||
Keywords | MEMBRANE PROTEIN / MITOCHONDRIAL TRANSPORT | ||||||
Function / homology | Function and homology information positive regulation of heme biosynthetic process / Mitochondrial ABC transporters / positive regulation of hemoglobin biosynthetic process / mitochondrial unfolded protein response / heme biosynthetic process / mitochondrial transport / ABC-type transporter activity / erythrocyte development / positive regulation of erythrocyte differentiation / mitochondrial membrane ...positive regulation of heme biosynthetic process / Mitochondrial ABC transporters / positive regulation of hemoglobin biosynthetic process / mitochondrial unfolded protein response / heme biosynthetic process / mitochondrial transport / ABC-type transporter activity / erythrocyte development / positive regulation of erythrocyte differentiation / mitochondrial membrane / mitochondrial inner membrane / protein homodimerization activity / ATP hydrolysis activity / mitochondrion / ATP binding Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Pike, A.C.W. / Shintre, C.A. / Li, Q. / Kim, J. / von Delft, F. / Barr, A.J. / Das, S. / Chaikuad, A. / Xia, X. / Quigley, A. ...Pike, A.C.W. / Shintre, C.A. / Li, Q. / Kim, J. / von Delft, F. / Barr, A.J. / Das, S. / Chaikuad, A. / Xia, X. / Quigley, A. / Dong, Y. / Dong, L. / Krojer, T. / Vollmar, M. / Muniz, J.R.C. / Bray, J.E. / Berridge, G. / Chalk, R. / Gileadi, O. / Burgess-Brown, N. / Shrestha, L. / Goubin, S. / Yang, J. / Mahajan, P. / Mukhopadhyay, S. / Bullock, A.N. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Edwards, A.M. / Carpenter, E.P. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Structures of Abcb10, a Human ATP-Binding Cassette Transporter in Apo- and Nucleotide-Bound States Authors: Shintre, C.A. / Pike, A.C.W. / Li, Q. / Kim, J. / Barr, A.J. / Goubin, S. / Shrestha, L. / Yang, J. / Berridge, G. / Ross, J. / Stansfeld, P.J. / Sansom, M.S.P. / Edwards, A.M. / Bountra, C. ...Authors: Shintre, C.A. / Pike, A.C.W. / Li, Q. / Kim, J. / Barr, A.J. / Goubin, S. / Shrestha, L. / Yang, J. / Berridge, G. / Ross, J. / Stansfeld, P.J. / Sansom, M.S.P. / Edwards, A.M. / Bountra, C. / Marsden, B.D. / von Delft, F. / Bullock, A.N. / Gileadi, O. / Burgess-Brown, N.A. / Carpenter, E.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ayx.cif.gz | 238 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ayx.ent.gz | 186.8 KB | Display | PDB format |
PDBx/mmJSON format | 4ayx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ayx_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 4ayx_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 4ayx_validation.xml.gz | 22.6 KB | Display | |
Data in CIF | 4ayx_validation.cif.gz | 31 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/4ayx ftp://data.pdbj.org/pub/pdb/validation_reports/ay/4ayx | HTTPS FTP |
-Related structure data
Related structure data | 3zdqC 4aytSC 4aywC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 3 molecules A
#1: Protein | Mass: 64816.684 Da / Num. of mol.: 1 / Fragment: ABC TRANSPORTER, RESIDUES 152-738 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFB-LIC-BSE / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q9NRK6 |
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#5: Sugar |
-Non-polymers , 5 types, 38 molecules
#2: Chemical | ChemComp-GLY / | ||
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#3: Chemical | ChemComp-MG / | ||
#4: Chemical | ChemComp-ACP / | ||
#6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.56 Å3/Da / Density % sol: 65.44 % / Description: NONE |
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Crystal grow | pH: 9.5 Details: 0.1 M SODIUM CHLORIDE, 0.1 M GLYCINE PH 9.5, 33% (V/V) PEG 300. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→39 Å / Num. obs: 21011 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 96.44 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 1.8 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4AYT Resolution: 2.9→39 Å / Cor.coef. Fo:Fc: 0.8942 / Cor.coef. Fo:Fc free: 0.8641 / SU R Cruickshank DPI: 0.749 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.681 / SU Rfree Blow DPI: 0.344 / SU Rfree Cruickshank DPI: 0.355 Details: REFINEMENT NOTE 1: IDEAL-DIST CONTACT T CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY= MG NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=4427. NUMBER OF ATOMS WITH APPROX ...Details: REFINEMENT NOTE 1: IDEAL-DIST CONTACT T CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY= MG NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=4427. NUMBER OF ATOMS WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON- BONDED CONTACTS=1. NCS TARGET REPRESENTATION: LSSR (-TARGET_
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Displacement parameters | Biso mean: 90.84 Å2
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Refine analyze | Luzzati coordinate error obs: 0.525 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.04 Å / Total num. of bins used: 11
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Refinement TLS params. | Method: refined / Origin x: -40.3783 Å / Origin y: 46.4598 Å / Origin z: 4.9489 Å
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Refinement TLS group | Selection details: CHAIN A AND RESID(154 - 724) |