+Open data
-Basic information
Entry | Database: PDB / ID: 1yq3 | |||||||||
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Title | Avian respiratory complex ii with oxaloacetate and ubiquinone | |||||||||
Components |
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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 / TIM22 mitochondrial import inner membrane insertion complex / : / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase / succinate dehydrogenase (quinone) activity / protein insertion into mitochondrial inner membrane / oxidoreductase activity, acting on the CH-CH group of donors / anaerobic respiration ...The tricarboxylic acid cycle / succinate metabolic process / TIM22 mitochondrial import inner membrane insertion complex / : / mitochondrial electron transport, succinate to ubiquinone / succinate dehydrogenase / succinate dehydrogenase (quinone) activity / protein insertion into mitochondrial inner membrane / oxidoreductase activity, acting on the CH-CH group of donors / anaerobic respiration / 3 iron, 4 sulfur cluster binding / protein transmembrane transporter activity / 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 / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Gallus gallus (chicken) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Huang, L. / Cobessi, D. / Tung, E.Y. / Berry, E.A. | |||||||||
Citation | 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. / Sun, G. / Cobessi, D. / Wang, A.C. / Shen, J.T. / Tung, E.Y. / Anderson, V.E. / Berry, E.A. #1: 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. #2: 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 |
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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 |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yq3.cif.gz | 264.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yq3.ent.gz | 200.6 KB | Display | PDB format |
PDBx/mmJSON format | 1yq3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1yq3_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 1yq3_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 1yq3_validation.xml.gz | 58.1 KB | Display | |
Data in CIF | 1yq3_validation.cif.gz | 82.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yq/1yq3 ftp://data.pdbj.org/pub/pdb/validation_reports/yq/1yq3 | HTTPS FTP |
-Related structure data
Related structure data | 1yq4C 2fbwC 1nekS C: citing same article (ref.) S: Starting model for refinement |
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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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Details | THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH IS ALSO THE BIOLOGICAL ASSEMBLY |
-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 68256.922 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: Q9YHT1, succinate dehydrogenase |
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#2: Protein | Mass: 28685.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: Q9YHT2, succinate dehydrogenase |
-SUCCINATE DEHYDROGENASE CYTOCHROME B, ... , 2 types, 2 molecules CD
#3: Protein | Mass: 15433.147 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: D0VWW3*PLUS, succinate dehydrogenase |
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#4: Protein | Mass: 10971.604 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: Q5ZIS0, succinate dehydrogenase |
-Sugars , 1 types, 1 molecules
#13: Sugar | ChemComp-JZR / |
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-Non-polymers , 11 types, 874 molecules
#5: Chemical | ChemComp-FAD / | ||||||||||||||||
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#6: Chemical | ChemComp-TEO / | ||||||||||||||||
#7: Chemical | ChemComp-UNL / Num. of mol.: 30 / Source method: obtained synthetically #8: Chemical | ChemComp-FES / | #9: Chemical | ChemComp-SF4 / | #10: Chemical | ChemComp-F3S / | #11: Chemical | ChemComp-UQ / | #12: Chemical | ChemComp-GOL / | #14: Chemical | ChemComp-HEM / | #15: Chemical | #16: 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: 3.5 Å3/Da / Density % sol: 64.54 % |
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Crystal grow | Temperature: 278 K / 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, 0.0016 M MNCL2, 0.0013 M MGCL2, 0.0015 M NA-AZIDE, 0.00025 M NA-EDTA, OXALOACETATE , pH 7.50, VAPOR ...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, 0.0016 M MNCL2, 0.0013 M MGCL2, 0.0015 M NA-AZIDE, 0.00025 M NA-EDTA, OXALOACETATE , pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979462 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 20, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979462 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→99 Å / Num. obs: 79236 / % possible obs: 87.5 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Biso Wilson estimate: 34.4 Å2 / Rsym value: 0.119 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.19→2.27 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.61 / Rsym value: 0.27 / % possible all: 49 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1NEK Resolution: 2.2→38.66 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 72.0779 Å2 / ksol: 0.309824 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→38.66 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.24 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 15
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Xplor file |
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