+Open data
-Basic information
Entry | Database: PDB / ID: 1w63 | ||||||
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Title | AP1 clathrin adaptor core | ||||||
Components |
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Keywords | ENDOCYTOSIS / CLATHRIN ADAPTOR / TRANSPORT / COATED PITS | ||||||
Function / homology | Function and homology information basolateral protein secretion / endosome to melanosome transport / AP-1 adaptor complex / Lysosome Vesicle Biogenesis / platelet dense granule organization / clathrin adaptor complex / clathrin coat / Lysosome Vesicle Biogenesis / melanosome assembly / Golgi Associated Vesicle Biogenesis ...basolateral protein secretion / endosome to melanosome transport / AP-1 adaptor complex / Lysosome Vesicle Biogenesis / platelet dense granule organization / clathrin adaptor complex / clathrin coat / Lysosome Vesicle Biogenesis / melanosome assembly / Golgi Associated Vesicle Biogenesis / MHC class II antigen presentation / Golgi to vacuole transport / Golgi Associated Vesicle Biogenesis / clathrin coat assembly / clathrin-coated vesicle membrane / clathrin adaptor activity / MHC class II antigen presentation / retrograde transport, endosome to Golgi / determination of left/right symmetry / clathrin-coated vesicle / clathrin binding / clathrin-coated pit / vesicle-mediated transport / Neutrophil degranulation / trans-Golgi network membrane / kidney development / intracellular protein transport / trans-Golgi network / terminal bouton / presynapse / heart development / early endosome / lysosomal membrane / intracellular membrane-bounded organelle / synapse / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / cytosol Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) RATTUS NORVEGICUS (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å | ||||||
Authors | Heldwein, E. / Macia, E. / Wang, J. / Yin, H.L. / Kirchhausen, T. / Harrison, S.C. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2004 Title: Crystal Structure of the Clathrin Adaptor Protein 1 Core Authors: Heldwein, E. / Macia, E. / Wang, J. / Yin, H.L. / Kirchhausen, T. / Harrison, S.C. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w63.cif.gz | 1.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb1w63.ent.gz | 1.5 MB | Display | PDB format |
PDBx/mmJSON format | 1w63.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1w63_validation.pdf.gz | 600.3 KB | Display | wwPDB validaton report |
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Full document | 1w63_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 1w63_validation.xml.gz | 357.1 KB | Display | |
Data in CIF | 1w63_validation.cif.gz | 509.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w6/1w63 ftp://data.pdbj.org/pub/pdb/validation_reports/w6/1w63 | HTTPS FTP |
-Related structure data
Related structure data | 1gw5 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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2 |
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3 |
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4 |
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5 |
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6 |
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Unit cell |
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-Components
#1: Protein | Mass: 69728.781 Da / Num. of mol.: 6 / Fragment: CORE, RESIDUES 0-612 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PFASTBAC1, PFASTBACHTB / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P22892 #2: Protein | Mass: 66086.398 Da / Num. of mol.: 6 / Fragment: CORE, RESIDUE 1-584 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PFASTBAC1, PFASTBACHTB / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P52303 #3: Protein | Mass: 48590.730 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PFASTBAC1, PFASTBACHTB / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P35585 #4: Protein | Mass: 18757.994 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PFASTBAC1, PFASTBACHTB / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P61967 Sequence details | FIRST 5 RESIDUES (GAGMS) OF CHAIN A ORIGINATE FROM EXPRESSION | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 7 |
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-Sample preparation
Crystal | Density Matthews: 4.27 Å3/Da / Density % sol: 70.97 % Description: DATA WERE COLLECTED USING DOUBLE CCD DETECTOR SETUP |
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Crystal grow | pH: 7 Details: 8-9% ETHANOL, 0.1 M NA HEPES, PH 7.5, 2 MM CYSTEINE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 1.1808 |
Detector | Type: ADSC CCD / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1808 Å / Relative weight: 1 |
Reflection | Resolution: 4.01→39.84 Å / Num. obs: 141015 / % possible obs: 81.3 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 4→4.1 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.5 / % possible all: 69.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GW5 1gw5 Resolution: 4→40 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 Details: CHAIN A IS MISSING RESIDUES 590-613 CHAIN B IS MISSING RESIDUES 1, 268-274, AND 584 CHAIN M IS MISSING RESIDUES 1, 146-156, 219-231, AND 363-372 CHAIN S IS MISSING RESIDUES 149-158
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Solvent computation | Bsol: 41.3296 Å2 / ksol: 0.32 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 4→40 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM |