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- PDB-2iad: CLASS II MHC I-AD IN COMPLEX WITH AN INFLUENZA HEMAGGLUTININ PEPT... -

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Basic information

Entry
Database: PDB / ID: 2iad
TitleCLASS II MHC I-AD IN COMPLEX WITH AN INFLUENZA HEMAGGLUTININ PEPTIDE 126-138
Components(MHC CLASS II I-AD) x 2
KeywordsMHC II / CLASS II MHC I-AD
Function / homology
Function and homology information


Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / Co-inhibition by PD-1 / Generation of second messenger molecules / Downstream TCR signaling / antigen processing and presentation of peptide antigen / MHC class II antigen presentation / positive regulation of T cell differentiation / antigen processing and presentation / multivesicular body ...Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / Co-inhibition by PD-1 / Generation of second messenger molecules / Downstream TCR signaling / antigen processing and presentation of peptide antigen / MHC class II antigen presentation / positive regulation of T cell differentiation / antigen processing and presentation / multivesicular body / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / adaptive immune response / early endosome / lysosome / immune response / external side of plasma membrane / Golgi apparatus / membrane / plasma membrane
Similarity search - Function
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 ...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
H-2 class II histocompatibility antigen, A-D beta chain / H-2 class II histocompatibility antigen, A-D alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsScott, C.A. / Peterson, P.A. / Teyton, L. / Wilson, I.A.
Citation
Journal: Immunity / Year: 1998
Title: Crystal structures of two I-Ad-peptide complexes reveal that high affinity can be achieved without large anchor residues.
Authors: Scott, C.A. / Peterson, P.A. / Teyton, L. / Wilson, I.A.
#1: Journal: Protein Sci. / Year: 1998
Title: Engineering Protein for X-Ray Crystallography: The Murine Major Histocompatibility Complex Class II Molecule I-Ad
Authors: Scott, C.A. / Garcia, K.C. / Stura, E.A. / Peterson, P.A. / Wilson, I.A. / Teyton, L.
#2: Journal: J.Exp.Med. / Year: 1996
Title: Role of Chain Pairing for the Production of Functional Soluble Ia Major Histocompatibility Complex Class II Molecules
Authors: Scott, C.A. / Garcia, K.C. / Carbone, F.R. / Wilson, I.A. / Teyton, L.
History
DepositionMar 13, 1998Processing site: BNL
Revision 1.0Nov 18, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MHC CLASS II I-AD
B: MHC CLASS II I-AD


Theoretical massNumber of molelcules
Total (without water)45,7092
Polymers45,7092
Non-polymers00
Water2,054114
1
A: MHC CLASS II I-AD
B: MHC CLASS II I-AD

A: MHC CLASS II I-AD
B: MHC CLASS II I-AD


Theoretical massNumber of molelcules
Total (without water)91,4174
Polymers91,4174
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
MethodPQS
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-22 kcal/mol
Surface area18510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.200, 100.200, 53.100
Angle α, β, γ (deg.)90.00, 100.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MHC CLASS II I-AD


Mass: 22091.631 Da / Num. of mol.: 1
Fragment: RESIDUES 126P - 138P OF CHAIN B ARE COVALENTLY LINKED INFLUENZA HEMAGGLUTININ PEPTIDE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB-C / Cell line: S2 / Fragment: RESIDUES 126P - 138P OF CHAIN B / Organ: TAIL / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P04228
#2: Protein MHC CLASS II I-AD


Mass: 23617.074 Da / Num. of mol.: 1
Fragment: RESIDUES 126P - 138P OF CHAIN B ARE COVALENTLY LINKED INFLUENZA HEMAGGLUTININ PEPTIDE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/C / Cell line: S2 / Fragment: RESIDUES 126P - 138P OF CHAIN B / Organ: TAIL / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01921
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
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: 3.76 Å3/Da / Density % sol: 67 %
Crystal growpH: 7.4 / Details: 19% PEG 8000 0.2 M TRIS, PH 7.4
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 22 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-9 mg/mlprotein1drop
219 %PEG80001reservoir
30.2 MTris1reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1997
Details: 58 CM LONG, PT-COATED, FUSED SILICA, VERTICAL FOCUS
RadiationMonochromator: CYLINDRICALLY BENT TRIANGULAR SI(111) ASYMMETRIC CUT, HORIZONTAL FOCUS
Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.4→24 Å / Num. obs: 22555 / % possible obs: 89 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.076 / Rsym value: 0.076
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 2 % / Rmerge(I) obs: 0.259 / Rsym value: 0.259 / % possible all: 88
Reflection shell
*PLUS
% possible obs: 88 % / Num. unique obs: 2820

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.8refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DLH

1dlh


Resolution: 2.4→24 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.308 2241 10 %RANDOM
Rwork0.253 ---
obs0.253 22555 89 %-
Displacement parametersBiso mean: 30 Å2
Refinement stepCycle: LAST / Resolution: 2.4→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3129 0 0 114 3243
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.8
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d29.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.4→2.51 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.375 280 10 %
Rwork0.356 2540 -
obs--88 %
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg29.7

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