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Open data
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Basic information
Entry | Database: PDB / ID: 1w63 | ||||||
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Title | AP1 clathrin adaptor core | ||||||
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![]() | ENDOCYTOSIS / CLATHRIN ADAPTOR / TRANSPORT / COATED PITS | ||||||
Function / homology | ![]() 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 / heart development / early endosome / lysosomal membrane / intracellular membrane-bounded organelle / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Heldwein, E. / Macia, E. / Wang, J. / Yin, H.L. / Kirchhausen, T. / Harrison, S.C. | ||||||
![]() | ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.8 MB | Display | ![]() |
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PDB format | ![]() | 1.5 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 600.3 KB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 357.1 KB | Display | |
Data in CIF | ![]() | 509.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1gw5 S: Starting model for refinement |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() #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.) ![]() ![]() ![]() #3: Protein | Mass: 48590.730 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Protein | Mass: 18757.994 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Sequence details | FIRST 5 RESIDUES (GAGMS) OF CHAIN A ORIGINATE FROM EXPRESSION | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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 |