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- PDB-9cyl: Structure of LAG3 loop1 deletion bound to the MHC class II molecu... -

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Basic information

Entry
Database: PDB / ID: 9cyl
TitleStructure of LAG3 loop1 deletion bound to the MHC class II molecule I-A(b)
Components
  • Class-II-associated invariant chain peptide
  • H-2 class II histocompatibility antigen, A beta chain
  • H-2 class II histocompatibility antigen, A-B alpha chain
  • Secreted lymphocyte activation gene 3 protein
KeywordsIMMUNE SYSTEM / LAG3 / Immune checkpoint / T cell / complex / MHCII / immune therapy
Function / homology
Function and homology information


positive regulation of antigen processing and presentation / positive regulation of alpha-beta T cell activation / plasmacytoid dendritic cell activation / negative regulation of peptide secretion / macrophage migration inhibitory factor signaling pathway / NOS2-CD74 complex / MHC class II protein binding, via antigen binding groove / antigen processing and presentation of endogenous antigen / positive regulation of dendritic cell antigen processing and presentation / negative regulation of T cell differentiation ...positive regulation of antigen processing and presentation / positive regulation of alpha-beta T cell activation / plasmacytoid dendritic cell activation / negative regulation of peptide secretion / macrophage migration inhibitory factor signaling pathway / NOS2-CD74 complex / MHC class II protein binding, via antigen binding groove / antigen processing and presentation of endogenous antigen / positive regulation of dendritic cell antigen processing and presentation / negative regulation of T cell differentiation / macrophage migration inhibitory factor binding / positive regulation of macrophage migration inhibitory factor signaling pathway / protein trimerization / macrophage migration inhibitory factor receptor complex / negative regulation of regulatory T cell differentiation / positive regulation of cytokine-mediated signaling pathway / positive regulation of T-helper 1 type immune response / T cell activation involved in immune response / positive regulation of prostaglandin biosynthetic process / T cell selection / negative regulation of T cell activation / positive regulation of type 2 immune response / positive regulation of natural killer cell mediated cytotoxicity / antigen processing and presentation of peptide antigen / B cell affinity maturation / host-mediated suppression of symbiont invasion / negative thymic T cell selection / protein antigen binding / MHC class II protein binding / negative regulation of mature B cell apoptotic process / MHC class II antigen presentation / positive regulation of kinase activity / CD4 receptor binding / positive regulation of monocyte differentiation / positive thymic T cell selection / vacuole / cytokine receptor activity / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of neutrophil chemotaxis / prostaglandin biosynthetic process / positive regulation of macrophage cytokine production / positive regulation of T cell differentiation / negative regulation of interleukin-2 production / regulation of macrophage activation / nitric-oxide synthase binding / natural killer cell mediated cytotoxicity / transport vesicle membrane / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / antigen processing and presentation / cytokine binding / negative regulation of DNA damage response, signal transduction by p53 class mediator / immunoglobulin mediated immune response / : / response to type II interferon / toxic substance binding / regulation of immune response / positive regulation of chemokine production / positive regulation of B cell proliferation / multivesicular body / protein folding chaperone / MHC class II antigen presentation / lysosomal lumen / T cell activation / negative regulation of cell migration / trans-Golgi network membrane / positive regulation of interleukin-8 production / lumenal side of endoplasmic reticulum membrane / Cell surface interactions at the vascular wall / intracellular protein transport / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / cellular response to type II interferon / positive regulation of interleukin-6 production / positive regulation of fibroblast proliferation / MHC class II protein complex binding / endocytic vesicle membrane / transmembrane signaling receptor activity / late endosome / amyloid-beta binding / positive regulation of protein phosphorylation / protein-containing complex assembly / adaptive immune response / positive regulation of canonical NF-kappaB signal transduction / positive regulation of viral entry into host cell / early endosome / lysosome / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / protein stabilization / immune response / Golgi membrane / external side of plasma membrane / lysosomal membrane / ubiquitin protein ligase binding / positive regulation of gene expression / negative regulation of apoptotic process
Similarity search - Function
MHC class II-associated invariant chain, trimerisation / MHC class II-associated invariant chain/CLIP, MHC II-interacting / MHC class II-associated invariant chain / MHC class II-associated invariant chain, trimerisation domain superfamily / HLA class II histocompatibility antigen, gamma subunit / Class II MHC-associated invariant chain trimerisation domain / CLIP, MHC2 interacting / : / Interleukin-1 receptor family / Thyroglobulin type-1 repeat signature. ...MHC class II-associated invariant chain, trimerisation / MHC class II-associated invariant chain/CLIP, MHC II-interacting / MHC class II-associated invariant chain / MHC class II-associated invariant chain, trimerisation domain superfamily / HLA class II histocompatibility antigen, gamma subunit / Class II MHC-associated invariant chain trimerisation domain / CLIP, MHC2 interacting / : / Interleukin-1 receptor family / Thyroglobulin type-1 repeat signature. / Thyroglobulin type-1 / Thyroglobulin type-1 superfamily / Thyroglobulin type-1 repeat / Thyroglobulin type-1 domain profile. / Thyroglobulin type I repeats. / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
HLA class II histocompatibility antigen gamma chain / H-2 class II histocompatibility antigen, A-B alpha chain / H-2 class II histocompatibility antigen, A beta chain / Lymphocyte activation gene 3 protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 4.66 Å
AuthorsMing, Q. / Tran, T.H. / Antfolk, D. / Luca, V.C.
Funding support United States, 2items
OrganizationGrant numberCountry
Other governmentFlorida Department of Health Bankhead-Coley 22B07 United States
Rita Allen Foundation United States
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis for mouse LAG3 interactions with the MHC class II molecule I-A b.
Authors: Ming, Q. / Antfolk, D. / Price, D.A. / Manturova, A. / Medina, E. / Singh, S. / Mason, C. / Tran, T.H. / Smalley, K.S.M. / Leung, D.W. / Luca, V.C.
History
DepositionAug 2, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H-2 class II histocompatibility antigen, A-B alpha chain
B: H-2 class II histocompatibility antigen, A beta chain
P: Class-II-associated invariant chain peptide
L: Secreted lymphocyte activation gene 3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5468
Polymers69,6614
Non-polymers8854
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)184.994, 184.994, 122.672
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein H-2 class II histocompatibility antigen, A-B alpha chain / IAalpha


Mass: 22026.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Aa / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P14434
#2: Protein H-2 class II histocompatibility antigen, A beta chain


Mass: 22637.221 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Ab1, H2-iabeta / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P14483
#3: Protein/peptide Class-II-associated invariant chain peptide / CLIP


Mass: 1676.118 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD74, DHLAG / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P04233
#4: Protein Secreted lymphocyte activation gene 3 protein / sLAG-3


Mass: 23321.643 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lag3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q61790
#5: 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.: 4 / Source method: obtained synthetically / 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
Has ligand of interestN
Has protein modificationY

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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: 4.21 Å3/Da / Density % sol: 70.82 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 1% w/v Tryptone, 0.001 M Sodium azide, 0.05 M HEPES sodium pH 7.0, 12% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Mar 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 4.66→92.5 Å / Num. obs: 7006 / % possible obs: 99.8 % / Redundancy: 10.5 % / Biso Wilson estimate: 232.6 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.187 / Rrim(I) all: 0.198 / Net I/σ(I): 10.91
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2% possible all
4.66-4.9411.22.571.1310980.38799.4
4.94-5.2811.151.8771.5910360.57599.9
5.28-5.7110.841.581.859600.605100
5.71-6.2510.320.9672.948980.825100
6.25-6.989.350.5514.668210.924100
6.98-8.059.980.22110.657340.991100
8.05-9.8511.040.08726.056280.99100
9.85-13.8610.370.04546.495120.999100

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Processing

Software
NameVersionClassification
PHENIX(1.21.1_5286: ???)refinement
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 4.66→92.5 Å / SU ML: 0.87 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 43.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3257 351 5.02 %
Rwork0.268 --
obs0.2709 6998 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.66→92.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4643 0 56 0 4699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034827
X-RAY DIFFRACTIONf_angle_d0.5696594
X-RAY DIFFRACTIONf_dihedral_angle_d11.5571792
X-RAY DIFFRACTIONf_chiral_restr0.045738
X-RAY DIFFRACTIONf_plane_restr0.005854
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.66-5.340.39781140.33192148X-RAY DIFFRACTION100
5.34-6.720.37321150.35442184X-RAY DIFFRACTION100
6.72-92.50.29831220.23162315X-RAY DIFFRACTION100

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