[English] 日本語
Yorodumi
- PDB-8ath: CRYSTAL STRUCTURE OF LAMP1 IN COMPLEX WITH FAB-B. -

+
Open data


ID or keywords:

Loading...

-
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 / azurophil granule membrane ...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 / azurophil granule membrane / ion channel inhibitor activity / autolysosome / autophagosome membrane / ficolin-1-rich granule membrane / multivesicular body / sarcolemma / late endosome / melanosome / synaptic vesicle / 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 / cytosol / cytoplasm
Similarity search - Function
Lysosome-associated membrane glycoprotein, conserved site / : / Lysosome-associated membrane glycoprotein 2, transmembrane segment / 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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
Has protein modificationY

-
Experimental details

-
Experiment

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

-
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

-
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

-
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more