[English] 日本語
Yorodumi- PDB-4akm: Crystal structure of the human lysosome-associated membrane prote... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4akm | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the human lysosome-associated membrane protein LAMP-3 (aka DC-LAMP) | ||||||
Components | LYSOSOME-ASSOCIATED MEMBRANE GLYCOPROTEIN 3 | ||||||
Keywords | MEMBRANE PROTEIN / GLYCOSYLATION / BETA PRISM | ||||||
Function / homology | Function and homology information regulation of viral life cycle / alveolar lamellar body membrane / establishment of protein localization to organelle / response to interferon-alpha / negative regulation of proteasomal protein catabolic process / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / regulation of autophagy / late endosome membrane / adaptive immune response / vesicle ...regulation of viral life cycle / alveolar lamellar body membrane / establishment of protein localization to organelle / response to interferon-alpha / negative regulation of proteasomal protein catabolic process / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / regulation of autophagy / late endosome membrane / adaptive immune response / vesicle / membrane => GO:0016020 / early endosome / lysosomal membrane / intracellular membrane-bounded organelle / positive regulation of gene expression / perinuclear region of cytoplasm / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.687 Å | ||||||
Authors | Krausze, J. / Wilke, S. / Buessow, K. | ||||||
Citation | Journal: Bmc Biol. / Year: 2012 Title: Crystal Structure of the Conserved Domain of the Dc Lysosomal Associated Membrane Protein: Implications for the Lysosomal Glycocalyx. Authors: Wilke, S. / Krausze, J. / Bussow, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4akm.cif.gz | 70.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4akm.ent.gz | 56.1 KB | Display | PDB format |
PDBx/mmJSON format | 4akm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4akm_validation.pdf.gz | 454.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4akm_full_validation.pdf.gz | 457.1 KB | Display | |
Data in XML | 4akm_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 4akm_validation.cif.gz | 17.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ak/4akm ftp://data.pdbj.org/pub/pdb/validation_reports/ak/4akm | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.9291, 0.35759, 0.09437), Vector: |
-Components
#1: Protein | Mass: 18656.707 Da / Num. of mol.: 2 Fragment: MEMBRANE-PROXIMAL PART OF LUMINAL DOMAIN, RESIDUES 222-381 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): CHO LEC3.2.8.1 / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: Q9UQV4 #2: Chemical | ChemComp-IR3 / #3: Sugar | #4: Water | ChemComp-HOH / | Nonpolymer details | N-ACETYL-D-GLUCOSAMIN | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.28 Å3/Da / Density % sol: 62.5 % / Description: NONE |
---|---|
Crystal grow | pH: 5 Details: PROTEIN WAS CRYSTALLIZED FROM 5% PEG 6000, 0.1 M CITRIC ACID, PH 5.0; THEN SOAKED IN 0.014 M AMMONIUM HEXACHLOROIRIDATE(III)HYDRATE AND CRYO-PROTECTED IN 30% PEG 6000. |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.10371, 1.1042, 1.1009 | ||||||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 7, 2010 / Details: MIRROR | ||||||||||||
Radiation | Monochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
| ||||||||||||
Reflection | Resolution: 2.7→20 Å / Num. obs: 11238 / % possible obs: 91.1 % / Observed criterion σ(I): 2.5 / Redundancy: 2.86 % / Biso Wilson estimate: 55.49 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.48 | ||||||||||||
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 2.84 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.47 / % possible all: 97.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 2.687→19.295 Å / SU ML: 0.87 / σ(F): 1.98 / Phase error: 29.06 / Stereochemistry target values: MLHL
| |||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 10.238 Å2 / ksol: 0.235 e/Å3 | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.3 Å2
| |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.687→19.295 Å
| |||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||
LS refinement shell |
|