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- PDB-5gv0: Crystal structure of the membrane-proximal domain of mouse lysoso... -

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Basic information

Entry
Database: PDB / ID: 5gv0
TitleCrystal structure of the membrane-proximal domain of mouse lysosome-associated membrane protein 1 (LAMP-1)
ComponentsLysosome-associated membrane glycoprotein 1
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


regulation of organelle transport along microtubule / : / granzyme-mediated programmed cell death signaling pathway / phagolysosome membrane / autophagic cell death / alveolar lamellar body / cytolytic granule membrane / cytolytic granule / positive regulation of natural killer cell degranulation / establishment of protein localization to organelle ...regulation of organelle transport along microtubule / : / granzyme-mediated programmed cell death signaling pathway / phagolysosome membrane / autophagic cell death / alveolar lamellar body / cytolytic granule membrane / cytolytic granule / positive regulation of natural killer cell degranulation / establishment of protein localization to organelle / Golgi to lysosome transport / vacuole / autolysosome / positive regulation of natural killer cell mediated cytotoxicity / autophagosome membrane / phagocytic vesicle / Neutrophil degranulation / multivesicular body / sarcolemma / melanosome / synaptic vesicle / late endosome / late endosome membrane / cytoplasmic vesicle / spermatogenesis / vesicle / lysosome / protein stabilization / endosome membrane / endosome / lysosomal membrane / protein domain specific binding / external side of plasma membrane / neuronal cell body / dendrite / perinuclear region of cytoplasm / enzyme binding / cell surface / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Porin - #110 / Lysosome-associated membrane glycoprotein, conserved site / Lysosome-associated membrane glycoproteins duplicated domain signature. / LAMP glycoproteins transmembrane and cytoplasmic domain signature. / Lysosome-associated membrane glycoprotein / Lysosome-associated membrane glycoprotein (Lamp) / Lysosome-associated membrane glycoprotein family profile. / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Lysosome-associated membrane glycoprotein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsTomabechi, Y. / Ehara, H. / Kukimoto-Niino, M. / Shirouzu, M.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2016
Title: Lysosome-associated membrane proteins-1 and -2 (LAMP-1 and LAMP-2) assemble via distinct modes
Authors: Terasawa, K. / Tomabechi, Y. / Ikeda, M. / Ehara, H. / Kukimoto-Niino, M. / Wakiyama, M. / Podyma-Inoue, K.A. / Rajapakshe, A.R. / Watabe, T. / Shirouzu, M. / Hara-Yokoyama, M.
History
DepositionSep 1, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / citation ...chem_comp / citation / diffrn_source / pdbx_struct_oper_list
Item: _chem_comp.type / _citation.journal_id_CSD ..._chem_comp.type / _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysosome-associated membrane glycoprotein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3317
Polymers18,2541
Non-polymers1,0776
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-6 kcal/mol
Surface area8790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.596, 50.047, 95.144
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lysosome-associated membrane glycoprotein 1 / / Lysosome-associated membrane protein 1 / 120 kDa lysosomal membrane glycoprotein / CD107 antigen- ...Lysosome-associated membrane protein 1 / 120 kDa lysosomal membrane glycoprotein / CD107 antigen-like family member A / LGP-120 / Lysosomal membrane glycoprotein A / LGP-A / P2B


Mass: 18253.611 Da / Num. of mol.: 1 / Fragment: UNP residues 208-370
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lamp1, Lamp-1 / Plasmid: pOriP / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P11438
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: SO4
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 2M ammonium sulphate, 0.1M sodium HEPES (pH 7.5), 2% (v/v) polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 24809 / % possible obs: 99.3 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.059 / Net I/av σ(I): 50.639 / Net I/σ(I): 16.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.5-1.534.50.1480.98194.1
1.53-1.554.90.1530.982199.3
1.55-1.585.70.1430.987199.8
1.58-1.6270.1360.992199.9
1.62-1.657.10.1180.99199.8
1.65-1.697.10.1140.9921100
1.69-1.7370.1080.9911100
1.73-1.7870.0970.993199.9
1.78-1.8370.0880.993199.7
1.83-1.896.90.0850.994199.8
1.89-1.966.80.0760.995199.9
1.96-2.046.80.0710.995199.8
2.04-2.136.90.0670.995199.9
2.13-2.2470.0650.9961100
2.24-2.3870.0660.996199.9
2.38-2.5670.0670.995199.9
2.56-2.826.60.0660.997199.9
2.82-3.236.30.0610.9971100
3.23-4.076.50.0520.997199.2
4.07-506.30.0370.999195.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1690refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→34.48 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 18.62
RfactorNum. reflection% reflection
Rfree0.1963 2000 8.08 %
Rwork0.1743 --
obs0.1761 24751 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.35 Å2 / Biso mean: 19.8439 Å2 / Biso min: 7.86 Å2
Refinement stepCycle: final / Resolution: 1.5→34.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1236 0 66 201 1503
Biso mean--29.73 30.52 -
Num. residues----162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051323
X-RAY DIFFRACTIONf_angle_d1.0371795
X-RAY DIFFRACTIONf_chiral_restr0.043223
X-RAY DIFFRACTIONf_plane_restr0.004227
X-RAY DIFFRACTIONf_dihedral_angle_d11.691472
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5003-1.53780.2391350.18711529166495
1.5378-1.57940.22471410.179816161757100
1.5794-1.62590.20771400.175615881728100
1.6259-1.67840.20481430.168316211764100
1.6784-1.73830.21461410.171515991740100
1.7383-1.80790.20071400.173416051745100
1.8079-1.89020.17371430.160616171760100
1.8902-1.98990.20091420.165816321774100
1.9899-2.11450.16861450.161716381783100
2.1145-2.27780.21291440.162216331777100
2.2778-2.50690.19441420.172516301772100
2.5069-2.86950.20711470.184216641811100
2.8695-3.61470.1991460.166416621808100
3.6147-34.48940.18261510.19091717186897

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