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Basic information

Entry
Database: PDB / ID: 6g9r
TitleMurine class I major histocompatibility complex H-2 Db in complex with self-antigen derived from dopamine monooxygenase.
Components
  • Beta-2-microglobulin
  • Dopamine beta-hydroxylase
  • H-2 class I histocompatibility antigen, D-B alpha chain
KeywordsIMMUNE SYSTEM / LCMV / cross-reactivity / MHC class I / TCR / APL
Function / homology
Function and homology information


Catecholamine biosynthesis / dopamine beta-monooxygenase / leukocyte mediated immunity / dopamine beta-monooxygenase activity / regulation of vascular associated smooth muscle cell proliferation / regulation of vascular endothelial cell proliferation / chromaffin granule lumen / homoiothermy / regulation of extrinsic apoptotic signaling pathway / norepinephrine biosynthetic process ...Catecholamine biosynthesis / dopamine beta-monooxygenase / leukocyte mediated immunity / dopamine beta-monooxygenase activity / regulation of vascular associated smooth muscle cell proliferation / regulation of vascular endothelial cell proliferation / chromaffin granule lumen / homoiothermy / regulation of extrinsic apoptotic signaling pathway / norepinephrine biosynthetic process / chromaffin granule membrane / 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 / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / leukocyte migration / response to pain / transport vesicle membrane / positive regulation of vasoconstriction / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / associative learning / blood vessel remodeling / cellular defense response / 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 / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / 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 / centriolar satellite / memory / phagocytic vesicle membrane / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / glucose homeostasis / T cell differentiation in thymus / negative regulation of neuron projection development / positive regulation of cold-induced thermogenesis / protein refolding / secretory granule lumen / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / copper ion binding / external side of plasma membrane / structural molecule activity / endoplasmic reticulum / 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, histidine-cluster-2 conserved site / Copper type II, ascorbate-dependent monooxygenases signature 2. / Copper type II, ascorbate-dependent monooxygenase, N-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, histidine-cluster-2 conserved site / Copper type II, ascorbate-dependent monooxygenases signature 2. / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsAchour, A. / Sandalova, T. / Allerbring, E.
CitationJournal: to be published
Title: Structural basis for CD8+ T cells auto-reactivity in LCMV infection
Authors: Allerbring, E. / Duru, A.D. / Nygren, P.A. / Sandalova, T. / Achour, A.
History
DepositionApr 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 23, 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: H-2 class I histocompatibility antigen, D-B alpha chain
D: Beta-2-microglobulin
E: H-2 class I histocompatibility antigen, D-B alpha chain
F: Beta-2-microglobulin
G: H-2 class I histocompatibility antigen, D-B alpha chain
H: Beta-2-microglobulin
P: Dopamine beta-hydroxylase
I: Dopamine beta-hydroxylase
J: Dopamine beta-hydroxylase
K: Dopamine beta-hydroxylase


Theoretical massNumber of molelcules
Total (without water)179,32112
Polymers179,32112
Non-polymers00
Water1629
1
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
P: Dopamine beta-hydroxylase


Theoretical massNumber of molelcules
Total (without water)44,8303
Polymers44,8303
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-16 kcal/mol
Surface area19530 Å2
MethodPISA
2
C: H-2 class I histocompatibility antigen, D-B alpha chain
D: Beta-2-microglobulin
I: Dopamine beta-hydroxylase


Theoretical massNumber of molelcules
Total (without water)44,8303
Polymers44,8303
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-17 kcal/mol
Surface area19580 Å2
MethodPISA
3
E: H-2 class I histocompatibility antigen, D-B alpha chain
F: Beta-2-microglobulin
J: Dopamine beta-hydroxylase


Theoretical massNumber of molelcules
Total (without water)44,8303
Polymers44,8303
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-18 kcal/mol
Surface area19650 Å2
MethodPISA
4
G: H-2 class I histocompatibility antigen, D-B alpha chain
H: Beta-2-microglobulin
K: Dopamine beta-hydroxylase


Theoretical massNumber of molelcules
Total (without water)44,8303
Polymers44,8303
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-18 kcal/mol
Surface area19630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.245, 123.597, 99.262
Angle α, β, γ (deg.)90.00, 103.07, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22E
13A
23G
14B
24D
15B
25F
16B
26H
17C
27E
18C
28G
19D
29F
110D
210H
111E
211G
112F
212H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYPROPROAA1 - 2761 - 276
21GLYGLYPROPROCC1 - 2761 - 276
12GLYGLYPROPROAA1 - 2761 - 276
22GLYGLYPROPROEE1 - 2761 - 276
13GLYGLYPROPROAA1 - 2761 - 276
23GLYGLYPROPROGG1 - 2761 - 276
14ILEILEMETMETBB1 - 991 - 99
24ILEILEMETMETDD1 - 991 - 99
15ILEILEMETMETBB1 - 991 - 99
25ILEILEMETMETFF1 - 991 - 99
16ILEILEMETMETBB1 - 991 - 99
26ILEILEMETMETHH1 - 991 - 99
17GLYGLYPROPROCC1 - 2761 - 276
27GLYGLYPROPROEE1 - 2761 - 276
18GLYGLYPROPROCC1 - 2761 - 276
28GLYGLYPROPROGG1 - 2761 - 276
19ILEILEMETMETDD1 - 991 - 99
29ILEILEMETMETFF1 - 991 - 99
110ILEILEMETMETDD1 - 991 - 99
210ILEILEMETMETHH1 - 991 - 99
111GLYGLYPROPROEE1 - 2761 - 276
211GLYGLYPROPROGG1 - 2761 - 276
112ILEILEMETMETFF1 - 991 - 99
212ILEILEMETMETHH1 - 991 - 99

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12

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Components

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


Mass: 32087.703 Da / Num. of mol.: 4 / Fragment: UNP residues 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01899
#2: Protein
Beta-2-microglobulin


Mass: 11704.359 Da / Num. of mol.: 4 / Fragment: UNP residues 21-119
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
Dopamine beta-hydroxylase / Dopamine beta-monooxygenase / mDBM


Mass: 1038.173 Da / Num. of mol.: 4 / Fragment: UNP residues 557-565 / Mutation: L3P / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: Q64237, dopamine beta-monooxygenase
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.07 Å3/Da / Density % sol: 59.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 1.5-2.0M ammonium sulfate 0.1M TRIS HCL, pH 8.0 / PH range: 7.5-9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.072 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 4, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 135709 / Num. obs: 56263 / % possible obs: 94.5 % / Redundancy: 2.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.059 / Net I/σ(I): 8.2
Reflection shellResolution: 2.7→2.77 Å / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 11115 / CC1/2: 0.64 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1s7u

1s7u


Resolution: 2.7→45 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.922 / SU B: 16.871 / SU ML: 0.323 / Cross valid method: THROUGHOUT / ESU R: 1.415 / ESU R Free: 0.361 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26441 2843 5.1 %RANDOM
Rwork0.23407 ---
obs0.23562 53380 94.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 82.239 Å2
Baniso -1Baniso -2Baniso -3
1--2.01 Å20 Å21.79 Å2
2--2.57 Å2-0 Å2
3----1.26 Å2
Refinement stepCycle: 1 / Resolution: 2.7→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12632 0 0 9 12641
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01913058
X-RAY DIFFRACTIONr_bond_other_d0.0050.0211806
X-RAY DIFFRACTIONr_angle_refined_deg1.5221.93717750
X-RAY DIFFRACTIONr_angle_other_deg1.109327237
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.34751530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.49223.594679
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.61152131
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0281596
X-RAY DIFFRACTIONr_chiral_restr0.0890.21779
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02114806
X-RAY DIFFRACTIONr_gen_planes_other0.0050.023184
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.5157.9616141
X-RAY DIFFRACTIONr_mcbond_other6.5157.9616140
X-RAY DIFFRACTIONr_mcangle_it10.21311.9287658
X-RAY DIFFRACTIONr_mcangle_other10.21311.9277659
X-RAY DIFFRACTIONr_scbond_it6.2538.3776917
X-RAY DIFFRACTIONr_scbond_other6.2528.3776917
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.88912.37810090
X-RAY DIFFRACTIONr_long_range_B_refined13.71461.29114049
X-RAY DIFFRACTIONr_long_range_B_other13.71461.2914050
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 / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A321940.01
12C321940.01
21A320420.04
22E320420.04
31A320800.03
32G320800.03
41B116720
42D116720
51B116620.01
52F116620.01
61B116580.01
62H116580.01
71C320880.04
72E320880.04
81C321280.03
82G321280.03
91D116620.01
92F116620.01
101D116600.01
102H116600.01
111E320280.04
112G320280.04
121F116600.01
122H116600.01
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 211 -
Rwork0.375 3984 -
obs--95.89 %

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