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- PDB-3cch: H-2Db complex with murine gp100 -

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Basic information

Entry
Database: PDB / ID: 3cch
TitleH-2Db complex with murine gp100
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • H-2 class I histocompatibility antigen, D-B alpha chain
  • nonameric peptide murine gp100
KeywordsIMMUNE SYSTEM / murine MHC / Glycoprotein / Immune response / Membrane / MHC I / Transmembrane / 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: 2.6 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
DepositionFeb 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 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

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


Theoretical massNumber of molelcules
Total (without water)181,97537
Polymers179,58912
Non-polymers2,38625
Water1,47782
1
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: nonameric peptide murine gp100
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3748
Polymers44,8973
Non-polymers4765
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-73.1 kcal/mol
Surface area19250 Å2
MethodPISA
2
D: H-2 class I histocompatibility antigen, D-B alpha chain
E: Beta-2-microglobulin
F: nonameric peptide murine gp100
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,66211
Polymers44,8973
Non-polymers7658
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19240 Å2
ΔGint-75.2 kcal/mol
Surface area5560 Å2
MethodPISA
3
G: H-2 class I histocompatibility antigen, D-B alpha chain
H: Beta-2-microglobulin
I: nonameric peptide murine gp100
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4709
Polymers44,8973
Non-polymers5726
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-92.9 kcal/mol
Surface area19430 Å2
MethodPISA
4
J: H-2 class I histocompatibility antigen, D-B alpha chain
K: Beta-2-microglobulin
L: nonameric peptide murine gp100
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4709
Polymers44,8973
Non-polymers5726
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-94.5 kcal/mol
Surface area19380 Å2
MethodPISA
5
D: H-2 class I histocompatibility antigen, D-B alpha chain
E: Beta-2-microglobulin
F: nonameric peptide murine gp100
hetero molecules

J: H-2 class I histocompatibility antigen, D-B alpha chain
K: Beta-2-microglobulin
L: nonameric peptide murine gp100
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,13120
Polymers89,7946
Non-polymers1,33714
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area12650 Å2
ΔGint-184.1 kcal/mol
Surface area37490 Å2
MethodPISA
6
G: H-2 class I histocompatibility antigen, D-B alpha chain
H: Beta-2-microglobulin
I: nonameric peptide murine gp100
hetero molecules

A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: nonameric peptide murine gp100
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,84317
Polymers89,7946
Non-polymers1,04911
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area12540 Å2
ΔGint-180.1 kcal/mol
Surface area37540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.500, 176.600, 85.500
Angle α, β, γ (deg.)90.00, 120.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
31G
41J
12A
22D
32G
42J
13B
23E
33H
43K
14C
24F
34I
44L
15B
25E
35H
45K
16B
26E
36H
46K

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYALAAA1 - 1771 - 177
21GLYALADD1 - 1771 - 177
31GLYGLYGG1 - 1751 - 175
41GLYGLYJJ1 - 1751 - 175
12THRPROAA200 - 276200 - 276
22THRPRODD200 - 276200 - 276
32THRPROGG200 - 276200 - 276
42THRPROJJ200 - 276200 - 276
13ILEPROBB1 - 331 - 33
23ILEPROEE1 - 331 - 33
33ILEPROHH1 - 331 - 33
43ILEPROKK1 - 331 - 33
14GLULEUCC1 - 91 - 9
24GLULEUFF1 - 91 - 9
34GLULEUII1 - 91 - 9
44GLULEULL1 - 91 - 9
15ILESERBB35 - 5735 - 57
25ILESEREE35 - 5735 - 57
35ILESERHH35 - 5735 - 57
45ILESERKK35 - 5735 - 57
16ASPMETBB59 - 9959 - 99
26ASPMETEE59 - 9959 - 99
36ASPMETHH59 - 9959 - 99
46ASPMETKK59 - 9959 - 99

NCS ensembles :
ID
1
2
3
4
5
6

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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 / H-2D(B)


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 murine gp100


Mass: 1105.139 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Synthetic peptide

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Non-polymers , 3 types, 107 molecules

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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 60.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 1.8M Ammonium Sulfate, 0.1M Tris, 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: 2.6→19.6 Å / Num. all: 67578 / Num. obs: 65171 / % possible obs: 96.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.6→2.7 Å / % possible all: 89.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→19.6 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.898 / SU B: 12.978 / SU ML: 0.274 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.655 / ESU R Free: 0.332 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27859 3379 5.1 %RANDOM
Rwork0.24079 ---
all0.2456 67578 --
obs0.24266 63514 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.524 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12590 0 129 82 12801
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02113123
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.94517835
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6551526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.47423.634688
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.994152151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.12315100
X-RAY DIFFRACTIONr_chiral_restr0.0970.21764
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210276
X-RAY DIFFRACTIONr_nbd_refined0.2720.36106
X-RAY DIFFRACTIONr_nbtor_refined0.3330.58649
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.220.5830
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2690.3112
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4360.59
X-RAY DIFFRACTIONr_mcbond_it1.19627807
X-RAY DIFFRACTIONr_mcangle_it2.058312348
X-RAY DIFFRACTIONr_scbond_it0.89526174
X-RAY DIFFRACTIONr_scangle_it1.40735481
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1438tight positional0.050.05
12D1438tight positional0.040.05
13G1438tight positional0.040.05
14J1438tight positional0.040.05
21A620tight positional0.030.05
22D620tight positional0.040.05
23G620tight positional0.040.05
24J620tight positional0.040.05
31B271tight positional0.040.05
32E271tight positional0.040.05
33H271tight positional0.040.05
34K271tight positional0.040.05
41C78tight positional0.020.05
42F78tight positional0.030.05
43I78tight positional0.030.05
44L78tight positional0.020.05
51B182tight positional0.050.05
52E182tight positional0.050.05
53H182tight positional0.050.05
54K182tight positional0.050.05
61B349tight positional0.050.05
62E349tight positional0.040.05
63H349tight positional0.050.05
64K349tight positional0.040.05
11A1438tight thermal0.110.5
12D1438tight thermal0.10.5
13G1438tight thermal0.10.5
14J1438tight thermal0.110.5
21A620tight thermal0.080.5
22D620tight thermal0.080.5
23G620tight thermal0.080.5
24J620tight thermal0.080.5
31B271tight thermal0.10.5
32E271tight thermal0.090.5
33H271tight thermal0.090.5
34K271tight thermal0.10.5
41C78tight thermal0.060.5
42F78tight thermal0.060.5
43I78tight thermal0.060.5
44L78tight thermal0.060.5
51B182tight thermal0.090.5
52E182tight thermal0.080.5
53H182tight thermal0.090.5
54K182tight thermal0.080.5
61B349tight thermal0.080.5
62E349tight thermal0.090.5
63H349tight thermal0.090.5
64K349tight thermal0.080.5
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 220 -
Rwork0.361 4646 -
obs--99.2 %

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