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Yorodumi- PDB-5w1c: Crystal structure of MBP fused activation-induced cytidine deamin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5w1c | ||||||
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Title | Crystal structure of MBP fused activation-induced cytidine deaminase (AID) in complex with cytidine | ||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA / Class switch recombination / Cytidine deaminase / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | Function and homology information somatic diversification of immunoglobulins / regulation of nuclear cell cycle DNA replication / single-stranded DNA cytosine deaminase / DNA cytosine deamination / cytidine to uridine editing / deoxycytidine deaminase activity / cytidine deaminase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / negative regulation of DNA methylation-dependent heterochromatin formation / isotype switching ...somatic diversification of immunoglobulins / regulation of nuclear cell cycle DNA replication / single-stranded DNA cytosine deaminase / DNA cytosine deamination / cytidine to uridine editing / deoxycytidine deaminase activity / cytidine deaminase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / negative regulation of DNA methylation-dependent heterochromatin formation / isotype switching / DNA demethylation / carbohydrate transmembrane transporter activity / somatic hypermutation of immunoglobulin genes / B cell differentiation / Chromatin modifications during the maternal to zygotic transition (MZT) / P-body / mRNA processing / outer membrane-bounded periplasmic space / defense response to virus / cellular response to lipopolysaccharide / defense response to bacterium / ubiquitin protein ligase binding / protein-containing complex / RNA binding / zinc ion binding / identical protein binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli O157:H7 (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.18 Å | ||||||
Authors | Qiao, Q. / Wang, L. / Wu, H. | ||||||
Citation | Journal: Mol. Cell / Year: 2017 Title: AID Recognizes Structured DNA for Class Switch Recombination. Authors: Qiao, Q. / Wang, L. / Meng, F.L. / Hwang, J.K. / Alt, F.W. / Wu, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5w1c.cif.gz | 244.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5w1c.ent.gz | 190.4 KB | Display | PDB format |
PDBx/mmJSON format | 5w1c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w1/5w1c ftp://data.pdbj.org/pub/pdb/validation_reports/w1/5w1c | HTTPS FTP |
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-Related structure data
Related structure data | 5w0rSC 5w0uC 5w0zC 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 , 1 types, 2 molecules BA
#1: Protein | Mass: 62081.289 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O157:H7 (bacteria), (gene. exp.) Homo sapiens (human) Gene: malE, Z5632, ECs5017, AICDA, AID / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P0AEY0, UniProt: Q9GZX7, single-stranded DNA cytosine deaminase |
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-DNA chain , 2 types, 2 molecules DG
#2: DNA chain | Mass: 3687.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
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#3: DNA chain | Mass: 3638.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
-Non-polymers , 4 types, 8 molecules
#4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.92 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 0.1 M MES at pH 6.2, 3% PEG3350, 10 mM CaCl2 and 20mM Cytidine |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 3.18→155.3 Å / Num. obs: 28767 / % possible obs: 99.3 % / Redundancy: 6.5 % / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 3.18→3.36 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4138 / CC1/2: 0.974 / Rpim(I) all: 0.335 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5W0R Resolution: 3.18→125.455 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.1 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.18→125.455 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1801→3.2937 Å
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