[English] 日本語
Yorodumi
- PDB-1ufu: Crystal structure of ligand binding domain of immunoglobulin-like... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ufu
TitleCrystal structure of ligand binding domain of immunoglobulin-like transcript 2 (ILT2; LIR-1)
ComponentsImmunoglobulin-like transcript 2
KeywordsIMMUNE SYSTEM / Immunoglobulin-like folds
Function / homology
Function and homology information


HLA-A specific inhibitory MHC class I receptor activity / positive regulation of gamma-delta T cell activation involved in immune response / MHC class Ib protein complex binding / inhibitory MHC class I receptor activity / HLA-B specific inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation / immune response-inhibiting cell surface receptor signaling pathway / MHC class Ib protein binding / Fc receptor mediated inhibitory signaling pathway / negative regulation of mononuclear cell proliferation ...HLA-A specific inhibitory MHC class I receptor activity / positive regulation of gamma-delta T cell activation involved in immune response / MHC class Ib protein complex binding / inhibitory MHC class I receptor activity / HLA-B specific inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation / immune response-inhibiting cell surface receptor signaling pathway / MHC class Ib protein binding / Fc receptor mediated inhibitory signaling pathway / negative regulation of mononuclear cell proliferation / MHC class Ib receptor activity / negative regulation of T cell mediated cytotoxicity / MHC class I receptor activity / negative regulation of CD8-positive, alpha-beta T cell activation / negative regulation of transforming growth factor beta production / negative regulation of alpha-beta T cell activation / negative regulation of serotonin secretion / negative regulation of cytokine production involved in immune response / dendritic cell differentiation / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / protein phosphatase 1 binding / negative regulation of osteoclast development / negative regulation of interleukin-12 production / negative regulation of endocytosis / negative regulation of interferon-beta production / negative regulation of dendritic cell apoptotic process / positive regulation of macrophage cytokine production / T cell proliferation involved in immune response / negative regulation of natural killer cell mediated cytotoxicity / negative regulation of interleukin-10 production / negative regulation of calcium ion transport / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / negative regulation of cell cycle / MHC class I protein binding / negative regulation of T cell proliferation / positive regulation of defense response to virus by host / SH2 domain binding / response to virus / receptor internalization / cytokine-mediated signaling pathway / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of type II interferon production / defense response to virus / cellular response to lipopolysaccharide / adaptive immune response / positive regulation of apoptotic process / external side of plasma membrane / positive regulation of gene expression / signal transduction / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily ...Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Leukocyte immunoglobulin-like receptor subfamily B member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsShiroishi, M. / Amano, K. / Rasubala, L. / Tsumoto, K. / Kumagai, I. / Kohda, D. / Maenaka, K.
CitationJournal: To be Published
Title: Kinetic and thermodynamic properties of the interaction between Immunoglobulin like transcript (ILT) and MHC class I
Authors: Shiroishi, M. / Amano, K. / Rasubala, L. / Tsumoto, K. / Kumagai, I. / Kohda, D. / Maenaka, K.
History
DepositionJun 10, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Immunoglobulin-like transcript 2


Theoretical massNumber of molelcules
Total (without water)21,9991
Polymers21,9991
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.220, 104.400, 53.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Immunoglobulin-like transcript 2 / ILT2


Mass: 21998.645 Da / Num. of mol.: 1 / Fragment: Ligand binding domain (domain1 and 2)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGMT7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8NHL6

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.6M Sodium Formate, 0.08M Na-acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 4406 / % possible obs: 88.8 % / Observed criterion σ(I): 1 / Redundancy: 12.2 % / Biso Wilson estimate: 41.9 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 6.7
Reflection shellResolution: 3→3.11 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 5.6 / Num. unique all: 411 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G0X

1g0x


Resolution: 3→8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3 339 -RANDOM
Rwork0.232 ---
obs0.232 3607 87.5 %-
Displacement parametersBiso mean: 37.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1355 0 0 0 1355
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d26.9
X-RAY DIFFRACTIONc_improper_angle_d1.02
LS refinement shellResolution: 3→3.18 Å / Rfactor Rfree error: 0.042
RfactorNum. reflection% reflection
Rfree0.343 68 -
Rwork0.309 --
obs--97 %

+
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