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- PDB-1zhb: Crystal Structure Of The Murine Class I Major Histocompatibility ... -

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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-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 / octopamine biosynthetic process / dopamine beta-monooxygenase / leukocyte mediated immunity / dopamine beta-monooxygenase activity / regulation of vascular associated smooth muscle cell proliferation / Catecholamine biosynthesis / regulation of vascular endothelial cell proliferation / chromaffin granule lumen / homoiothermy ...octopamine metabolic process / octopamine biosynthetic process / dopamine beta-monooxygenase / leukocyte mediated immunity / dopamine beta-monooxygenase activity / regulation of vascular associated smooth muscle cell proliferation / Catecholamine biosynthesis / regulation of vascular endothelial cell proliferation / chromaffin granule lumen / homoiothermy / regulation of extrinsic apoptotic signaling pathway / varicosity / norepinephrine biosynthetic process / chromaffin granule membrane / response to ozone / catecholamine metabolic process / behavioral response to ethanol / vasoconstriction / dopamine catabolic process / fear response / maternal behavior / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / L-ascorbic acid binding / ER-Phagosome pathway / DAP12 signaling / response to iron ion / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / response to pain / leukocyte migration / response to copper ion / transport vesicle membrane / response to isolation stress / positive regulation of vasoconstriction / response to immobilization stress / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / associative learning / social behavior / blood vessel remodeling / cellular defense response / cellular response to manganese ion / Neutrophil degranulation / secretory granule membrane / response to amphetamine / lumenal side of endoplasmic reticulum membrane / locomotory behavior / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / response to peptide hormone / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / bone development / visual learning / MHC class I protein complex / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / memory / phagocytic vesicle membrane / terminal bouton / negative regulation of epithelial cell proliferation / apical part of cell / sensory perception of smell / positive regulation of cellular senescence / response to estradiol / glucose homeostasis / T cell differentiation in thymus / negative regulation of neuron projection development / positive regulation of cold-induced thermogenesis / protein refolding / response to ethanol / secretory granule lumen / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / response to xenobiotic stimulus / copper ion binding / axon / external side of plasma membrane / neuronal cell body / dendrite / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / plasma membrane / cytosol
Similarity search - Function
Dopamine beta-hydroxylase-like / Tyramine beta-hydroxylase/Dopamine beta-hydroxylase / Copper-dependent monooxygenases, DOMON domain / DOMON domain / 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 ...Dopamine beta-hydroxylase-like / Tyramine beta-hydroxylase/Dopamine beta-hydroxylase / Copper-dependent monooxygenases, DOMON domain / DOMON domain / 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 / Immunoglobulin-like fold / Immunoglobulins / 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
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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


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


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
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: 3.3 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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