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- PDB-4akm: Crystal structure of the human lysosome-associated membrane prote... -

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Basic information

Entry
Database: PDB / ID: 4akm
TitleCrystal structure of the human lysosome-associated membrane protein LAMP-3 (aka DC-LAMP)
ComponentsLYSOSOME-ASSOCIATED MEMBRANE GLYCOPROTEIN 3
KeywordsMEMBRANE 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 / late endosome membrane / early endosome membrane / vesicle / adaptive immune response / early endosome ...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 / late endosome membrane / early endosome membrane / vesicle / adaptive immune response / early endosome / regulation of autophagy / lysosomal membrane / intracellular membrane-bounded organelle / positive regulation of gene expression / perinuclear region of cytoplasm / cell surface / plasma membrane
Similarity search - Function
Porin - #110 / Lysosome-associated membrane glycoprotein / : / Lysosome-associated membrane glycoprotein 2-like, luminal domains / Lysosome-associated membrane glycoprotein family profile. / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
IRIDIUM (III) ION / Lysosome-associated membrane glycoprotein 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.687 Å
AuthorsKrausze, J. / Wilke, S. / Buessow, K.
CitationJournal: 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
DepositionFeb 24, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Jul 17, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LYSOSOME-ASSOCIATED MEMBRANE GLYCOPROTEIN 3
B: LYSOSOME-ASSOCIATED MEMBRANE GLYCOPROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5258
Polymers37,3132
Non-polymers1,2116
Water18010
1
A: LYSOSOME-ASSOCIATED MEMBRANE GLYCOPROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2624
Polymers18,6571
Non-polymers6063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LYSOSOME-ASSOCIATED MEMBRANE GLYCOPROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2624
Polymers18,6571
Non-polymers6063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.600, 52.600, 141.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9291, 0.35759, 0.09437), (0.35585, -0.93388, 0.03526), (0.10074, 0.00082, -0.99491)
Vector: -11.6267, 17.47254, 153.64288)

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Components

#1: Protein LYSOSOME-ASSOCIATED MEMBRANE GLYCOPROTEIN 3 / LAMP-3 / LYSOSOMAL-ASSOCIATED MEMBRANE PROTEIN 3 / DC-LYSOSOME-ASSOCIATED MEMBRANE GLYCOPROTEIN / ...LAMP-3 / LYSOSOMAL-ASSOCIATED MEMBRANE PROTEIN 3 / DC-LYSOSOME-ASSOCIATED MEMBRANE GLYCOPROTEIN / DC LAMP / PROTEIN TSC403 / CD_ANTIGEN=CD208


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 / IRIDIUM (III) ION


Mass: 192.217 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ir
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsN-ACETYL-D-GLUCOSAMINE (NAG): N-ACETYL-D-GLUCOSAMINE IS COVALENTLY ATTACHED TO N291

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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: 3.28 Å3/Da / Density % sol: 62.5 % / Description: NONE
Crystal growpH: 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.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.10371, 1.1042, 1.1009
DetectorType: MARRESEARCH / Detector: CCD / Date: May 7, 2010 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.103711
21.10421
31.10091
ReflectionResolution: 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 shellResolution: 2.7→2.85 Å / Redundancy: 2.84 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.47 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.2492 562 5 %
Rwork0.2265 --
obs0.2277 11232 92.05 %
Solvent computationShrinkage 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 parametersBiso mean: 61.3 Å2
Baniso -1Baniso -2Baniso -3
1-6.4177 Å20 Å20 Å2
2--6.4177 Å20 Å2
3----12.8354 Å2
Refinement stepCycle: LAST / Resolution: 2.687→19.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2438 0 32 10 2480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062516
X-RAY DIFFRACTIONf_angle_d1.0233394
X-RAY DIFFRACTIONf_dihedral_angle_d26.2061528
X-RAY DIFFRACTIONf_chiral_restr0.073386
X-RAY DIFFRACTIONf_plane_restr0.003442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6873-2.95690.36371510.32612885X-RAY DIFFRACTION99
2.9569-3.38280.3531520.2762878X-RAY DIFFRACTION100
3.3828-4.25440.27841050.21861988X-RAY DIFFRACTION69
4.2544-19.29590.17831540.18952919X-RAY DIFFRACTION100

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