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- PDB-5dmk: Crystal Structure of IAg7 in complex with RLGL-WE14 -

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Basic information

Entry
Database: PDB / ID: 5dmk
TitleCrystal Structure of IAg7 in complex with RLGL-WE14
Components
  • H-2 class II histocompatibility antigen, A-D alpha chain
  • beta chain of Major Histocompatibility Complex Class II, I-Ag7,H2-Ab1 protein
KeywordsIMMUNE SYSTEM / Chromogranin A / Type I Diabetes / T cell / fusion protein
Function / homology
Function and homology information


protein localization to secretory granule / positive regulation of relaxation of cardiac muscle / Antimicrobial peptides / negative regulation of catecholamine secretion / positive regulation of dense core granule biogenesis / mast cell chemotaxis / mast cell activation / chromaffin granule / antigen processing and presentation of peptide antigen / regulation of the force of heart contraction ...protein localization to secretory granule / positive regulation of relaxation of cardiac muscle / Antimicrobial peptides / negative regulation of catecholamine secretion / positive regulation of dense core granule biogenesis / mast cell chemotaxis / mast cell activation / chromaffin granule / antigen processing and presentation of peptide antigen / regulation of the force of heart contraction / positive regulation of T cell differentiation / mast cell degranulation / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / antigen processing and presentation / neuronal dense core vesicle / transport vesicle / multivesicular body / positive regulation of cardiac muscle contraction / secretory granule / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / defense response to Gram-negative bacterium / adaptive immune response / early endosome / lysosome / defense response to Gram-positive bacterium / external side of plasma membrane / perinuclear region of cytoplasm / cell surface / Golgi apparatus / extracellular space / plasma membrane
Similarity search - Function
Chromogranin A/B / Chromogranin A/B/C / Chromogranin, conserved site / Granin (chromogranin or secretogranin) / Granins signature 1. / Granins signature 2. / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain ...Chromogranin A/B / Chromogranin A/B/C / Chromogranin, conserved site / Granin (chromogranin or secretogranin) / Granins signature 1. / Granins signature 2. / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / 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 / Roll / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / H-2 class II histocompatibility antigen, A-D alpha chain / Chromogranin-A / H2-Ab1 protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.45 Å
AuthorsWang, Y. / Jin, N. / Dai, S. / Kappler, J.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: N-terminal additions to the WE14 peptide of chromogranin A create strong autoantigen agonists in type 1 diabetes.
Authors: Jin, N. / Wang, Y. / Crawford, F. / White, J. / Marrack, P. / Dai, S. / Kappler, J.W.
History
DepositionSep 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 1.2Apr 6, 2016Group: Source and taxonomy
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: H-2 class II histocompatibility antigen, A-D alpha chain
B: beta chain of Major Histocompatibility Complex Class II, I-Ag7,H2-Ab1 protein
C: H-2 class II histocompatibility antigen, A-D alpha chain
D: beta chain of Major Histocompatibility Complex Class II, I-Ag7,H2-Ab1 protein
E: H-2 class II histocompatibility antigen, A-D alpha chain
F: beta chain of Major Histocompatibility Complex Class II, I-Ag7,H2-Ab1 protein
G: H-2 class II histocompatibility antigen, A-D alpha chain
H: beta chain of Major Histocompatibility Complex Class II, I-Ag7,H2-Ab1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)178,71810
Polymers178,3408
Non-polymers3782
Water5,999333
1
A: H-2 class II histocompatibility antigen, A-D alpha chain
B: beta chain of Major Histocompatibility Complex Class II, I-Ag7,H2-Ab1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7743
Polymers44,5852
Non-polymers1891
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-25 kcal/mol
Surface area17930 Å2
MethodPISA
2
C: H-2 class II histocompatibility antigen, A-D alpha chain
D: beta chain of Major Histocompatibility Complex Class II, I-Ag7,H2-Ab1 protein


Theoretical massNumber of molelcules
Total (without water)44,5852
Polymers44,5852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-25 kcal/mol
Surface area18120 Å2
MethodPISA
3
E: H-2 class II histocompatibility antigen, A-D alpha chain
F: beta chain of Major Histocompatibility Complex Class II, I-Ag7,H2-Ab1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7743
Polymers44,5852
Non-polymers1891
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6070 Å2
ΔGint-24 kcal/mol
Surface area18030 Å2
MethodPISA
4
G: H-2 class II histocompatibility antigen, A-D alpha chain
H: beta chain of Major Histocompatibility Complex Class II, I-Ag7,H2-Ab1 protein


Theoretical massNumber of molelcules
Total (without water)44,5852
Polymers44,5852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint-25 kcal/mol
Surface area18000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.765, 161.765, 204.162
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11D-306-

HOH

21F-419-

HOH

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Components

#1: Protein
H-2 class II histocompatibility antigen, A-D alpha chain


Mass: 19659.947 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: NOD / Gene: I-Ag7 / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P04228
#2: Protein
beta chain of Major Histocompatibility Complex Class II, I-Ag7,H2-Ab1 protein / MHC class II H2-IA-beta chain (haplotype NOD)


Mass: 24924.953 Da / Num. of mol.: 4 / Fragment: UNP residues 31-215
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Ab1 / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q31135, UniProt: P26339*PLUS
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsChain B,D,F,H are fusion protein, 19 residues of hybrid peptide (half from mouse Chromogranin A ...Chain B,D,F,H are fusion protein, 19 residues of hybrid peptide (half from mouse Chromogranin A gene, half from artificial peptide sequence library) linked to beta chain f of Chromogranin A

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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: 3.97 Å3/Da / Density % sol: 69.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1M Ammonium Citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.45→44.866 Å / Num. obs: 93185 / % possible obs: 93.58 % / Redundancy: 2.8 % / Net I/σ(I): 1.92

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.45→44.866 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.26 4697 5.04 %
Rwork0.2113 --
obs0.2138 93185 93.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.594 Å2 / ksol: 0.348 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.0343 Å2-0 Å20 Å2
2---3.0343 Å20 Å2
3---6.0687 Å2
Refinement stepCycle: LAST / Resolution: 2.45→44.866 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11846 0 26 333 12205
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912193
X-RAY DIFFRACTIONf_angle_d1.21316548
X-RAY DIFFRACTIONf_dihedral_angle_d16.664427
X-RAY DIFFRACTIONf_chiral_restr0.0811788
X-RAY DIFFRACTIONf_plane_restr0.0052142
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.47780.40231280.33772635X-RAY DIFFRACTION85
2.4778-2.50690.3951210.34112643X-RAY DIFFRACTION84
2.5069-2.53750.41941870.33832944X-RAY DIFFRACTION96
2.5375-2.56960.4091630.32443011X-RAY DIFFRACTION96
2.5696-2.60340.35141410.31653010X-RAY DIFFRACTION97
2.6034-2.63910.39441590.31262986X-RAY DIFFRACTION96
2.6391-2.67680.35931490.29833012X-RAY DIFFRACTION96
2.6768-2.71670.3311620.2982991X-RAY DIFFRACTION96
2.7167-2.75920.34391520.28812990X-RAY DIFFRACTION96
2.7592-2.80440.35871560.28112992X-RAY DIFFRACTION96
2.8044-2.85280.33761610.27892976X-RAY DIFFRACTION96
2.8528-2.90460.33681660.26392949X-RAY DIFFRACTION95
2.9046-2.96050.30661470.27132983X-RAY DIFFRACTION95
2.9605-3.02090.32321660.26132913X-RAY DIFFRACTION94
3.0209-3.08660.30281700.25252868X-RAY DIFFRACTION92
3.0866-3.15840.32691640.24852850X-RAY DIFFRACTION91
3.1584-3.23730.341280.23862613X-RAY DIFFRACTION83
3.2373-3.32480.28551550.21812888X-RAY DIFFRACTION92
3.3248-3.42260.25611590.21453046X-RAY DIFFRACTION97
3.4226-3.53310.25471710.21513025X-RAY DIFFRACTION97
3.5331-3.65930.26281690.2013040X-RAY DIFFRACTION96
3.6593-3.80570.21811340.18773029X-RAY DIFFRACTION96
3.8057-3.97880.22951630.18363010X-RAY DIFFRACTION95
3.9788-4.18850.21281870.16562963X-RAY DIFFRACTION94
4.1885-4.45070.19461350.14422964X-RAY DIFFRACTION93
4.4507-4.79390.2041240.1362698X-RAY DIFFRACTION84
4.7939-5.27570.16971750.14843076X-RAY DIFFRACTION96
5.2757-6.03750.21681740.17653123X-RAY DIFFRACTION97
6.0375-7.60060.25521650.20673111X-RAY DIFFRACTION95
7.6006-44.8730.20421660.19653149X-RAY DIFFRACTION91

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