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- PDB-8ath: CRYSTAL STRUCTURE OF LAMP1 IN COMPLEX WITH FAB-B. -

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Basic information

Entry
Database: PDB / ID: 8ath
TitleCRYSTAL STRUCTURE OF LAMP1 IN COMPLEX WITH FAB-B.
Components
  • Fab B Heavy Chain
  • Fab B Light Chain
  • Lysosome-associated membrane glycoprotein 1
KeywordsPROTEIN BINDING / ANTIGEN / FAB / COMPLEX
Function / homology
Function and homology information


regulation of organelle transport along microtubule / positive regulation of natural killer cell degranulation / granzyme-mediated programmed cell death signaling pathway / phagolysosome membrane / cytolytic granule membrane / Golgi to lysosome transport / establishment of protein localization to organelle / lysosomal lumen acidification / positive regulation of natural killer cell mediated cytotoxicity / autolysosome ...regulation of organelle transport along microtubule / positive regulation of natural killer cell degranulation / granzyme-mediated programmed cell death signaling pathway / phagolysosome membrane / cytolytic granule membrane / Golgi to lysosome transport / establishment of protein localization to organelle / lysosomal lumen acidification / positive regulation of natural killer cell mediated cytotoxicity / autolysosome / azurophil granule membrane / ion channel inhibitor activity / autophagosome membrane / ficolin-1-rich granule membrane / multivesicular body / sarcolemma / melanosome / synaptic vesicle / late endosome / late endosome membrane / virus receptor activity / lysosome / protein stabilization / endosome membrane / protein domain specific binding / lysosomal membrane / external side of plasma membrane / Neutrophil degranulation / perinuclear region of cytoplasm / enzyme binding / extracellular exosome / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / : / Lysosome-associated membrane glycoprotein 2, transmembrane segment / 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 2-like, luminal domains / Lysosome-associated membrane glycoprotein family profile.
Similarity search - Domain/homology
Lysosome-associated membrane glycoprotein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.366 Å
AuthorsMathieu, M. / Dupuy, A.
Funding support France, 1items
OrganizationGrant numberCountry
Other private France
CitationJournal: Mabs / Year: 2023
Title: Deciphering cross-species reactivity of LAMP-1 antibodies using deep mutational epitope mapping and AlphaFold.
Authors: Pruvost, T. / Mathieu, M. / Dubois, S. / Maillere, B. / Vigne, E. / Nozach, H.
History
DepositionAug 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysosome-associated membrane glycoprotein 1
B: Lysosome-associated membrane glycoprotein 1
E: Fab B Heavy Chain
F: Fab B Light Chain
H: Fab B Heavy Chain
L: Fab B Light Chain


Theoretical massNumber of molelcules
Total (without water)134,7066
Polymers134,7066
Non-polymers00
Water4,846269
1
A: Lysosome-associated membrane glycoprotein 1
H: Fab B Heavy Chain
L: Fab B Light Chain


Theoretical massNumber of molelcules
Total (without water)67,3533
Polymers67,3533
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysosome-associated membrane glycoprotein 1
E: Fab B Heavy Chain
F: Fab B Light Chain


Theoretical massNumber of molelcules
Total (without water)67,3533
Polymers67,3533
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.932, 93.68, 108.009
Angle α, β, γ (deg.)90, 115.93, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Lysosome-associated membrane glycoprotein 1 / LAMP-1 / Lysosome-associated membrane protein 1 / CD107 antigen-like family member A


Mass: 18863.150 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LAMP1 / Plasmid: pXL5907 / Details (production host): TrxA-His-Thr-LAMP1-29-195 / Cell line (production host): 293 / Production host: Human adenovirus 5 / Variant (production host): 293-F / References: UniProt: P11279
#2: Antibody Fab B Heavy Chain


Mass: 24981.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: AbVec2.0-IGHG1 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / Strain (production host): HEK293
#3: Antibody Fab B Light Chain


Mass: 23508.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: AbVec1.1-IGLC / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 2.53 Å3/Da / Density % sol: 51.42 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG 3350 20% - NaF 0.2M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 2.37→72.08 Å / Num. obs: 54397 / % possible obs: 99.1 % / Redundancy: 3.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.034 / Net I/σ(I): 14.4
Reflection shellResolution: 2.37→2.65 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.475 / Num. unique obs: 15415 / CC1/2: 0.837 / Rpim(I) all: 0.305 / % possible all: 99.3

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Fab domains

Resolution: 2.366→72.08 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.885 / SU R Cruickshank DPI: 0.415 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.4 / SU Rfree Blow DPI: 0.272 / SU Rfree Cruickshank DPI: 0.279
RfactorNum. reflection% reflectionSelection details
Rfree0.2898 2767 -RANDOM
Rwork0.2514 ---
obs0.2534 54389 99 %-
Displacement parametersBiso mean: 62.6 Å2
Baniso -1Baniso -2Baniso -3
1-8.6462 Å20 Å2-2.9876 Å2
2--5.2562 Å20 Å2
3----13.9025 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: LAST / Resolution: 2.366→72.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8703 0 0 269 8972
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0088900HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0412100HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2963SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes1486HARMONIC5
X-RAY DIFFRACTIONt_it8900HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1210SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6470SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.38
X-RAY DIFFRACTIONt_other_torsion17.17
LS refinement shellResolution: 2.37→2.38 Å
RfactorNum. reflection% reflection
Rfree0.3497 58 -
Rwork0.3346 --
obs0.3354 1088 99.64 %

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