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- PDB-3f8u: Tapasin/ERp57 heterodimer -

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Basic information

Entry
Database: PDB / ID: 3f8u
TitleTapasin/ERp57 heterodimer
Components
  • Protein disulfide-isomerase A3ERp57
  • Tapasin
KeywordsIMMUNE SYSTEM/ISOMERASE / Endoplasmic reticulum / Glycoprotein / Immunoglobulin domain / Membrane / Microsome / protein disulfide isomerase / thioredoxin-like fold / Ig-like domain / beta barrel / Isomerase / Redox-active cente / IMMUNE SYSTEM-ISOMERASE COMPLEX
Function / homology
Function and homology information


MHC class Ib protein complex assembly / peptide antigen stabilization / Tapasin-ERp57 complex / Calnexin/calreticulin cycle / MHC class I protein complex binding / TAP1 binding / TAP2 binding / protein disulfide-isomerase / disulfide oxidoreductase activity / protein folding in endoplasmic reticulum ...MHC class Ib protein complex assembly / peptide antigen stabilization / Tapasin-ERp57 complex / Calnexin/calreticulin cycle / MHC class I protein complex binding / TAP1 binding / TAP2 binding / protein disulfide-isomerase / disulfide oxidoreductase activity / protein folding in endoplasmic reticulum / regulation of protein complex stability / phospholipase C activity / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / positive regulation of extrinsic apoptotic signaling pathway / cellular response to interleukin-7 / TAP complex binding / protein disulfide isomerase activity / MHC class I protein binding / protein-disulfide reductase activity / extrinsic apoptotic signaling pathway / protein folding chaperone / phagocytic vesicle / endoplasmic reticulum-Golgi intermediate compartment membrane / response to endoplasmic reticulum stress / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / platelet aggregation / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / unfolded protein binding / melanosome / protein folding / ER-Phagosome pathway / regulation of gene expression / protein-containing complex assembly / adaptive immune response / molecular adaptor activity / endoplasmic reticulum lumen / Golgi membrane / cysteine-type endopeptidase activity / focal adhesion / endoplasmic reticulum membrane / cell surface / endoplasmic reticulum / RNA binding / extracellular space / extracellular exosome / identical protein binding / nucleus
Similarity search - Function
Protein disulfide-isomerase A3, first redox inactive TRX-like domain b / Tapasin / Protein disulphide isomerase / Thioredoxin-like domain / Disulphide isomerase / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain ...Protein disulfide-isomerase A3, first redox inactive TRX-like domain b / Tapasin / Protein disulphide isomerase / Thioredoxin-like domain / Disulphide isomerase / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Thioredoxin-like superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Tapasin / Protein disulfide-isomerase A3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsDong, G. / Reinisch, K.M.
CitationJournal: Immunity / Year: 2009
Title: Insights into MHC class I peptide loading from the structure of the tapasin-ERp57 thiol oxidoreductase heterodimer.
Authors: Dong, G. / Wearsch, P.A. / Peaper, D.R. / Cresswell, P. / Reinisch, K.M.
History
DepositionNov 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 20, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein disulfide-isomerase A3ERp57
B: Tapasin
C: Protein disulfide-isomerase A3ERp57
D: Tapasin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,6286
Polymers194,1864
Non-polymers4422
Water2,018112
1
A: Protein disulfide-isomerase A3ERp57
B: Tapasin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,3143
Polymers97,0932
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-3 kcal/mol
Surface area40900 Å2
MethodPISA
2
C: Protein disulfide-isomerase A3ERp57
D: Tapasin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,3143
Polymers97,0932
Non-polymers2211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-5 kcal/mol
Surface area40520 Å2
MethodPISA
3
A: Protein disulfide-isomerase A3ERp57
B: Tapasin
hetero molecules

C: Protein disulfide-isomerase A3ERp57
D: Tapasin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,6286
Polymers194,1864
Non-polymers4422
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area6710 Å2
ΔGint-17 kcal/mol
Surface area79680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.101, 72.295, 200.193
Angle α, β, γ (deg.)90.00, 94.613, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein disulfide-isomerase A3ERp57 / E.C.5.3.4.1 / ERp57 / Disulfide isomerase ER-60 / ERp60 / 58 kDa microsomal protein / p58 / ERp57 / 58 kDa ...ERp57 / Disulfide isomerase ER-60 / ERp60 / 58 kDa microsomal protein / p58 / ERp57 / 58 kDa glucose-regulated protein


Mass: 54309.035 Da / Num. of mol.: 2 / Mutation: C60A
Source method: isolated from a genetically manipulated source
Details: covalently linked to tapasin via sulfide bond / Source: (gene. exp.) Homo sapiens (human) / Gene: PDIA3, ERP57, ERP60, GRP58 / Plasmid: pFastbac Dual / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF21 / References: UniProt: P30101, protein disulfide-isomerase
#2: Antibody Tapasin / TPSN / TPN / TAP-binding protein / TAP-associated protein / NGS-17


Mass: 42783.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Asn233 glycosylated, glycan is only partly visible / Source: (gene. exp.) Homo sapiens (human) / Gene: TAPBP, NGS17, TAPA / Plasmid: pFastbac Dual / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF21 / References: UniProt: O15533
#3: 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.: 2
Source method: isolated from a genetically manipulated source
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.75 Å3/Da / Density % sol: 55.31 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: reservoir contained 100 mM HEPES (@pH 7.5), 20% PEG 3K, 200 mM CaCl2. protein was concentrated to 10mg/ml in 150 mM NaCl, 20 mM Tris (@ pH 7.4), 5% glycerol. The hanging drop was ...Details: reservoir contained 100 mM HEPES (@pH 7.5), 20% PEG 3K, 200 mM CaCl2. protein was concentrated to 10mg/ml in 150 mM NaCl, 20 mM Tris (@ pH 7.4), 5% glycerol. The hanging drop was supplemented to contain 100 mM guanidine HCl; seeding was used to obtain larger crystals., VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 63580 / Num. obs: 63580 / % possible obs: 97.4 % / Observed criterion σ(I): -2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 19.4
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 6.5 / Num. unique all: 5852 / Rsym value: 0.207 / % possible all: 91.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.6→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.285 3257 5.1 %random
Rwork0.245 ---
all0.247 63580 --
obs0.247 63580 97.4 %-
Displacement parametersBiso mean: 63 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12911 0 28 112 13051
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
LS refinement shellResolution: 2.6→2.76 Å
RfactorNum. reflection% reflection
Rfree0.465 538 -
Rwork0.373 --
obs-10314 95.5 %

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