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- PDB-7tug: Crystal structure of Tapasin in complex with PaSta2-Fab -

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Basic information

Entry
Database: PDB / ID: 7tug
TitleCrystal structure of Tapasin in complex with PaSta2-Fab
Components
  • PaSta2 Fab heavy chain
  • PaSta2 Fab kappa light chain
  • Tapasin
KeywordsIMMUNE SYSTEM / PaSta / Fab / Antibody / IgG / MHC-I / HLA / peptide loading complex / PLC / antigen presentation / immune response
Function / homology
Function and homology information


MHC class Ib protein complex assembly / peptide antigen stabilization / Tapasin-ERp57 complex / MHC class I protein complex binding / TAP2 binding / TAP1 binding / regulation of protein complex stability / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / TAP complex binding / MHC class I protein binding ...MHC class Ib protein complex assembly / peptide antigen stabilization / Tapasin-ERp57 complex / MHC class I protein complex binding / TAP2 binding / TAP1 binding / regulation of protein complex stability / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / TAP complex binding / MHC class I protein binding / endoplasmic reticulum-Golgi intermediate compartment membrane / protein folding chaperone / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class I protein complex / MHC class I peptide loading complex / antigen processing and presentation of endogenous peptide antigen via MHC class I / peptide antigen binding / phagocytic vesicle membrane / unfolded protein binding / ER-Phagosome pathway / regulation of gene expression / protein-containing complex assembly / molecular adaptor activity / Golgi membrane / endoplasmic reticulum membrane / endoplasmic reticulum
Similarity search - Function
Tapasin / : / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like ...Tapasin / : / 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 / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsJiang, J. / Natarajan, K. / Taylor, D.K. / Boyd, L.F. / Margulies, D.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Nat Commun / Year: 2022
Title: Structural mechanism of tapasin-mediated MHC-I peptide loading in antigen presentation.
Authors: Jiang, J. / Taylor, D.K. / Kim, E.J. / Boyd, L.F. / Ahmad, J. / Mage, M.G. / Truong, H.V. / Woodward, C.H. / Sgourakis, N.G. / Cresswell, P. / Margulies, D.H. / Natarajan, K.
History
DepositionFeb 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2022Group: Database references
Category: citation / citation_author / pdbx_database_related
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Tapasin
H: PaSta2 Fab heavy chain
L: PaSta2 Fab kappa light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,0334
Polymers93,8113
Non-polymers2211
Water00
1
D: Tapasin
hetero molecules

H: PaSta2 Fab heavy chain
L: PaSta2 Fab kappa light chain


Theoretical massNumber of molelcules
Total (without water)94,0334
Polymers93,8113
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_444-x-1/2,-y-1/2,z-1/21
Buried area4210 Å2
ΔGint-25 kcal/mol
Surface area37030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.090, 168.820, 108.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Antibody Tapasin / TPN / TPSN / NGS-17 / TAP-associated protein / TAP-binding protein


Mass: 44739.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TAPBP, NGS17, TAPA / Plasmid: pET21b / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: O15533
#2: Antibody PaSta2 Fab heavy chain


Mass: 24792.748 Da / Num. of mol.: 1 / Fragment: Variable and Constant CH1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET21b / Cell line (production host): Expi 293S / Production host: Homo sapiens (human)
#3: Antibody PaSta2 Fab kappa light chain


Mass: 24278.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET21b / Cell line (production host): Expi 293S / Production host: Homo sapiens (human)
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
Has ligand of interestN
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: 2.47 Å3/Da / Density % sol: 50.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 17% PEG 10000, 0.1M Bis-Tris, 0.1M Am Acetate / PH range: 5.5-8.5

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Data collection

DiffractionMean temperature: 273 K / Ambient temp details: LN blow / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.9→54.33 Å / Num. obs: 8241 / % possible obs: 95.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 67.65 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.065 / Rrim(I) all: 0.127 / Net I/σ(I): 7.5
Reflection shellResolution: 3.9→4.04 Å / Mean I/σ(I) obs: 0.85 / Num. unique obs: 692 / CC1/2: 0.477 / Rpim(I) all: 0.851 / % possible all: 80.75

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F8U

3f8u


Resolution: 3.9→54.33 Å / SU ML: 0.6412 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 34.8533
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3319 409 4.97 %
Rwork0.2822 7826 -
obs0.2846 8235 93.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 78.23 Å2
Refinement stepCycle: LAST / Resolution: 3.9→54.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5290 0 14 0 5304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00215450
X-RAY DIFFRACTIONf_angle_d0.50717501
X-RAY DIFFRACTIONf_chiral_restr0.0402879
X-RAY DIFFRACTIONf_plane_restr0.0053967
X-RAY DIFFRACTIONf_dihedral_angle_d10.33371803
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9-4.470.35211270.30092456X-RAY DIFFRACTION90.09
4.47-5.620.31761400.28112593X-RAY DIFFRACTION94.31
5.63-54.330.32871420.27052777X-RAY DIFFRACTION97.01

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