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- PDB-3zhf: gamma 2 adaptin EAR domain crystal structure with preS1 site1 pep... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3zhf | ||||||
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Title | gamma 2 adaptin EAR domain crystal structure with preS1 site1 peptide NPDWDFN | ||||||
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![]() | PROTEIN TRANSPORT/VIRAL PROTEIN / PROTEIN TRANSPORT-VIRAL PROTEIN COMPLEX / GAE | ||||||
Function / homology | ![]() AP-1 adaptor complex / caveolin-mediated endocytosis of virus by host cell / Golgi to vacuole transport / clathrin adaptor activity / Lysosome Vesicle Biogenesis / Golgi-associated vesicle / vesicle-mediated transport / transport vesicle / intracellular protein transport / membrane => GO:0016020 ...AP-1 adaptor complex / caveolin-mediated endocytosis of virus by host cell / Golgi to vacuole transport / clathrin adaptor activity / Lysosome Vesicle Biogenesis / Golgi-associated vesicle / vesicle-mediated transport / transport vesicle / intracellular protein transport / membrane => GO:0016020 / endosome membrane / Golgi membrane / fusion of virus membrane with host endosome membrane / virion attachment to host cell / virion membrane / Golgi apparatus / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Juergens, M.C. / Voros, J. / Rautureau, G. / Shepherd, D. / Pye, V.E. / Muldoon, J. / Johnson, C.M. / Ashcroft, A. / Freund, S.M.V. / Ferguson, N. | ||||||
![]() | ![]() Title: The Hepatitis B Virus Pres1 Domain Hijacks Host Trafficking Proteins by Motif Mimicry. Authors: Jurgens, M.C. / Voros, J. / Rautureau, G.J.P. / Shepherd, D.A. / Pye, V.E. / Muldoon, J. / Johnson, C.M. / Ashcroft, A.E. / Freund, S.M.V. / Ferguson, N. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 43 KB | Display | ![]() |
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PDB format | ![]() | 29 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.4 KB | Display | ![]() |
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Full document | ![]() | 455.4 KB | Display | |
Data in XML | ![]() | 8.4 KB | Display | |
Data in CIF | ![]() | 10.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ymtC ![]() 4bcxSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 13762.746 Da / Num. of mol.: 1 / Fragment: EAR DOMAIN, RESIDUES 665-785 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 930.940 Da / Num. of mol.: 1 / Fragment: PRES1 DOMAIN, RESIDUES 85-91 / Source method: obtained synthetically / Details: AMIDATED C-TERMINUS, CARBOXYLATED N-TERMINUS / Source: (synth.) ![]() ![]() |
#3: Chemical | ChemComp-PEG / |
#4: Chemical | ChemComp-EDO / |
#5: Water | ChemComp-HOH / |
Nonpolymer details | AMINO GROUP (NH2): PEPTIDE C TERMINUS IS AMIDATED |
Sequence details | GGS IS A CLONING ARTEFACT AT THE PROTEIN N-TERMINUS |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.07 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 100 MM MES/IMIDAZOLE PH 6.5, 0.02 M 1,6-HEXANEDIOL, 0.02 M 1-BUTANOL, 0.02 M (RS)-1, 2-PROPANEDIOL, 0.02 M 2-PROPANOL, 0.02 M 1,4-BUTANEDIOL, 0.02 M 1,3-PROPANEDIOL, 10% (W/V) PEG 20000 AND ...Details: 100 MM MES/IMIDAZOLE PH 6.5, 0.02 M 1,6-HEXANEDIOL, 0.02 M 1-BUTANOL, 0.02 M (RS)-1, 2-PROPANEDIOL, 0.02 M 2-PROPANOL, 0.02 M 1,4-BUTANEDIOL, 0.02 M 1,3-PROPANEDIOL, 10% (W/V) PEG 20000 AND 24% (V/V) PEG400 (USING A 2:1 RATIO OF PROTEIN TO MOTHER LIQUOR), PEPTIDE WAS AT ABOUT 50 FOLD MOLAR EXCESS |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2395 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→37.46 Å / Num. obs: 15669 / % possible obs: 98.8 % / Observed criterion σ(I): 2.7 / Redundancy: 4.1 % / Biso Wilson estimate: 20.34 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.3 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.7 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 4BCX Resolution: 1.7→35.298 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 23.82 / 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: 1.7→35.298 Å
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Refine LS restraints |
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LS refinement shell |
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