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Entry
Database: PDB / ID: 1zhb
TitleCrystal Structure Of The Murine Class I Major Histocompatibility Complex Of H-2Db, B2-Microglobulin, and a 9-Residue Peptide Derived from rat dopamine beta-monooxigenase
Components
  • 9-mer peptide from Dopamine beta-monooxygenase
  • Beta-2-microglobulinBeta-2 microglobulin
  • H-2 class I histocompatibility antigen, D-B alpha chain
KeywordsIMMUNE SYSTEM / MHC / TCR-crossreactivity / self-ligand / autoimmunity
Function / homology
Function and homology information


octopamine metabolic process / dopamine beta-monooxygenase / leukocyte mediated immunity / dopamine beta-monooxygenase activity / octopamine biosynthetic process / Catecholamine biosynthesis / homoiothermy / : / chromaffin granule lumen / regulation of extrinsic apoptotic signaling pathway ...octopamine metabolic process / dopamine beta-monooxygenase / leukocyte mediated immunity / dopamine beta-monooxygenase activity / octopamine biosynthetic process / Catecholamine biosynthesis / homoiothermy / : / chromaffin granule lumen / regulation of extrinsic apoptotic signaling pathway / norepinephrine biosynthetic process / varicosity / chromaffin granule membrane / response to ozone / response to xenobiotic stimulus => GO:0009410 / response to isolation stress / behavioral response to ethanol / catecholamine metabolic process / maternal behavior / dopamine catabolic process / fear response / TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / L-ascorbic acid binding / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / response to iron ion / response to copper ion / cis-Golgi network membrane / positive regulation of natural killer cell activation / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / negative regulation of natural killer cell mediated cytotoxicity / response to pain / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / transport vesicle membrane / positive regulation of interleukin-13 production / leukocyte migration / positive regulation of natural killer cell mediated cytotoxicity / regulation of membrane depolarization / social behavior / positive regulation of natural killer cell proliferation / associative learning / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of memory T cell activation / positive regulation of immunoglobulin production / TAP complex binding / response to immobilization stress / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of interleukin-4 production / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / blood vessel remodeling / MHC class I protein binding / cellular response to manganese ion / cellular defense response / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / positive regulation of vasoconstriction / protection from natural killer cell mediated cytotoxicity / negative regulation of T cell proliferation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / response to amphetamine / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / detection of bacterium / Neutrophil degranulation / T cell receptor binding / secretory granule membrane / 14-3-3 protein binding / locomotory behavior / lumenal side of endoplasmic reticulum membrane / peptide binding / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / visual learning / bone development / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / terminal bouton / HFE-transferrin receptor complex
Similarity search - Function
DOMON domain / Dopamine beta-hydroxylase-like / Tyramine beta-hydroxylase/Dopamine beta-hydroxylase / DOMON domain profile. / DOMON domain / Possible catecholamine-binding domain present in a variety of eukaryotic proteins. / Copper type II, ascorbate-dependent monooxygenase, N-terminal / Copper type II, ascorbate-dependent monooxygenase, histidine-cluster-1 conserved site / Copper type II ascorbate-dependent monooxygenase, C-terminal / Copper type II, ascorbate-dependent monooxygenase, N-terminal domain superfamily ...DOMON domain / Dopamine beta-hydroxylase-like / Tyramine beta-hydroxylase/Dopamine beta-hydroxylase / DOMON domain profile. / DOMON domain / Possible catecholamine-binding domain present in a variety of eukaryotic proteins. / Copper type II, ascorbate-dependent monooxygenase, N-terminal / Copper type II, ascorbate-dependent monooxygenase, histidine-cluster-1 conserved site / Copper type II ascorbate-dependent monooxygenase, C-terminal / Copper type II, ascorbate-dependent monooxygenase, N-terminal domain superfamily / Copper type II ascorbate-dependent monooxygenase, N-terminal domain / Copper type II ascorbate-dependent monooxygenase, C-terminal domain / Copper type II, ascorbate-dependent monooxygenases signature 1. / PHM/PNGase F domain superfamily / Copper type II, ascorbate-dependent monooxygenase-like, C-terminal / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-B alpha chain / Dopamine beta-hydroxylase
Similarity search - Component
Biological speciesMus musculus (house mouse)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsSandalova, T. / Michaelsson, J. / Harris, R.A. / Odeberg, J. / Schneider, G. / Karre, K. / Achour, A.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: A structural basis for CD8+ T cell-dependent recognition of non-homologous peptide ligands: implications for molecular mimicry in autoreactivity
Authors: Sandalova, T. / Michaelsson, J. / Harris, R.A. / Odeberg, J. / Schneider, G. / Karre, K. / Achour, A.
#1: Journal: Immunity / Year: 2002
Title: A structural basis for LCMV immune evasion: subversion of H-2D(b) and H-2K(b) presentation of gp33 revealed by comparative crystal structure.Analyses
Authors: Achour, A. / Michaelsson, J. / Harris, R.A. / Odeberg, J. / Grufman, P. / Sandberg, J.K. / Levitsky, V. / Karre, K. / Sandalova, T. / Schneider, G.
History
DepositionApr 25, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Data collection / Database references / Source and taxonomy
Category: diffrn_source / pdbx_database_related / pdbx_entity_src_syn
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_entity_src_syn.details ..._diffrn_source.pdbx_synchrotron_site / _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific
Revision 1.4Oct 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: 9-mer peptide from Dopamine beta-monooxygenase
D: H-2 class I histocompatibility antigen, D-B alpha chain
E: Beta-2-microglobulin
F: 9-mer peptide from Dopamine beta-monooxygenase
G: H-2 class I histocompatibility antigen, D-B alpha chain
H: Beta-2-microglobulin
I: 9-mer peptide from Dopamine beta-monooxygenase
J: H-2 class I histocompatibility antigen, D-B alpha chain
K: Beta-2-microglobulin
L: 9-mer peptide from Dopamine beta-monooxygenase


Theoretical massNumber of molelcules
Total (without water)179,38112
Polymers179,38112
Non-polymers00
Water1,964109
1
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: 9-mer peptide from Dopamine beta-monooxygenase


Theoretical massNumber of molelcules
Total (without water)44,8453
Polymers44,8453
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-18 kcal/mol
Surface area19170 Å2
MethodPISA
2
D: H-2 class I histocompatibility antigen, D-B alpha chain
E: Beta-2-microglobulin
F: 9-mer peptide from Dopamine beta-monooxygenase


Theoretical massNumber of molelcules
Total (without water)44,8453
Polymers44,8453
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-18 kcal/mol
Surface area19460 Å2
MethodPISA
3
G: H-2 class I histocompatibility antigen, D-B alpha chain
H: Beta-2-microglobulin
I: 9-mer peptide from Dopamine beta-monooxygenase


Theoretical massNumber of molelcules
Total (without water)44,8453
Polymers44,8453
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-21 kcal/mol
Surface area19500 Å2
MethodPISA
4
J: H-2 class I histocompatibility antigen, D-B alpha chain
K: Beta-2-microglobulin
L: 9-mer peptide from Dopamine beta-monooxygenase


Theoretical massNumber of molelcules
Total (without water)44,8453
Polymers44,8453
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-21 kcal/mol
Surface area19380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.063, 122.715, 99.403
Angle α, β, γ (deg.)90.00, 103.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
31G
41J
12B
22E
32H
42K
13C
23F
33I
43L

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROTRPTRP5AA2 - 2742 - 274
21PROPROTRPTRP5DD2 - 2742 - 274
31PROPROTRPTRP5GG2 - 2742 - 274
41PROPROTRPTRP5JJ2 - 2742 - 274
12ILEILEMETMET4BB1 - 991 - 99
22ILEILEMETMET4EE1 - 991 - 99
32ILEILEMETMET4HH1 - 991 - 99
42ILEILEMETMET4KK1 - 991 - 99
13LYSLYSILEILE4CC1 - 91 - 9
23LYSLYSILEILE4FF1 - 91 - 9
33LYSLYSILEILE4II1 - 91 - 9
43LYSLYSILEILE4LL1 - 91 - 9

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
H-2 class I histocompatibility antigen, D-B alpha chain / H- 2DB


Mass: 32087.703 Da / Num. of mol.: 4 / Fragment: EXTRAcellular part
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D / Production host: Escherichia coli (E. coli) / References: UniProt: P01899
#2: Protein
Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11704.359 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: P01887
#3: Protein/peptide
9-mer peptide from Dopamine beta-monooxygenase / Dopamine beta- hydroxylase / DBH


Mass: 1053.231 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: Q05754, dopamine beta-monooxygenase
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 3.3 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: ammonium sulphate, Tris HCl, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.0292 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 28, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0292 Å / Relative weight: 1
ReflectionResolution: 2.7→25 Å / Num. all: 203819 / Num. obs: 58548 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 66.2 Å2 / Rsym value: 0.081 / Net I/σ(I): 14.4
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2 / Num. unique all: 2200 / Rsym value: 0.502 / % possible all: 93.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N5A

1n5a


Resolution: 2.7→24.92 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.907 / SU B: 23.57 / SU ML: 0.222 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.378 / ESU R Free: 0.329 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26176 2231 4 %RANDOM
Rwork0.22533 ---
all0.22607 53240 --
obs0.226 53240 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 47.366 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å2-0.08 Å2
2--0.03 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 2.7→24.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12552 0 0 109 12661
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02112940
X-RAY DIFFRACTIONr_bond_other_d0.0050.0211140
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.93617572
X-RAY DIFFRACTIONr_angle_other_deg0.795325992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.37151512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.40223.571672
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.902152136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9461596
X-RAY DIFFRACTIONr_chiral_restr0.0790.21772
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214376
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022756
X-RAY DIFFRACTIONr_nbd_refined0.2040.22356
X-RAY DIFFRACTIONr_nbd_other0.1970.210703
X-RAY DIFFRACTIONr_nbtor_refined0.1880.25833
X-RAY DIFFRACTIONr_nbtor_other0.0890.27622
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2321
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1350.23
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.244
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2460.2160
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1310.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1721.59765
X-RAY DIFFRACTIONr_mcbond_other0.1081.53068
X-RAY DIFFRACTIONr_mcangle_it1.121212284
X-RAY DIFFRACTIONr_scbond_it1.57936494
X-RAY DIFFRACTIONr_scangle_it2.3014.55288
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1597medium positional0.340.5
12D1597medium positional0.220.5
13G1597medium positional0.340.5
14J1597medium positional0.220.5
21B1526medium positional0.30.5
22E1526medium positional0.340.5
23H1526medium positional0.450.5
24K1526medium positional0.340.5
31C145medium positional0.640.5
32F145medium positional0.530.5
33I145medium positional0.610.5
34L145medium positional0.710.5
11A2610loose positional0.965
12D2610loose positional0.635
13G2610loose positional0.645
14J2610loose positional0.685
11A1597medium thermal0.512
12D1597medium thermal0.412
13G1597medium thermal0.442
14J1597medium thermal0.442
21B1526medium thermal0.442
22E1526medium thermal0.382
23H1526medium thermal0.482
24K1526medium thermal0.42
31C145medium thermal0.332
32F145medium thermal0.272
33I145medium thermal0.432
34L145medium thermal0.442
11A2610loose thermal1.2710
12D2610loose thermal1.1710
13G2610loose thermal1.2410
14J2610loose thermal1.1810
LS refinement shellResolution: 2.7→2.765 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 130 -
Rwork0.332 3126 -
obs--100 %

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