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- PDB-5wlg: Crystal Structure of H-2Db with the GAP501 peptide (SQL) -

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Basic information

Entry
Database: PDB / ID: 5wlg
TitleCrystal Structure of H-2Db with the GAP501 peptide (SQL)
Components
  • Beta-2-microglobulin
  • GAP50 peptide
  • H-2 class I histocompatibility antigen, D-B alpha chain
  • T cell receptor alpha variable 8D-2,Human nkt tcr alpha chain
  • T-cell receptor beta chain V region C5,Human nkt tcr beta chain
KeywordsIMMUNE SYSTEM / H-2Db / malaria / GAP50 / Immune response gene / TCR / T cell / Vb8.1
Function / homology
Function and homology information


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 / T cell receptor complex / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response ...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 / T cell receptor complex / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / Neutrophil degranulation / 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 / lumenal side of endoplasmic reticulum membrane / peptide binding / response to bacterium / 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 / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / 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 / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / sensory perception of smell / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / cell surface receptor signaling pathway / hydrolase activity / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / protein-containing complex binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / membrane / metal ion binding / plasma membrane / cytosol
Similarity search - Function
T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 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 ...T-cell receptor alpha chain, constant domain / Domain of unknown function (DUF1968) / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / 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 / Immunoglobulin V-Type / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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
T cell receptor alpha variable 8D-2 / Secreted acid phosphatase, putative / Human nkt tcr alpha chain / Human nkt tcr beta chain / Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-B alpha chain / T-cell receptor beta chain V region C5
Similarity search - Component
Biological speciesMus musculus (house mouse)
Plasmodium berghei (eukaryote)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsGras, S. / Farenc, C. / Josephs, T. / Rossjohn, J.
CitationJournal: Immunity / Year: 2017
Title: A T Cell Receptor Locus Harbors a Malaria-Specific Immune Response Gene.
Authors: Van Braeckel-Budimir, N. / Gras, S. / Ladell, K. / Josephs, T.M. / Pewe, L. / Urban, S.L. / Miners, K.L. / Farenc, C. / Price, D.A. / Rossjohn, J. / Harty, J.T.
History
DepositionJul 26, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_end
Revision 1.2May 29, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Oct 4, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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: GAP50 peptide
D: T cell receptor alpha variable 8D-2,Human nkt tcr alpha chain
E: T-cell receptor beta chain V region C5,Human nkt tcr beta chain
F: H-2 class I histocompatibility antigen, D-B alpha chain
G: Beta-2-microglobulin
H: GAP50 peptide
I: T cell receptor alpha variable 8D-2,Human nkt tcr alpha chain
J: T-cell receptor beta chain V region C5,Human nkt tcr beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,10214
Polymers184,99810
Non-polymers1044
Water16,033890
1
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: GAP50 peptide
D: T cell receptor alpha variable 8D-2,Human nkt tcr alpha chain
E: T-cell receptor beta chain V region C5,Human nkt tcr beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,5577
Polymers92,4995
Non-polymers582
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10940 Å2
ΔGint-73 kcal/mol
Surface area37920 Å2
MethodPISA
2
F: H-2 class I histocompatibility antigen, D-B alpha chain
G: Beta-2-microglobulin
H: GAP50 peptide
I: T cell receptor alpha variable 8D-2,Human nkt tcr alpha chain
J: T-cell receptor beta chain V region C5,Human nkt tcr beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,5457
Polymers92,4995
Non-polymers462
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10850 Å2
ΔGint-72 kcal/mol
Surface area37950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.735, 70.210, 116.488
Angle α, β, γ (deg.)90.00, 108.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 4 types, 8 molecules AFBGDIEJ

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


Mass: 32281.930 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P01899
#2: Protein Beta-2-microglobulin


Mass: 11660.350 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P01887
#4: Protein T cell receptor alpha variable 8D-2,Human nkt tcr alpha chain / Human nkt tcr beta chain


Mass: 20203.350 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Gene: Trav8d-2, B2M, HDCMA22P / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0A075B616, UniProt: K7N5M3
#5: Protein T-cell receptor beta chain V region C5,Human nkt tcr beta chain


Mass: 27303.146 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Plasmid: pET30 / Gene: B2M, HDCMA22P / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P04213, UniProt: K7N5M4

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Protein/peptide , 1 types, 2 molecules CH

#3: Protein/peptide GAP50 peptide


Mass: 1050.229 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium berghei (eukaryote)
Gene: GAP50, PBK173_000161900, PBNK65E_000154900, PBNK65NY_000154100, PBSP11A_000154100, PBSP11RLL_000154100
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0Y9W4B5

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Non-polymers , 3 types, 894 molecules

#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 890 / 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: 2.43 Å3/Da / Density % sol: 49.43 % / Mosaicity: 0.07 °
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.2
Details: 18%PEG3350, 2% ethylen glycol, 0.2M CaCl2, 0.1M HEPES pH 7.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.1→47.05 Å / Num. obs: 103846 / % possible obs: 99.9 % / Redundancy: 5.2 % / Biso Wilson estimate: 36.87 Å2 / Rpim(I) all: 0.034 / Net I/σ(I): 15.3
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.722 / Num. unique obs: 5143 / CC1/2: 0.844 / Rpim(I) all: 0.346 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
Aimless0.5.21data scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
XDSdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L8D, 1KGC

4l8d

1kgc


Resolution: 2.1→47.05 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.897 / SU R Cruickshank DPI: 0.245 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.25 / SU Rfree Blow DPI: 0.191 / SU Rfree Cruickshank DPI: 0.191
RfactorNum. reflection% reflectionSelection details
Rfree0.249 5105 4.92 %RANDOM
Rwork0.218 ---
obs0.22 103824 99.9 %-
Displacement parametersBiso mean: 52.77 Å2
Baniso -1Baniso -2Baniso -3
1-11.0156 Å20 Å2-1.716 Å2
2---19.2465 Å20 Å2
3---8.231 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: 1 / Resolution: 2.1→47.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12943 0 4 890 13837
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00813371HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0918190HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4556SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes365HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1934HARMONIC5
X-RAY DIFFRACTIONt_it13371HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.45
X-RAY DIFFRACTIONt_other_torsion19.14
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1682SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact15221SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2873 373 4.88 %
Rwork0.2673 7274 -
all0.2682 7647 -
obs--99.96 %

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