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- PDB-3ch1: Crystal structure of H-2Db in complex with chimeric gp100 -

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Basic information

Entry
Database: PDB / ID: 3ch1
TitleCrystal structure of H-2Db in complex with chimeric gp100
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • H-2 class I histocompatibility antigen, D-B alpha chain
  • nonameric peptide chimeric gp100
KeywordsIMMUNE SYSTEM / MHC / H-2Db / Glycoprotein / Immune response / Membrane / MHC I / Transmembrane / Immunoglobulin domain / Secreted / Disease mutation / Melanin biosynthesis
Function / homology
Function and homology information


TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / 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 ...TAP1 binding / TAP2 binding / positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / 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 / 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 / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of interleukin-13 production / positive regulation of natural killer cell mediated cytotoxicity / regulation of membrane depolarization / positive regulation of natural killer cell proliferation / 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 / 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 / MHC class I protein binding / cellular defense response / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / detection of bacterium / Neutrophil degranulation / T cell receptor binding / 14-3-3 protein binding / 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 / 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 / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / negative regulation of epithelial cell proliferation / positive regulation of T cell activation / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of type II interferon production / sensory perception of smell / negative regulation of neuron projection development / positive regulation of tumor necrosis factor production / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / antibacterial humoral response / iron ion transport / T cell receptor signaling pathway / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization / cellular response to lipopolysaccharide / intracellular iron ion homeostasis / defense response to Gram-negative bacterium / amyloid fibril formation / adaptive immune response
Similarity search - Function
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 ...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
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBadia-Martinez, D. / Achour, A.
CitationJournal: Cancer Res. / Year: 2009
Title: Design of agonistic altered peptides for the robust induction of CTL directed towards H-2Db in complex with the melanoma-associated epitope gp100.
Authors: van Stipdonk, M.J. / Badia-Martinez, D. / Sluijter, M. / Offringa, R. / van Hall, T. / Achour, A.
History
DepositionMar 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance

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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
D: H-2 class I histocompatibility antigen, D-B alpha chain
E: Beta-2-microglobulin
G: H-2 class I histocompatibility antigen, D-B alpha chain
H: Beta-2-microglobulin
J: H-2 class I histocompatibility antigen, D-B alpha chain
K: Beta-2-microglobulin
C: nonameric peptide chimeric gp100
F: nonameric peptide chimeric gp100
I: nonameric peptide chimeric gp100
L: nonameric peptide chimeric gp100
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,50443
Polymers179,62912
Non-polymers2,87531
Water8,683482
1
D: H-2 class I histocompatibility antigen, D-B alpha chain
E: Beta-2-microglobulin
F: nonameric peptide chimeric gp100
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,64811
Polymers44,9073
Non-polymers7418
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-26.4 kcal/mol
Surface area19460 Å2
MethodPISA
2
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: nonameric peptide chimeric gp100
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,83213
Polymers44,9073
Non-polymers92510
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-27.9 kcal/mol
Surface area19240 Å2
MethodPISA
3
G: H-2 class I histocompatibility antigen, D-B alpha chain
H: Beta-2-microglobulin
I: nonameric peptide chimeric gp100
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2767
Polymers44,9073
Non-polymers3684
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-15.7 kcal/mol
Surface area19770 Å2
MethodPISA
4
J: H-2 class I histocompatibility antigen, D-B alpha chain
K: Beta-2-microglobulin
L: nonameric peptide chimeric gp100
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,74812
Polymers44,9073
Non-polymers8419
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6400 Å2
ΔGint-55 kcal/mol
Surface area19510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.500, 105.400, 126.690
Angle α, β, γ (deg.)90.00, 90.08, 90.00
Int Tables number3
Space group name H-MP121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
31G
41J
12B
22E
32H
42K
13C
23F
33I
43L

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 15
2111D1 - 15
3111G1 - 15
4111J1 - 15
1211A32 - 57
2211D32 - 57
3211G32 - 57
4211J32 - 57
1311A59 - 60
2311D59 - 60
3311G59 - 60
4311J59 - 60
1411A63 - 74
2411D63 - 74
3411G63 - 74
4411J63 - 74
1511A76 - 153
2511D76 - 153
3511G76 - 153
4511J76 - 153
1611A155 - 175
2611D155 - 175
3611G155 - 175
4611J155 - 175
1712A183 - 190
2712D183 - 190
3712G183 - 190
4712J183 - 190
1812A225 - 276
2812D225 - 276
3812G225 - 276
4812J225 - 276
1911A20 - 30
2911D20 - 30
3911G20 - 30
4911J20 - 30
11011A200 - 220
21011D200 - 220
31011G200 - 220
41011J200 - 220
1121B2 - 15
2121E2 - 15
3121H2 - 15
4121K2 - 15
1221B20 - 38
2221E20 - 38
3221H20 - 38
4221K20 - 38
1321B40 - 47
2321E40 - 47
3321H40 - 47
4321K40 - 47
1421B49 - 68
2421E49 - 68
3421H49 - 68
4421K49 - 68
1521B76 - 99
2521E76 - 99
3521H76 - 99
4521K76 - 99
1131C1 - 3
2131F1 - 3
3131I1 - 3
4131L1 - 3
1233C4
2233F4
3233I4
4233L4
1331C5 - 9
2331F5 - 9
3331I5 - 9
4331L5 - 9

NCS ensembles :
ID
1
2
3

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Components

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Protein , 2 types, 8 molecules ADGJBEHK

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


Mass: 32087.703 Da / Num. of mol.: 4 / Fragment: UNP residues 25-300
Source method: isolated from a genetically manipulated source
Details: Extracellular part / Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / 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

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Protein/peptide , 1 types, 4 molecules CFIL

#3: Protein/peptide
nonameric peptide chimeric gp100


Mass: 1115.176 Da / Num. of mol.: 4 / Source method: obtained synthetically

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Non-polymers , 3 types, 513 molecules

#4: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 482 / 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: 3.88 Å3/Da / Density % sol: 68.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 1.8M ammonium sulfate, 0.1M Tris Cl, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 4, 2007
RadiationMonochromator: Diamond (111), Ge (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.3→48.6 Å / Num. all: 122100 / Num. obs: 116802 / % possible obs: 95.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.3→2.4 Å / % possible all: 89.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→48.6 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.911 / SU B: 7.213 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.248 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26402 6122 5 %RANDOM
Rwork0.23108 ---
obs0.23269 115851 99.91 %-
all-122100 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.039 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12561 0 181 482 13224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02113123
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3251.94717756
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3651512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92123.623690
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.979152138
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.17515102
X-RAY DIFFRACTIONr_chiral_restr0.090.21751
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210250
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.25557
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.28556
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2667
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.280
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2020.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.831.57826
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.434212292
X-RAY DIFFRACTIONr_scbond_it1.50536202
X-RAY DIFFRACTIONr_scangle_it2.4714.55460
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
11A1777tight positional0.030.05
12D1777tight positional0.030.05
13G1777tight positional0.030.05
14J1777tight positional0.040.05
21B703tight positional0.040.05
22E703tight positional0.040.05
23H703tight positional0.040.05
24K703tight positional0.040.05
31C71tight positional0.030.05
32F71tight positional0.030.05
33I71tight positional0.030.05
34L71tight positional0.030.05
11A240medium positional0.210.5
12D240medium positional0.270.5
13G240medium positional0.220.5
14J240medium positional0.230.5
11A1777tight thermal0.090.5
12D1777tight thermal0.090.5
13G1777tight thermal0.090.5
14J1777tight thermal0.090.5
21B703tight thermal0.10.5
22E703tight thermal0.110.5
23H703tight thermal0.10.5
24K703tight thermal0.120.5
31C71tight thermal0.150.5
32F71tight thermal0.160.5
33I71tight thermal0.160.5
34L71tight thermal0.140.5
11A240medium thermal0.282
12D240medium thermal0.312
13G240medium thermal0.312
14J240medium thermal0.262
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 472 -
Rwork0.327 8485 -
obs--99.81 %

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