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- PDB-1iao: CLASS II MHC I-AD IN COMPLEX WITH OVALBUMIN PEPTIDE 323-339 -

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Basic information

Entry
Database: PDB / ID: 1iao
TitleCLASS II MHC I-AD IN COMPLEX WITH OVALBUMIN PEPTIDE 323-339
Components(MHC CLASS II I-AD) x 2
KeywordsMHC II / CLASS II MHC / I-A / OVALBUMIN PEPTIDE
Function / homology
Function and homology information


Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / PD-1 signaling / 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 / negative regulation of T cell proliferation ...Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / PD-1 signaling / 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 / negative regulation of T cell proliferation / multivesicular body / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / adaptive immune response / lysosome / early endosome / immune response / lysosomal membrane / external side of plasma membrane / protein-containing complex binding / Golgi apparatus / cell surface / 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 / Immunoglobulins / Roll / Immunoglobulin-like fold / 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: 2.6 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: Immunity / Year: 1998
Title: Erratum. 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.
#2: 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.
#3: 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 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / 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 / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Aug 9, 2023Group: Database references / Refinement description / Structure summary
Category: chem_comp / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)47,6383
Polymers47,4172
Non-polymers2211
Water1448
1
A: MHC CLASS II I-AD
B: MHC CLASS II I-AD
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)95,2766
Polymers94,8334
Non-polymers4422
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
MethodPQS
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-23 kcal/mol
Surface area18360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.300, 101.300, 92.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein MHC CLASS II I-AD


Mass: 22091.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: BOTH THE A AND B CHAINS HAVE AN 8-RESIDUE (SSADLVPR) PEPTIDE BOUND TO THE C-TERMINUS. THE B CHAIN ALSO HAS A 24-RESIDUE PEPTIDE CONSISTING OF A 2-RESIDUE (RG) SIGNAL SEQUENCE, RESIDUES 323 - ...Details: BOTH THE A AND B CHAINS HAVE AN 8-RESIDUE (SSADLVPR) PEPTIDE BOUND TO THE C-TERMINUS. THE B CHAIN ALSO HAS A 24-RESIDUE PEPTIDE CONSISTING OF A 2-RESIDUE (RG) SIGNAL SEQUENCE, RESIDUES 323 - 339 OF HEN EGG OVALBUMIN AND A 6-RESIDUE (GSGSGS) LINKER, COVALENTLY BONDED TO THE N-TERMINUS.
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/C / Description: HETEROLOGOUS EXPRESSION / Cell line: S2 / Organ: EGG / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P04228
#2: Protein MHC CLASS II I-AD


Mass: 25324.998 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: BOTH THE A AND B CHAINS HAVE AN 8-RESIDUE (SSADLVPR) PEPTIDE BOUND TO THE C-TERMINUS. THE B CHAIN ALSO HAS A 24-RESIDUE PEPTIDE CONSISTING OF A 2-RESIDUE (RG) SIGNAL SEQUENCE, RESIDUES 323 - ...Details: BOTH THE A AND B CHAINS HAVE AN 8-RESIDUE (SSADLVPR) PEPTIDE BOUND TO THE C-TERMINUS. THE B CHAIN ALSO HAS A 24-RESIDUE PEPTIDE CONSISTING OF A 2-RESIDUE (RG) SIGNAL SEQUENCE, RESIDUES 323 - 339 OF HEN EGG OVALBUMIN AND A 6-RESIDUE (GSGSGS) LINKER, COVALENTLY BONDED TO THE N-TERMINUS.
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/C / Description: HETEROLOGOUS EXPRESSION / Cell line: S2 / Organ: EGG / Cell line (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P04228, UniProt: P01921*PLUS
#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.: 1
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.: 8 / 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: 2.79 Å3/Da / Density % sol: 56 %
Crystal growpH: 5.5 / Details: 32% PEG 600, 0.1 IMIDAZOLE MALATE, PH 5.5
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
232 %PEG6001reservoir
30.1 Mimidazole malate1reservoir

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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: 2.6→27 Å / Num. obs: 14777 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 9 % / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 10
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 2 / Rsym value: 0.383 / % possible all: 91
Reflection shell
*PLUS
% possible obs: 91 % / Num. unique obs: 1690

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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: 2.6→27 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.01 / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.32 1464 10 %RANDOM
Rwork0.255 ---
obs0.255 14777 99 %-
Displacement parametersBiso mean: 51 Å2
Refinement stepCycle: LAST / Resolution: 2.6→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3013 0 14 8 3035
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg2.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d29.2
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: 2.6→2.72 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.456 176 10 %
Rwork0.412 1513 -
obs--91 %
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.32
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg29.2

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