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- PDB-5gv3: Crystal structure of the membrane-distal domain of mouse lysosome... -

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Basic information

Entry
Database: PDB / ID: 5gv3
TitleCrystal structure of the membrane-distal domain of mouse lysosome-associated membrane protein 2 (LAMP-2)
ComponentsLysosome-associated membrane glycoprotein 2
KeywordsMEMBRANE PROTEIN
Function / homology
Function and homology information


: / chaperone-mediated autophagy translocation complex / lysosomal matrix / lysosomal protein catabolic process / establishment of protein localization to organelle / platelet dense granule membrane / protein targeting to lysosome involved in chaperone-mediated autophagy / Platelet degranulation / autolysosome / muscle cell cellular homeostasis ...: / chaperone-mediated autophagy translocation complex / lysosomal matrix / lysosomal protein catabolic process / establishment of protein localization to organelle / platelet dense granule membrane / protein targeting to lysosome involved in chaperone-mediated autophagy / Platelet degranulation / autolysosome / muscle cell cellular homeostasis / chaperone-mediated autophagy / autophagosome maturation / protein targeting / negative regulation of protein-containing complex assembly / cellular response to starvation / Neutrophil degranulation / regulation of protein stability / trans-Golgi network / autophagy / phagocytic vesicle membrane / late endosome / late endosome membrane / lysosome / protein stabilization / endosome / lysosomal membrane / protein domain specific binding / perinuclear region of cytoplasm / enzyme binding / extracellular space / extracellular exosome / membrane / plasma membrane
Similarity search - Function
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.
Similarity search - Domain/homology
Lysosome-associated membrane glycoprotein 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.096 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 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysosome-associated membrane glycoprotein 2
B: Lysosome-associated membrane glycoprotein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,64127
Polymers37,4482
Non-polymers3,19325
Water1,47782
1
A: Lysosome-associated membrane glycoprotein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,41915
Polymers18,7241
Non-polymers1,69514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysosome-associated membrane glycoprotein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,22212
Polymers18,7241
Non-polymers1,49811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.610, 103.930, 129.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-327-

HOH

21B-328-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA25 - 189
211chain BB25 - 187

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Components

#1: Protein Lysosome-associated membrane glycoprotein 2 / / Lysosome-associated membrane protein 2 / CD107 antigen-like family member B / Lysosomal membrane ...Lysosome-associated membrane protein 2 / CD107 antigen-like family member B / Lysosomal membrane glycoprotein type B / LGP-B


Mass: 18723.883 Da / Num. of mol.: 2 / Fragment: UNP residues 26-189
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lamp2, Lamp-2 / Plasmid: pOriP / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P17047
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Zn
#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.: 10
Source method: isolated from a genetically manipulated source
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.: 82 / 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: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 50mM zinc acetate, 20% (v/v) polyethylene glycol 3500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1.2 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: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.096→50 Å / Num. obs: 23657 / % possible obs: 98.7 % / Redundancy: 7.7 % / Rsym value: 0.068 / Net I/σ(I): 16.31
Reflection shellResolution: 2.0965→2.1489 Å

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIX1.9_1690refinement
SOLVEphasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.096→40.488 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.7 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.3075 1979 8.37 %
Rwork0.2687 21678 -
obs0.272 23657 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.47 Å2 / Biso mean: 55.9428 Å2 / Biso min: 8.48 Å2
Refinement stepCycle: final / Resolution: 2.096→40.488 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2536 0 150 82 2768
Biso mean--67.41 59.36 -
Num. residues----324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012821
X-RAY DIFFRACTIONf_angle_d1.3423754
X-RAY DIFFRACTIONf_chiral_restr0.061463
X-RAY DIFFRACTIONf_plane_restr0.006468
X-RAY DIFFRACTIONf_dihedral_angle_d11.61940
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1428X-RAY DIFFRACTION15.117TORSIONAL
12B1428X-RAY DIFFRACTION15.117TORSIONAL
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 (%)
2.0965-2.14890.37491320.34631474160694
2.1489-2.2070.40141400.31081502164298
2.207-2.27190.35681330.31681521165499
2.2719-2.34530.34481370.29851533167099
2.3453-2.42910.38031430.2861514165799
2.4291-2.52630.34341430.29821540168399
2.5263-2.64130.37011430.30181537168099
2.6413-2.78050.32591440.31841533167799
2.7805-2.95470.38531410.28261570171199
2.9547-3.18270.34591370.28971551168899
3.1827-3.50280.28621450.262715671712100
3.5028-4.00930.27921480.247715781726100
4.0093-5.04980.25781470.229815901737100
5.0498-40.49560.29891460.26951668181499

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