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- PDB-8tbp: HLA-DRB1*15:01 in complex with smith antigen -

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Basic information

Entry
Database: PDB / ID: 8tbp
TitleHLA-DRB1*15:01 in complex with smith antigen
Components
  • HLA class II histocompatibility antigen, DR alpha chain
  • HLA class II histocompatibility antigen, DRB1 beta chain
  • Small nuclear ribonucleoprotein-associated protein N peptide
KeywordsIMMUNE SYSTEM / Human Leukocyte Antigen / HLA / Major Histocompatibility Complex / MHC
Function / homology
Function and homology information


regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II ...regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / positive regulation of kinase activity / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / inflammatory response to antigenic stimulus / snRNP binding / small nuclear ribonucleoprotein complex / CD4 receptor binding / intermediate filament / U4 snRNP / U2 snRNP / U1 snRNP / U2-type prespliceosome / T-helper 1 type immune response / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / polysaccharide binding / negative regulation of type II interferon production / humoral immune response / Generation of second messenger molecules / macrophage differentiation / immunological synapse / Co-inhibition by PD-1 / epidermis development / U5 snRNP / positive regulation of insulin secretion involved in cellular response to glucose stimulus / detection of bacterium / T cell receptor binding / U4/U6 x U5 tri-snRNP complex / negative regulation of T cell proliferation / catalytic step 2 spliceosome / MHC class II antigen presentation / mRNA Splicing - Major Pathway / RNA splicing / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / spliceosomal complex / peptide antigen assembly with MHC class II protein complex / negative regulation of inflammatory response to antigenic stimulus / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / mRNA splicing, via spliceosome / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / peptide antigen binding / structural constituent of cytoskeleton / positive regulation of T cell mediated cytotoxicity / cognition / endocytic vesicle membrane / positive regulation of protein phosphorylation / Interferon gamma signaling / MHC class II protein complex binding / Downstream TCR signaling / late endosome membrane / T cell receptor signaling pathway / early endosome membrane / adaptive immune response / positive regulation of viral entry into host cell / lysosome / positive regulation of ERK1 and ERK2 cascade / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / immune response / Golgi membrane / lysosomal membrane / external side of plasma membrane / positive regulation of DNA-templated transcription / cell surface / signal transduction / extracellular space / RNA binding / extracellular exosome / nucleoplasm / membrane / plasma membrane / cytoplasm
Similarity search - Function
: / Small ribonucleoprotein associated, SmB/SmN / 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 / LSM domain ...: / Small ribonucleoprotein associated, SmB/SmN / 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 / LSM domain / LSM domain, eukaryotic/archaea-type / snRNP Sm proteins / : / Sm domain profile. / LSM domain superfamily / MHC classes I/II-like antigen recognition protein / : / 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, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain / Small nuclear ribonucleoprotein-associated protein N
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1262111426 Å
AuthorsTing, Y.T. / Broury, A. / Ooi, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2024
Title: Smith-specific regulatory T cells halt the progression of lupus nephritis.
Authors: Eggenhuizen, P.J. / Cheong, R.M.Y. / Lo, C. / Chang, J. / Ng, B.H. / Ting, Y.T. / Monk, J.A. / Loh, K.L. / Broury, A. / Tay, E.S.V. / Shen, C. / Zhong, Y. / Lim, S. / Chung, J.X. / Kandane- ...Authors: Eggenhuizen, P.J. / Cheong, R.M.Y. / Lo, C. / Chang, J. / Ng, B.H. / Ting, Y.T. / Monk, J.A. / Loh, K.L. / Broury, A. / Tay, E.S.V. / Shen, C. / Zhong, Y. / Lim, S. / Chung, J.X. / Kandane-Rathnayake, R. / Koelmeyer, R. / Hoi, A. / Chaudhry, A. / Manzanillo, P. / Snelgrove, S.L. / Morand, E.F. / Ooi, J.D.
History
DepositionJun 29, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 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: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1 beta chain
C: HLA class II histocompatibility antigen, DR alpha chain
D: HLA class II histocompatibility antigen, DRB1 beta chain
E: Small nuclear ribonucleoprotein-associated protein N peptide
F: Small nuclear ribonucleoprotein-associated protein N peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2418
Polymers89,7996
Non-polymers4422
Water181
1
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1 beta chain
E: Small nuclear ribonucleoprotein-associated protein N peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1214
Polymers44,9003
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7440 Å2
ΔGint-33 kcal/mol
Surface area18120 Å2
MethodPISA
2
C: HLA class II histocompatibility antigen, DR alpha chain
D: HLA class II histocompatibility antigen, DRB1 beta chain
F: Small nuclear ribonucleoprotein-associated protein N peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1214
Polymers44,9003
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7540 Å2
ΔGint-35 kcal/mol
Surface area18000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.080, 95.080, 294.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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


Mass: 21185.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: P01903
#2: Protein HLA class II histocompatibility antigen, DRB1 beta chain / Human leukocyte antigen DRB1 / HLA-DRB1


Mass: 22073.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: P01911
#3: Protein/peptide Small nuclear ribonucleoprotein-associated protein N peptide / Smith Antigen / snRNP-N / Sm protein D / Sm-D / Sm protein N / Sm-N / SmN / Tissue-specific-splicing protein


Mass: 1639.982 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPN, HCERN3, SMN / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: P63162
#4: 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.: 2 / 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: H2O
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: 3.7 Å3/Da / Density % sol: 66.78 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 0.2M Disodium Malon 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 3.12→46.9312243917 Å / Num. obs: 24942 / % possible obs: 99.6 % / Redundancy: 16 % / Biso Wilson estimate: 66.3722339896 Å2 / CC1/2: 0.989 / Rpim(I) all: 0.136 / Net I/σ(I): 7.7
Reflection shellResolution: 3.12→3.33 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4343 / CC1/2: 0.736

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1262111426→46.9312243917 Å / SU ML: 0.407230754254 / Cross valid method: FREE R-VALUE / σ(F): 1.32617264364 / Phase error: 25.2040563935
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.253401102757 1222 4.93916979912 %
Rwork0.202752776344 23519 -
obs0.205258999018 24741 99.6134798889 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.20086933 Å2
Refinement stepCycle: LAST / Resolution: 3.1262111426→46.9312243917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6224 0 28 1 6253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00365956401826434
X-RAY DIFFRACTIONf_angle_d0.7323699630858769
X-RAY DIFFRACTIONf_chiral_restr0.0461341473894948
X-RAY DIFFRACTIONf_plane_restr0.004879819336341147
X-RAY DIFFRACTIONf_dihedral_angle_d17.27875306383791
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1262111426-3.25130.3526135533351420.300268992612478X-RAY DIFFRACTION97.8707508405
3.2513-3.39930.3197457042991210.2467321083562594X-RAY DIFFRACTION99.9631811487
3.3993-3.57840.267245542611340.2291053011922540X-RAY DIFFRACTION99.8879342548
3.5784-3.80250.2784023234511320.2085408798592611X-RAY DIFFRACTION99.9635568513
3.8025-4.0960.2727710346021320.201452293932570X-RAY DIFFRACTION99.9630040696
4.096-4.50790.2131849793221300.16931245882620X-RAY DIFFRACTION99.7822931785
4.5079-5.15950.2049178527321420.1639931676762617X-RAY DIFFRACTION99.8552298227
5.1595-6.49770.3005581166111370.1997891322842663X-RAY DIFFRACTION99.8573466476

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