[English] 日本語
Yorodumi- PDB-2h88: Avian Mitochondrial Respiratory Complex II at 1.8 Angstrom Resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 2h88 | ||||||
---|---|---|---|---|---|---|---|
Title | Avian Mitochondrial Respiratory Complex II at 1.8 Angstrom Resolution | ||||||
Components | (SUCCINATE DEHYDROGENASE ...) x 4 | ||||||
Keywords | OXIDOREDUCTASE / COMPLEX II / MEMBRANE PROTEIN / HEME PROTEIN / IRON SULFUR PROTEIN / CYTOCHROME B / REDOX ENZYME / RESPIRATORY CHAIN / OXALOACETATE / UBIQUINONE | ||||||
Function / homology | Function and homology information The tricarboxylic acid cycle / : / succinate metabolic process / Oxidoreductases; Acting on the CH-OH group of donors; With a quinone or similar compound as acceptor / respiratory chain complex II (succinate dehydrogenase) / : / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / 3 iron, 4 sulfur cluster binding ...The tricarboxylic acid cycle / : / succinate metabolic process / Oxidoreductases; Acting on the CH-OH group of donors; With a quinone or similar compound as acceptor / respiratory chain complex II (succinate dehydrogenase) / : / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase (quinone) activity / succinate dehydrogenase / 3 iron, 4 sulfur cluster binding / ubiquinone binding / tricarboxylic acid cycle / aerobic respiration / respiratory electron transport chain / mitochondrial membrane / 2 iron, 2 sulfur cluster binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / mitochondrial inner membrane / electron transfer activity / heme binding / mitochondrion / metal ion binding Similarity search - Function | ||||||
Biological species | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / rigid body refinement / Resolution: 1.74 Å | ||||||
Authors | Huang, L.S. / Shen, J.T. / Wang, A.C. / Berry, E.A. | ||||||
Citation | Journal: Biochim.Biophys.Acta Title: Crystallographic studies of the binding of ligands to the dicarboxylate site of Complex II, and the identity of the ligand in the Authors: Huang, L.S. / Shen, J.T. / Wang, A.C. / Berry, E.A. #1: Journal: J.Biol.Chem. / Year: 2006 Title: 3-nitropropionic acid is a suicide inhibitor of mitochondrial respiration that, upon oxidation by complex II, forms a covalent adduct with a catalytic base arginine in the active site of the enzyme. Authors: Huang, L.S. / Sun, G. / Cobessi, D. / Wang, A.C. / Shen, J.T. / Tung, E.Y. / Anderson, V.E. / Berry, E.A. #2: Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Crystallization of mitochondrial respiratory complex II from chicken heart: a membrane-protein complex diffracting to 2.0 A Authors: Huang, L.S. / Borders, T.M. / Shen, J.T. / Wang, C.J. / Berry, E.A. #3: Journal: Cell(Cambridge,Mass.) / Year: 2005 Title: Crystal structure of mitochondrial respiratory membrane protein complex II. Authors: Sun, F. / Huo, X. / Zhai, Y. / Wang, A. / Xu, J. / Su, D. / Bartlam, M. / Rao, Z. | ||||||
History |
| ||||||
Remark 999 | SEQUENCE SEQUENCE 1-71 OF SUCCINATE DEHYDROGENASE FP SUBUNIT DO NOT MATCH TO ANY OF THE DATABASE ...SEQUENCE SEQUENCE 1-71 OF SUCCINATE DEHYDROGENASE FP SUBUNIT DO NOT MATCH TO ANY OF THE DATABASE SEQUENCE. THE SEQUENCE OF SUCCINATE DEHYDROGENASE CYTOCHROME B, LARGE SUBUNIT IS NOT AVAILABLE IN ANY OF THE DATABASE SEQUENCE AT THE TIME OF PROCESSING. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2h88.cif.gz | 496.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2h88.ent.gz | 393.8 KB | Display | PDB format |
PDBx/mmJSON format | 2h88.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2h88_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2h88_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 2h88_validation.xml.gz | 102.5 KB | Display | |
Data in CIF | 2h88_validation.cif.gz | 151.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h8/2h88 ftp://data.pdbj.org/pub/pdb/validation_reports/h8/2h88 | HTTPS FTP |
-Related structure data
Related structure data | 2h89C 2fbwS 1zpo S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
-SUCCINATE DEHYDROGENASE ... , 4 types, 8 molecules ANBOCPDQ
#1: Protein | Mass: 68256.922 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: Q9YHT1, succinate dehydrogenase #2: Protein | Mass: 28685.221 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: Q9YHT2, succinate dehydrogenase #3: Protein | Mass: 15392.052 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: D0VWW3*PLUS, succinate dehydrogenase #4: Protein | Mass: 10971.604 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: Q5ZIS0, succinate dehydrogenase |
---|
-Sugars , 1 types, 2 molecules
#14: Sugar |
---|
-Non-polymers , 11 types, 2114 molecules
#5: Chemical | ChemComp-K / #6: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | ChemComp-UNL / Num. of mol.: 64 / Source method: obtained synthetically #10: Chemical | #11: Chemical | #12: Chemical | #13: Chemical | #15: Chemical | #16: Water | ChemComp-HOH / | |
---|
-Details
Has protein modification | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.72 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 50 G/L PEG-3350, 25 ML/L ISOPROPANOL, 15 ML/L PEG-400 0.05 M NA-HEPES, 0.01 M TRIS-HCL, 0.0025 M FUMARATE, 0.0005 M MNCL2, 0.0013 M MGCL2, 0.0015 M NA-AZIDE, 0.00025 M NA-EDTA. Type 1 ...Details: 50 G/L PEG-3350, 25 ML/L ISOPROPANOL, 15 ML/L PEG-400 0.05 M NA-HEPES, 0.01 M TRIS-HCL, 0.0025 M FUMARATE, 0.0005 M MNCL2, 0.0013 M MGCL2, 0.0015 M NA-AZIDE, 0.00025 M NA-EDTA. Type 1 orthorhombic crystalls grew initially, after 1 month these monoclinic crystals appeared., pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 12, 2005 |
Radiation | Monochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.74→60 Å / Num. all: 292236 / Num. obs: 292236 / % possible obs: 91.3 % / Observed criterion σ(F): -999 / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 23.6 Å2 / Rsym value: 0.122 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 1.74→1.77 Å / Redundancy: 2 % / Mean I/σ(I) obs: 0.89 / Num. unique all: 8881 / Rsym value: 0.99 / % possible all: 55.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: rigid body refinement Starting model: 2FBW Resolution: 1.74→45.14 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 85.5341 Å2 / ksol: 0.360845 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.7 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.74→45.14 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15
|