+Open data
-Basic information
Entry | Database: PDB / ID: 1r4m | ||||||
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Title | APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex | ||||||
Components |
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Keywords | CELL CYCLE | ||||||
Function / homology | Function and homology information E1 NEDD8-activating enzyme / NEDD8 activating enzyme activity / endomitotic cell cycle / ubiquitin activating enzyme activity / NEDD8 transferase activity / regulation of proteolysis / mitotic DNA replication checkpoint signaling / protein neddylation / TGF-beta receptor signaling activates SMADs / anatomical structure morphogenesis ...E1 NEDD8-activating enzyme / NEDD8 activating enzyme activity / endomitotic cell cycle / ubiquitin activating enzyme activity / NEDD8 transferase activity / regulation of proteolysis / mitotic DNA replication checkpoint signaling / protein neddylation / TGF-beta receptor signaling activates SMADs / anatomical structure morphogenesis / post-translational protein modification / regulation of neuron apoptotic process / NIK-->noncanonical NF-kB signaling / Dectin-1 mediated noncanonical NF-kB signaling / Iron uptake and transport / protein modification process / modification-dependent protein catabolic process / protein tag activity / Cargo recognition for clathrin-mediated endocytosis / UCH proteinases / protein localization / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / ubiquitin-dependent protein catabolic process / neuron apoptotic process / regulation of apoptotic process / regulation of cell cycle / protein ubiquitination / protein heterodimerization activity / DNA damage response / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / signal transduction / protein-containing complex / proteolysis / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Walden, H. / Podgorski, M.S. / Holton, J.M. / Schulman, B.A. | ||||||
Citation | Journal: Mol.Cell / Year: 2003 Title: The structure of the APPBP1-UBA3-NEDD8-ATP complex reveals the basis for selective ubiquitin-like protein activation by an E1. Authors: Walden, H. / Podgorski, M.S. / Huang, D.T. / Miller, D.W. / Howard, R.J. / Minor, D.L. / Holton, J.M. / Schulman, B.A. | ||||||
History |
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Remark 999 | SEQUENCE The residues 600-608, 700-706, 800-802 and 900-917 of the chains B,D,F,H were modelled ...SEQUENCE The residues 600-608, 700-706, 800-802 and 900-917 of the chains B,D,F,H were modelled originally as alanines due to poor electron density. The residue names were assigned arbitrarily and the connectivity is unclear. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r4m.cif.gz | 715.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r4m.ent.gz | 589 KB | Display | PDB format |
PDBx/mmJSON format | 1r4m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1r4m_validation.pdf.gz | 467 KB | Display | wwPDB validaton report |
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Full document | 1r4m_full_validation.pdf.gz | 622.4 KB | Display | |
Data in XML | 1r4m_validation.xml.gz | 95.3 KB | Display | |
Data in CIF | 1r4m_validation.cif.gz | 139.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/1r4m ftp://data.pdbj.org/pub/pdb/validation_reports/r4/1r4m | HTTPS FTP |
-Related structure data
Related structure data | 1r4nC 1ngv 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 59829.652 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q13564 #2: Protein | Mass: 48394.219 Da / Num. of mol.: 4 / Mutation: C216A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TBC4 #3: Protein | Mass: 8573.978 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15843 #4: Chemical | ChemComp-ZN / |
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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: 3.02 Å3/Da / Density % sol: 59.3 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG10K, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / pH: 7.6 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 16, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 113653 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.8 / Redundancy: 24.6 % / Biso Wilson estimate: 84 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 3→3.1 Å / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 1.8 / % possible all: 99.9 |
Reflection | *PLUS Num. obs: 113171 / Num. measured all: 2787084 |
Reflection shell | *PLUS % possible obs: 99.9 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1NGV 1ngv Resolution: 3→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 80 Å2
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Refinement step | Cycle: LAST / Resolution: 3→50 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.24 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.35 |