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- PDB-1ieb: HISTOCOMPATIBILITY ANTIGEN -

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Basic information

Entry
Database: PDB / ID: 1ieb
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 / MHC class II antigen presentation / immunoglobulin mediated immune response / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding ...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 / MHC class II antigen presentation / immunoglobulin mediated immune response / 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 / 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 / Ig-like domain-containing protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral / software / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _software.name / _struct_asym.entity_id / _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 2.1Aug 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)98,68611
Polymers97,2634
Non-polymers1,4237
Water2,864159
1
A: MHC CLASS II I-EK
B: MHC CLASS II I-EK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2955
Polymers48,6312
Non-polymers6643
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7650 Å2
ΔGint-26 kcal/mol
Surface area18500 Å2
MethodPISA
2
C: MHC CLASS II I-EK
D: MHC CLASS II I-EK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3916
Polymers48,6312
Non-polymers7604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7520 Å2
ΔGint-18 kcal/mol
Surface area18550 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17420 Å2
ΔGint-55 kcal/mol
Surface area34800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.530, 77.530, 319.480
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsTHERE ARE TWO HETERODIMERS IN THE ASYMMETRIC UNIT RELATED BY AN APPROXIMATE TWO-FOLD AXIS. MOLECULE 1 : ALPHA CHAIN - RESIDUES A 1 THROUGH A 182 : BETA CHAIN - RESIDUES B 4N THROUGH B 188 : SUGARS - RESIDUES A 1, A 2, B 3 MOLECULE 2 : ALPHA CHAIN - RESIDUES C 1 THROUGH A 182 : BETA CHAIN - RESIDUES D 4N THROUGH B 188 : SUGARS - RESIDUES C 4, C 5, D 6 WATERS : 1 THROUGH 159

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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 HSP70 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: 26307.381 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: WITH COVALENTLY BOUND HSP70 PEPTIDE / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q31164
#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.: 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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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 HSP70 (236 - 248) COVALENTLY ATTACHED TO THE I-EK BETA CHAIN VIA A POLYPEPTIDE LINKER. NO ATTEMPT WAS MADE TO MODEL THREE RESIDUES AMINO TERMINAL TO THE PEPTIDE OR TEN RESIDUES CARBOXY TERMINAL TO EITHER THE ALPHA OR BETA CHAINS. DENSITY FOR RESIDUES B 107 - B 113 AND D 107 - D 113 WAS EXTREMELY WEAK. THESE RESIDUES ARE MODELLED AS ALANINE.

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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: 2.85 Å3/Da / Density % sol: 60 %
Crystal growpH: 5.2
Details: 18% 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: 0.9789
DetectorType: FUJI / Detector: IMAGE PLATE
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 29069 / % possible obs: 92.1 % / Redundancy: 2.95 % / Rsym value: 0.087
Reflection
*PLUS
Num. measured all: 85623 / Rmerge(I) obs: 0.087

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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 1IEA

1iea


Resolution: 2.7→6 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.01 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.321 1221 5.1 %RANDOM
Rwork0.222 ---
obs0.222 23940 83.6 %-
Displacement parametersBiso mean: 36.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 2.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6424 0 89 159 6672
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.73
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.49
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.851.5
X-RAY DIFFRACTIONx_mcangle_it3.172
X-RAY DIFFRACTIONx_scbond_it1.662
X-RAY DIFFRACTIONx_scangle_it2.682.5
Refine LS restraints NCSNCS model details: RESTRAINED
LS refinement shellResolution: 2.7→2.85 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.363 147 5.1 %
Rwork0.33 2754 -
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_deg26.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.49

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