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- PDB-1iea: HISTOCOMPATIBILITY ANTIGEN -

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Basic information

Entry
Database: PDB / ID: 1iea
TitleHISTOCOMPATIBILITY ANTIGEN
Components(MHC CLASS II I-EK) x 2
KeywordsHISTOCOMPATIBILITY ANTIGEN
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 / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / positive regulation of CD4-positive, alpha-beta T cell activation ...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 / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / MHC class II antigen presentation / positive regulation of memory T cell differentiation / polysaccharide binding / immunoglobulin mediated immune response / immunological synapse / T cell receptor binding / cognition / positive regulation of T cell mediated cytotoxicity / 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 / lysosomal membrane / external side of plasma membrane / cell surface / 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, E-D alpha chain / MHC class II antigen IEk-beta
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFremont, D.H. / Hendrickson, W.A. / Marrack, P. / Kappler, J.
CitationJournal: Science / Year: 1996
Title: Structures of an MHC class II molecule with covalently bound single peptides.
Authors: Fremont, D.H. / Hendrickson, W.A. / Marrack, P. / Kappler, J.
History
DepositionApr 5, 1996Processing site: BNL
Revision 1.0Jun 5, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Mar 22, 2017Group: Other
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / software / 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 / _software.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Aug 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-EK
B: MHC CLASS II I-EK
C: MHC CLASS II I-EK
D: MHC CLASS II I-EK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,76110
Polymers96,4344
Non-polymers1,3276
Water6,287349
1
A: MHC CLASS II I-EK
B: MHC CLASS II I-EK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8805
Polymers48,2172
Non-polymers6643
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7390 Å2
ΔGint-20 kcal/mol
Surface area18470 Å2
MethodPISA
2
C: MHC CLASS II I-EK
D: MHC CLASS II I-EK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8805
Polymers48,2172
Non-polymers6643
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7430 Å2
ΔGint-21 kcal/mol
Surface area18460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.020, 57.090, 117.010
Angle α, β, γ (deg.)90.00, 91.52, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MHC CLASS II I-EK


Mass: 22324.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: WITH COVALENTLY BOUND HB PEPTIDE / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P01904
#2: Protein MHC CLASS II I-EK


Mass: 25892.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: WITH COVALENTLY BOUND HB PEPTIDE / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q31163
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
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 / Water


Mass: 18.015 Da / Num. of mol.: 349 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS ENTRY CONTAINS COORDINATES FOR THE EXTRACELLULAR DOMAINS OF THE MURINE MHC CLASS II MOLECULE I- ...THIS ENTRY CONTAINS COORDINATES FOR THE EXTRACELLULAR DOMAINS OF THE MURINE MHC CLASS II MOLECULE I-EK WITH A PEPTIDE FROM MURINE HEMOGLOBIN (64 - 66) COVALENTLY ATTACHED TO THE I-EK BETA CHAIN VIA A POLYPEPTIDE LINKER. NO ATTEMPT WAS MADE TO MODEL FOUR RESIDUES AMINO TERMINAL TO THE BETA CHAIN OR TEN RESIDUES CARBOXY TERMINAL TO EITHER THE ALPHA OR BETA CHAINS. DENSITY FOR RESIDUES B 107 - B 113 AND D 1 - D 113 WAS EXTREMELY WEAK. THESE RESIDUES ARE MODELLED AS ALANINE. THERE ARE TWO HETERODIMERS IN THE ASYMMETRIC UNIT RELATED BY AN APPROXIMATE TWO-FOLD AXIS.
Sequence detailsCHAINS B AND D CONTAIN THE HB PEPTIDE AND LINKER REGIONS. THE BETA CHAIN AMINO TERMINUS, PEPTIDE P1 ...CHAINS B AND D CONTAIN THE HB PEPTIDE AND LINKER REGIONS. THE BETA CHAIN AMINO TERMINUS, PEPTIDE P1 - P9 AND LINKER ARE NOTED WITH THE INSERTION CODES N, P, AND L.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 55 %
Crystal growpH: 5.2
Details: 8% PEG 4000, 2% EG, 200MM A.S, 100MM CITRATE PH 5.2
Crystal grow
*PLUS
Method: unknown / PH range low: 5.6 / PH range high: 5.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-10 mg/mlprotein11
216-18 %PEG400012
32 %ethylene glycol12
4200 mMammonium sulfate12
5100 mMcitrate12

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9879, 1.0070
DetectorType: FUJI / Detector: IMAGE PLATE
RadiationScattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.98791
21.0071
ReflectionResolution: 2.3→20 Å / Num. obs: 38809 / % possible obs: 89.2 % / Redundancy: 4.35 % / Biso Wilson estimate: 34.2 Å2 / Rsym value: 0.075
Reflection
*PLUS
Num. measured all: 169034 / Rmerge(I) obs: 0.075

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Processing

Software
NameVersionClassification
HKLdata collection
DENZOdata reduction
SCALAdata scaling
Agrovatadata reduction
X-PLORmodel building
X-PLORrefinement
HKLdata reduction
CCP4(AGROVATAdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DLH

1dlh


Resolution: 2.3→6 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.01 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.274 1833 5 %RANDOM
Rwork0.202 ---
obs0.202 36317 88.7 %-
Displacement parametersBiso mean: 32.3 Å2
Baniso -1Baniso -2Baniso -3
1--4.37 Å20 Å2-2.27 Å2
2--5.65 Å20 Å2
3----1.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6336 0 84 349 6769
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.63
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.39
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.541.5
X-RAY DIFFRACTIONx_mcangle_it2.622
X-RAY DIFFRACTIONx_scbond_it1.532
X-RAY DIFFRACTIONx_scangle_it2.472.5
Refine LS restraints NCSNCS model details: RESTRAINED
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.325 205 4.9 %
Rwork0.277 3959 -
obs--61.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM3_MOD.CHOTOPH3.CHO
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.39

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