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- PDB-1a6a: THE STRUCTURE OF AN INTERMEDIATE IN CLASS II MHC MATURATION: CLIP... -

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Entry
Database: PDB / ID: 1a6a
TitleTHE STRUCTURE OF AN INTERMEDIATE IN CLASS II MHC MATURATION: CLIP BOUND TO HLA-DR3
Components
  • HLA class II histocompatibility antigen, DR alpha chain
  • HLA class II histocompatibility antigen, DR-1 beta chain
  • HLA class II histocompatibility antigen, gamma chain
KeywordsCOMPLEX (TRANSMEMBRANE/GLYCOPROTEIN) / MHC GLYCOPROTEIN / COMPLEX (TRANSMEMBRANE-GLYCOPROTEIN) / COMPLEX (TRANSMEMBRANE-GLYCOPROTEIN) complex
Function / homologyClass II MHC-associated invariant chain trimerisation domain / MHC class II antigen presentation / MHC class II, beta chain, N-terminal / Interferon gamma signaling / PD-1 signaling / Immunoglobulins and major histocompatibility complex proteins signature. / Thyroglobulin type-1 repeat signature. / Ig-like domain profile. / Thyroglobulin type-1 domain profile. / MHC class II, alpha chain, N-terminal ...Class II MHC-associated invariant chain trimerisation domain / MHC class II antigen presentation / MHC class II, beta chain, N-terminal / Interferon gamma signaling / PD-1 signaling / Immunoglobulins and major histocompatibility complex proteins signature. / Thyroglobulin type-1 repeat signature. / Ig-like domain profile. / Thyroglobulin type-1 domain profile. / MHC class II, alpha chain, N-terminal / Cell surface interactions at the vascular wall / Generation of second messenger molecules / CLIP, MHC2 interacting / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Downstream TCR signaling / Thyroglobulin type-1 / Immunoglobulin/major histocompatibility complex, conserved site / MHC class II-associated invariant chain / Immunoglobulin C1-set domain / Immunoglobulin-like domain / MHC classes I/II-like antigen recognition protein / MHC class II-associated invariant chain, trimerisation / Immunoglobulin-like fold / MHC class II, alpha/beta chain, N-terminal / MHC class II-associated invariant chain/CLIP, MHC II-interacting / Immunoglobulin C1-set / Immunoglobulin-like domain superfamily / MHC class II-associated invariant chain, trimerisation domain superfamily / Thyroglobulin type-1 superfamily / Thyroglobulin type-1 repeat / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, alpha domain / macrophage migration inhibitory factor signaling pathway / NOS2-CD74 complex / MHC class II protein binding, via antigen binding groove / negative regulation of peptide secretion / antigen processing and presentation of endogenous antigen / positive regulation of dendritic cell antigen processing and presentation / macrophage migration inhibitory factor binding / negative regulation of T cell differentiation / macrophage migration inhibitory factor receptor complex / positive regulation of cytokine-mediated signaling pathway / positive regulation of type 2 immune response / positive regulation of macrophage cytokine production / negative thymic T cell selection / immunoglobulin production involved in immunoglobulin mediated immune response / polysaccharide assembly with MHC class II protein complex / T cell selection / peptide antigen assembly with MHC class II protein complex / MHC class II protein binding / MHC class II receptor activity / positive regulation of neutrophil chemotaxis / positive regulation of T cell differentiation / positive thymic T cell selection / positive regulation of chemokine (C-X-C motif) ligand 2 production / regulation of macrophage activation / positive regulation of monocyte differentiation / negative regulation of mature B cell apoptotic process / positive regulation of kinase activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / protein trimerization / CD4 receptor binding / positive regulation of viral entry into host cell / MHC class II protein complex / immunoglobulin mediated immune response / cytokine receptor activity / vacuole / transport vesicle membrane / humoral immune response mediated by circulating immunoglobulin / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / prostaglandin biosynthetic process / clathrin-coated endocytic vesicle membrane / cytokine binding / nitric-oxide synthase binding / protein folding chaperone / negative regulation of DNA damage response, signal transduction by p53 class mediator / trans-Golgi network membrane / chaperone cofactor-dependent protein refolding / late endosome membrane / positive regulation of B cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class II protein complex binding / cognition / multivesicular body / lysosomal lumen / endocytic vesicle membrane / defense response / intracellular protein transport / integral component of lumenal side of endoplasmic reticulum membrane / peptide antigen binding / ER to Golgi transport vesicle membrane / protein heterotetramerization / lysosomal membrane / positive regulation of fibroblast proliferation / protein-containing complex assembly / interferon-gamma-mediated signaling pathway / intracellular / positive regulation of peptidyl-tyrosine phosphorylation / leukocyte migration
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 2.75 Å resolution
AuthorsGhosh, P. / Amaya, M. / Mellins, E. / Wiley, D.C.
CitationJournal: Nature / Year: 1995
Title: The structure of an intermediate in class II MHC maturation: CLIP bound to HLA-DR3.
Authors: Ghosh, P. / Amaya, M. / Mellins, E. / Wiley, D.C.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 22, 1998 / Release: May 27, 1998
RevisionDateData content typeGroupProviderType
1.0May 27, 1998Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelNon-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DR-1 beta chain
C: HLA class II histocompatibility antigen, gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5235
Polyers44,0813
Non-polymers4422
Water39622
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)7340
ΔGint (kcal/M)-42
Surface area (Å2)17990
MethodPISA
2
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DR-1 beta chain
C: HLA class II histocompatibility antigen, gamma chain
hetero molecules

A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DR-1 beta chain
C: HLA class II histocompatibility antigen, gamma chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,04610
Polyers88,1616
Non-polymers8854
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,x-y,-z1
Buried area (Å2)17000
ΔGint (kcal/M)-85
Surface area (Å2)33650
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)78.450, 78.450, 159.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP 32 1 2

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Components

#1: Protein/peptide HLA class II histocompatibility antigen, DR alpha chain


Mass: 20469.172 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Genus: Homo / Cell: B-LYMPHOCYTE / Cell line: 9.5.3 / Cellular location: PLASMA MEMBRANECell membrane / References: UniProt: P01903
#2: Protein/peptide HLA class II histocompatibility antigen, DR-1 beta chain


Mass: 21935.385 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / Genus: Homo / Cell: B-LYMPHOCYTE / Cell line: 9.5.3 / Cellular location: PLASMA MEMBRANECell membrane / References: UniProt: P01912
#3: Protein/peptide HLA class II histocompatibility antigen, gamma chain


Mass: 1676.118 Da / Num. of mol.: 1 / Fragment: CLIP FRAGMENT 87 - 101 OF INVARIANT CHAIN / Source: (natural) Homo sapiens (human) / Genus: Homo / Cell: B-LYMPHOCYTE / Cell line: 9.5.3 / Cellular location: PLASMA MEMBRANECell membrane / References: UniProt: P04233
#4: Chemical ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 2 / Formula: C8H15NO6 / N-Acetylglucosamine
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.7 / Density percent sol: 52 %
Crystal growpH: 4.5
Details: 12% PEG 4K, 100 MM MGCL2, 100 MM ACETATE BUFFER, PH 4.5
Crystal grow
*PLUS
Method: unknown
Details: conditions similar to: Gorga, J.C., (1991) Res. Immun., 142, 401.
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
112 %PEG400011
2100 mM11MgCl2
3100 mMacetate11

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: CHESS BEAMLINE F1 / Synchrotron site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: FUJI / Details: MIRRORS / Detector: IMAGE PLATE / Collection date: Jul 1, 1994
RadiationMonochromator: SI(111) / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 30.8 Å2 / D resolution high: 2.75 Å / D resolution low: 15 Å / Number obs: 14428 / Observed criterion sigma I: -3 / Rmerge I obs: 0.071 / NetI over sigmaI: 6.7 / Redundancy: 3.2 % / Percent possible obs: 96.9
Reflection shellRmerge I obs: 0.314 / Highest resolution: 2.75 Å / Lowest resolution: 3 Å / MeanI over sigI obs: 2.3 / Redundancy: 3 % / Percent possible all: 97.2
Reflection
*PLUS
Number obs: 13021
Reflection shell
*PLUS
Percent possible obs: 97.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
ROTAVATA/AGROVATAdata reduction
AMoREphasing
X-PLOR3.1refinement
CCP4(AGROVATAdata scaling
ROTAVATA)data scaling
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DLH
Details: RESIDUES 5 - 180 OF THE ALPHA SUBUNIT AND RESIDUES 5 - 191 OF THE BETA SUBUNIT ARE CLEARLY VISIBLE IN 2FO-FC ELECTRON DENSITY MAPS. THREE SMALL BREAKS IN MAIN-CHAIN DENSITY OCCUR IN LOOP REGIONS OF THE BETA 2 DOMAIN (AT BETA 109, 172, AND 189).
R Free selection details: RANDOM / Data cutoff high absF: 1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 0
Displacement parametersB iso mean: 47.6 Å2 / Aniso B11: -1 Å2 / Aniso B12: -1 Å2 / Aniso B13: 0 Å2 / Aniso B22: -1 Å2 / Aniso B23: 0 Å2 / Aniso B33: 1 Å2
Least-squares processR factor R free: 0.325 / R factor R free error: 0.009 / R factor R work: 0.246 / R factor obs: 0.246 / Highest resolution: 2.75 Å / Lowest resolution: 6 Å / Number reflection R free: 1323 / Number reflection obs: 13095 / Percent reflection R free: 10.1 / Percent reflection obs: 97.9
Refine analyzeLuzzati coordinate error free: 0.53 Å / Luzzati coordinate error obs: 0.39 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a free: 0.72 Å / Luzzati sigma a obs: 0.61 Å
Refine hist #LASTHighest resolution: 2.75 Å / Lowest resolution: 6 Å
Number of atoms included #LASTProtein: 3108 / Nucleic acid: 0 / Ligand: 28 / Solvent: 22 / Total: 3158
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.31
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.533.00
X-RAY DIFFRACTIONx_mcangle_it5.984.00
X-RAY DIFFRACTIONx_scbond_it5.524.00
X-RAY DIFFRACTIONx_scangle_it9.356.00
Refine LS shellHighest resolution: 2.75 Å / R factor R free: 0.444 / R factor R free error: 0.036 / R factor R work: 0.373 / Lowest resolution: 2.86 Å / Number reflection R free: 162 / Number reflection R work: 1442 / Total number of bins used: 8 / Percent reflection R free: 10.1 / Percent reflection obs: 96.7
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PARAM3_MOD.CHOTOPH3.CHO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.6
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.31
Refine LS shell
*PLUS
R factor obs: 0.373

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