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- PDB-4i5b: Structure of human MHC class II protein HLA-DR1 carrying an influ... -

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Basic information

Entry
Database: PDB / ID: 4i5b
TitleStructure of human MHC class II protein HLA-DR1 carrying an influenza hemagglutinin peptide partially filling the binding groove
Components
  • HLA class II histocompatibility antigen, DR alpha chain
  • HLA class II histocompatibility antigen, DRB1-1 beta chain
  • truncated hemagglutinin peptide
KeywordsIMMUNE SYSTEM / Immunoglobulin fold / Antigen presentation / peptide-MHC complex / membrane
Function / homology
Function and homology information


regulation of interleukin-4 production / regulation of interleukin-10 production / positive regulation of T cell mediated immune response to tumor cell / 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 ...regulation of interleukin-4 production / regulation of interleukin-10 production / positive regulation of T cell mediated immune response to tumor cell / 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 memory T cell differentiation / positive regulation of monocyte differentiation / CD4 receptor binding / positive regulation of kinase activity / inflammatory response to antigenic stimulus / transport vesicle membrane / intermediate filament / polysaccharide binding / T-helper 1 type immune response / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of insulin secretion involved in cellular response to glucose stimulus / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / Generation of second messenger molecules / immunological synapse / PD-1 signaling / epidermis development / detection of bacterium / T cell receptor binding / negative regulation of T cell proliferation / negative regulation of inflammatory response to antigenic stimulus / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cognition / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / peptide antigen binding / endocytic vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / Interferon gamma signaling / positive regulation of immune response / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / early endosome membrane / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / positive regulation of viral entry into host cell / lysosome / positive regulation of ERK1 and ERK2 cascade / immune response / positive regulation of protein phosphorylation / lysosomal membrane / external side of plasma membrane / Golgi membrane / positive regulation of DNA-templated transcription / cell surface / signal transduction / extracellular space / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / 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 ...Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / 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/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 / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain / HLA class II histocompatibility antigen, DRB1 beta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsSchulze, M.-S.E.D.
CitationJournal: Plos One / Year: 2013
Title: Disruption of hydrogen bonds between major histocompatibility complex class II and the peptide N-terminus is not sufficient to form a human leukocyte antigen-DM receptive state of major ...Title: Disruption of hydrogen bonds between major histocompatibility complex class II and the peptide N-terminus is not sufficient to form a human leukocyte antigen-DM receptive state of major histocompatibility complex class II.
Authors: Schulze, M.S. / Anders, A.K. / Sethi, D.K. / Call, M.J.
History
DepositionNov 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references

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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, DRB1-1 beta chain
C: truncated hemagglutinin peptide
D: HLA class II histocompatibility antigen, DR alpha chain
E: HLA class II histocompatibility antigen, DRB1-1 beta chain
F: truncated hemagglutinin peptide


Theoretical massNumber of molelcules
Total (without water)90,7926
Polymers90,7926
Non-polymers00
Water3,423190
1
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1-1 beta chain
C: truncated hemagglutinin peptide


Theoretical massNumber of molelcules
Total (without water)45,3963
Polymers45,3963
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-37 kcal/mol
Surface area18410 Å2
MethodPISA
2
D: HLA class II histocompatibility antigen, DR alpha chain
E: HLA class II histocompatibility antigen, DRB1-1 beta chain
F: truncated hemagglutinin peptide


Theoretical massNumber of molelcules
Total (without water)45,3963
Polymers45,3963
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-38 kcal/mol
Surface area19070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.811, 111.381, 211.544
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11E-207-

HOH

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Components

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


Mass: 21667.459 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P01903
#2: Protein HLA class II histocompatibility antigen, DRB1-1 beta chain / MHC class II antigen DRB1*1 / DR-1 / DR1


Mass: 22380.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P04229, UniProt: P01911*PLUS
#3: Protein/peptide truncated hemagglutinin peptide


Mass: 1347.688 Da / Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O

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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: 3.11 Å3/Da / Density % sol: 60.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.3
Details: 100 mM sodium acetate, 9% PEG 10000, pH 4.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 11, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.12→50 Å / Num. all: 64241 / Num. obs: 58717 / % possible obs: 91.4 % / Observed criterion σ(I): -3
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.12-2.15170
2.15-2.19179
2.19-2.23182
2.23-2.27187
2.27-2.32188
2.32-2.37190
2.37-2.42191
2.42-2.48193
2.48-2.55193
2.55-2.63194
2.63-2.71194
2.71-2.81194
2.81-2.92195
2.92-3.06195
3.06-3.22195
3.22-3.42195
3.42-3.68195
3.68-4.05196
4.05-4.64196
4.64-5.85198
5.85-49.29198

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→49.278 Å / SU ML: 0.23 / σ(F): 1.35 / Phase error: 22.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2368 2967 5.05 %RANDOM
Rwork0.199 ---
obs0.2009 58717 91.4 %-
all-64241 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.12→49.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6328 0 0 190 6518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086507
X-RAY DIFFRACTIONf_angle_d1.1448837
X-RAY DIFFRACTIONf_dihedral_angle_d14.1192392
X-RAY DIFFRACTIONf_chiral_restr0.076951
X-RAY DIFFRACTIONf_plane_restr0.0061156
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.15670.3091900.23632050X-RAY DIFFRACTION70
2.1567-2.19380.26741210.22052256X-RAY DIFFRACTION79
2.1938-2.23370.26161480.20872374X-RAY DIFFRACTION82
2.2337-2.27670.27731440.20592458X-RAY DIFFRACTION87
2.2767-2.32320.2661380.20272513X-RAY DIFFRACTION88
2.3232-2.37370.26521400.20632607X-RAY DIFFRACTION90
2.3737-2.42890.24911560.20332591X-RAY DIFFRACTION91
2.4289-2.48960.27231360.2112670X-RAY DIFFRACTION93
2.4896-2.5570.2451310.20632708X-RAY DIFFRACTION93
2.557-2.63220.25831460.21462705X-RAY DIFFRACTION94
2.6322-2.71710.25671510.21142711X-RAY DIFFRACTION94
2.7171-2.81420.2351250.20412730X-RAY DIFFRACTION94
2.8142-2.92690.29141380.21342752X-RAY DIFFRACTION95
2.9269-3.06010.27141430.22552760X-RAY DIFFRACTION95
3.0601-3.22140.26761430.22282741X-RAY DIFFRACTION95
3.2214-3.42320.2381570.20892750X-RAY DIFFRACTION95
3.4232-3.68740.23851530.19672792X-RAY DIFFRACTION95
3.6874-4.05830.22591500.19392799X-RAY DIFFRACTION96
4.0583-4.64520.18471460.16392839X-RAY DIFFRACTION96
4.6452-5.8510.18181340.16832934X-RAY DIFFRACTION98
5.851-49.29080.19941770.19053010X-RAY DIFFRACTION98

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