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- PDB-1i3r: CRYSTAL STRUCTURE OF A MUTANT IEK CLASS II MHC MOLECULE -

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Basic information

Entry
Database: PDB / ID: 1i3r
TitleCRYSTAL STRUCTURE OF A MUTANT IEK CLASS II MHC MOLECULE
Components
  • FUSION PROTEIN CONSISTING OF MHC E-BETA-K PRECURSOR, GLYCINE RICH LINKER, AND HEMOGLOBIN BETA-2 CHAIN
  • H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, E-K ALPHA CHAIN
KeywordsIMMUNE SYSTEM / MHC ClassII
Function / homology
Function and homology information


positive regulation of myeloid cell differentiation / myeloid cell differentiation / nitric oxide transport / erythrocyte development / hemoglobin complex / immunoglobulin mediated immune response / oxygen transport / oxygen carrier activity / peptide antigen assembly with MHC class II protein complex / carbon dioxide transport ...positive regulation of myeloid cell differentiation / myeloid cell differentiation / nitric oxide transport / erythrocyte development / hemoglobin complex / immunoglobulin mediated immune response / oxygen transport / oxygen carrier activity / peptide antigen assembly with MHC class II protein complex / carbon dioxide transport / MHC class II protein complex / regulation of erythrocyte differentiation / oxygen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / peptide antigen binding / MHC class II protein complex binding / late endosome membrane / lysosome / lysosomal membrane / external side of plasma membrane / heme binding / metal ion binding / 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 / 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 / Hemoglobin, beta-type / : / Globin/Protoglobin ...Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / 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 / Hemoglobin, beta-type / : / Globin/Protoglobin / Globin / Globin / Globin domain profile. / Globin-like superfamily / 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
: / Hemoglobin subunit beta-2 / H-2 class II histocompatibility antigen, E-K alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKappler, J.W. / Wilson, N.
CitationJournal: Immunity / Year: 2001
Title: Mutations changing the kinetics of class II MHC peptide exchange.
Authors: Wilson, N. / Fremont, D. / Marrack, P. / Kappler, J.
History
DepositionFeb 15, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq_dif / 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_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 2.1Oct 27, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Oct 30, 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: H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, E-K ALPHA CHAIN
B: FUSION PROTEIN CONSISTING OF MHC E-BETA-K PRECURSOR, GLYCINE RICH LINKER, AND HEMOGLOBIN BETA-2 CHAIN
C: H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, E-K ALPHA CHAIN
D: FUSION PROTEIN CONSISTING OF MHC E-BETA-K PRECURSOR, GLYCINE RICH LINKER, AND HEMOGLOBIN BETA-2 CHAIN
E: H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, E-K ALPHA CHAIN
F: FUSION PROTEIN CONSISTING OF MHC E-BETA-K PRECURSOR, GLYCINE RICH LINKER, AND HEMOGLOBIN BETA-2 CHAIN
G: H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, E-K ALPHA CHAIN
H: FUSION PROTEIN CONSISTING OF MHC E-BETA-K PRECURSOR, GLYCINE RICH LINKER, AND HEMOGLOBIN BETA-2 CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,47520
Polymers193,0088
Non-polymers3,46712
Water5,747319
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, E-K ALPHA CHAIN
D: FUSION PROTEIN CONSISTING OF MHC E-BETA-K PRECURSOR, GLYCINE RICH LINKER, AND HEMOGLOBIN BETA-2 CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1195
Polymers48,2522
Non-polymers8673
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7410 Å2
ΔGint-20 kcal/mol
Surface area19220 Å2
MethodPISA
3
E: H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, E-K ALPHA CHAIN
F: FUSION PROTEIN CONSISTING OF MHC E-BETA-K PRECURSOR, GLYCINE RICH LINKER, AND HEMOGLOBIN BETA-2 CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1195
Polymers48,2522
Non-polymers8673
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-20 kcal/mol
Surface area19310 Å2
MethodPISA
4
G: H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, E-K ALPHA CHAIN
H: FUSION PROTEIN CONSISTING OF MHC E-BETA-K PRECURSOR, GLYCINE RICH LINKER, AND HEMOGLOBIN BETA-2 CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1195
Polymers48,2522
Non-polymers8673
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7480 Å2
ΔGint-19 kcal/mol
Surface area19020 Å2
MethodPISA
5
A: H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, E-K ALPHA CHAIN
B: FUSION PROTEIN CONSISTING OF MHC E-BETA-K PRECURSOR, GLYCINE RICH LINKER, AND HEMOGLOBIN BETA-2 CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1195
Polymers48,2522
Non-polymers8673
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7340 Å2
ΔGint-19 kcal/mol
Surface area19250 Å2
MethodPISA
6
E: H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, E-K ALPHA CHAIN
F: FUSION PROTEIN CONSISTING OF MHC E-BETA-K PRECURSOR, GLYCINE RICH LINKER, AND HEMOGLOBIN BETA-2 CHAIN
G: H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, E-K ALPHA CHAIN
H: FUSION PROTEIN CONSISTING OF MHC E-BETA-K PRECURSOR, GLYCINE RICH LINKER, AND HEMOGLOBIN BETA-2 CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,23710
Polymers96,5044
Non-polymers1,7346
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
7
A: H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, E-K ALPHA CHAIN
B: FUSION PROTEIN CONSISTING OF MHC E-BETA-K PRECURSOR, GLYCINE RICH LINKER, AND HEMOGLOBIN BETA-2 CHAIN
C: H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, E-K ALPHA CHAIN
D: FUSION PROTEIN CONSISTING OF MHC E-BETA-K PRECURSOR, GLYCINE RICH LINKER, AND HEMOGLOBIN BETA-2 CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,23710
Polymers96,5044
Non-polymers1,7346
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)117.059, 58.020, 143.222
Angle α, β, γ (deg.)90.00, 93.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, E-K ALPHA CHAIN


Mass: 22359.082 Da / Num. of mol.: 4 / Mutation: E11Q, D66N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: IEK / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P04224
#2: Protein
FUSION PROTEIN CONSISTING OF MHC E-BETA-K PRECURSOR, GLYCINE RICH LINKER, AND HEMOGLOBIN BETA-2 CHAIN


Mass: 25892.832 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: IEK / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P02089, GenBank: 199396
#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: 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.: 8
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2.51 Å3/Da / Density % sol: 51.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 12.8% PEG4000, 80mM MgCl2, 80mM HEPES pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14.1 mg/mlprotein1drop
212.8 %PEG40001drop
380 mM1dropMgCl2
480 mMHEPES1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. all: 76526 / Num. obs: 74154 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 17.6
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.445 / % possible all: 90.8
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 25 Å
Reflection shell
*PLUS
% possible obs: 90.8 % / Num. unique obs: 6856

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→25 Å / Data cutoff high rms absF: 100000 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.27 3615 -Random
Rwork0.229 ---
all-76526 --
obs-74154 96.9 %-
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.43 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.4→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12782 0 224 319 13325
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.27
X-RAY DIFFRACTIONc_bond_d0.0066
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 25 Å / σ(F): 0 / Rfactor obs: 0.229 / Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 51.9 Å2
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.0066
LS refinement shell
*PLUS
Rfactor Rfree: 0.38 / Num. reflection Rfree: 316 / Rfactor Rwork: 0.331 / Num. reflection obs: 6212

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