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- PDB-3cc5: H-2Db complex with human gp100 -

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Basic information

Entry
Database: PDB / ID: 3cc5
TitleH-2Db complex with human gp100
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, D-B alpha chain
  • nonameric peptide from Melanocyte protein Pmel 17
KeywordsIMMUNE SYSTEM / murine MHC / Glycoprotein / Immune response / Membrane / MHC I / Transmembrane / Immunoglobulin domain / Secreted / Melanin biosynthesis
Function / homology
Function and homology information


cis-Golgi network membrane / positive regulation of melanin biosynthetic process / melanin biosynthetic process / melanosome membrane / melanosome organization / multivesicular body, internal vesicle / multivesicular body membrane / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC ...cis-Golgi network membrane / positive regulation of melanin biosynthetic process / melanin biosynthetic process / melanosome membrane / melanosome organization / multivesicular body, internal vesicle / multivesicular body membrane / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Regulation of MITF-M-dependent genes involved in pigmentation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / phagocytic vesicle membrane / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / sensory perception of smell / melanosome / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / external side of plasma membrane / endoplasmic reticulum membrane / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / identical protein binding / plasma membrane / cytosol
Similarity search - Function
PKD- and KLD-Associated Transmembrane / PKAT, KLD domain / PKAT, KLD domain / PKD domain / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / MHC class I, alpha chain, C-terminal ...PKD- and KLD-Associated Transmembrane / PKAT, KLD domain / PKAT, KLD domain / PKD domain / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / 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 / Melanocyte protein PMEL
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 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 24, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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 from Melanocyte protein Pmel 17
D: H-2 class I histocompatibility antigen, D-B alpha chain
E: Beta-2-microglobulin
F: nonameric peptide from Melanocyte protein Pmel 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,74015
Polymers89,8996
Non-polymers8419
Water10,935607
1
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: nonameric peptide from Melanocyte protein Pmel 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4188
Polymers44,9493
Non-polymers4685
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-39 kcal/mol
Surface area19020 Å2
MethodPISA
2
D: H-2 class I histocompatibility antigen, D-B alpha chain
E: Beta-2-microglobulin
F: nonameric peptide from Melanocyte protein Pmel 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3227
Polymers44,9493
Non-polymers3724
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-41 kcal/mol
Surface area19180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.200, 165.400, 161.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
31A
41D
51A
61D
12A
22D
32A
42D
52A
62D
72A
82D
13B
23E
14C
24F

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111HISHISVALVAL1AA3 - 343 - 34
211HISHISVALVAL1DD3 - 343 - 34
321PHEPHELEULEU1AA36 - 7836 - 78
421PHEPHELEULEU1DD36 - 7836 - 78
531ASNASNGLYGLY1AA80 - 17580 - 175
631ASNASNGLYGLY1DD80 - 17580 - 175
112THRTHRPROPRO1AA182 - 193182 - 193
212THRTHRPROPRO1DD182 - 193182 - 193
322METMETPROPRO1AA228 - 276228 - 276
422METMETPROPRO1DD228 - 276228 - 276
532GLUGLUASPASP2AA223 - 227223 - 227
632GLUGLUASPASP2DD223 - 227223 - 227
742SERSERGLUGLU1AA195 - 222195 - 222
842SERSERGLUGLU1DD195 - 222195 - 222
113LYSLYSMETMET1BB3 - 993 - 99
213LYSLYSMETMET1EE3 - 993 - 99
114LYSLYSLEULEU1CC1 - 91 - 9
214LYSLYSLEULEU1FF1 - 91 - 9

NCS ensembles :
ID
1
2
3
4

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Components

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Protein , 2 types, 4 molecules ADBE

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


Mass: 32087.703 Da / Num. of mol.: 2 / Fragment: Extracellular part, 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.: 2
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, 2 molecules CF

#3: Protein/peptide nonameric peptide from Melanocyte protein Pmel 17 / Silver locus protein homolog / Melanocyte lineage-specific antigen GP100 / Melanoma-associated ME20 ...Silver locus protein homolog / Melanocyte lineage-specific antigen GP100 / Melanoma-associated ME20 antigen / ME20M / ME20-M


Mass: 1157.321 Da / Num. of mol.: 2 / Fragment: Extracellular part, UNP residues 25-33 / Source method: obtained synthetically / Details: chemical synthesis / References: UniProt: P40967

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Non-polymers , 3 types, 616 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 607 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.49 Å3/Da / Density % sol: 50.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% PEG 6000, 0.1M Ammonium sulfate, 0.1M Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: 1.91→24.82 Å / Num. all: 71103 / Num. obs: 66186 / % possible obs: 93.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.91→2 Å / % possible all: 65.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N5A

1n5a


Resolution: 1.91→24.81 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.919 / SU B: 8.688 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.195 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2683 3432 5 %RANDOM
Rwork0.22762 ---
all0.2351 66190 --
obs0.22972 64542 97.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.891 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.91→24.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6336 0 51 607 6994
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0216574
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.9448924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3375762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65123.626342
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.717151080
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1191550
X-RAY DIFFRACTIONr_chiral_restr0.1110.2890
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025144
X-RAY DIFFRACTIONr_nbd_refined0.250.32930
X-RAY DIFFRACTIONr_nbtor_refined0.3210.54448
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2320.5889
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2660.358
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2360.532
X-RAY DIFFRACTIONr_mcbond_it1.16923935
X-RAY DIFFRACTIONr_mcangle_it1.82236208
X-RAY DIFFRACTIONr_scbond_it1.15723089
X-RAY DIFFRACTIONr_scangle_it1.77632716
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1420tight positional0.040.05
2A733tight positional0.040.05
3B804tight positional0.040.05
4C82tight positional0.030.05
2A21medium positional0.420.5
1A1420tight thermal0.150.5
2A733tight thermal0.130.5
3B804tight thermal0.130.5
4C82tight thermal0.150.5
2A21medium thermal0.262
LS refinement shellResolution: 1.912→1.961 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 193 -
Rwork0.277 3759 -
obs--77.87 %

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