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- PDB-1f3j: HISTOCOMPATIBILITY ANTIGEN I-AG7 -

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Basic information

Entry
Database: PDB / ID: 1f3j
TitleHISTOCOMPATIBILITY ANTIGEN I-AG7
Components
  • H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN
  • LYSOZYME C
  • MHC CLASS II NOD
KeywordsIMMUNE SYSTEM / HISTOCOMPATIBILITY ANTIGEN / MHC / PEPTIDE COMPLEX
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen / positive regulation of T cell differentiation / antigen processing and presentation / negative regulation of T cell proliferation / multivesicular body / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex ...antigen processing and presentation of peptide antigen / positive regulation of T cell differentiation / antigen processing and presentation / negative regulation of T cell proliferation / multivesicular body / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / 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 / cell wall macromolecule catabolic process / lysozyme / MHC class II protein complex binding / late endosome membrane / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / adaptive immune response / lysosome / early endosome / defense response to Gram-positive bacterium / defense response to bacterium / lysosomal membrane / external side of plasma membrane / protein-containing complex binding / Golgi apparatus / cell surface / endoplasmic reticulum / extracellular space / identical protein binding / plasma membrane / cytoplasm
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 / Glycoside hydrolase, family 22, lysozyme ...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 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / MHC classes I/II-like antigen recognition protein / Lysozyme-like domain superfamily / 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
Lysozyme C / H-2 class II histocompatibility antigen, A-D alpha chain / H2-Ab1 protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsLatek, R.R. / Unanue, E.R. / Fremont, D.H.
CitationJournal: Immunity / Year: 2000
Title: Structural basis of peptide binding and presentation by the type I diabetes-associated MHC class II molecule of NOD mice.
Authors: Latek, R.R. / Suri, A. / Petzold, S.J. / Nelson, C.A. / Kanagawa, O. / Unanue, E.R. / Fremont, D.H.
History
DepositionJun 4, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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 / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / 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

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Assembly

Deposited unit
A: H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN
B: MHC CLASS II NOD
P: LYSOZYME C
D: H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN
E: MHC CLASS II NOD
Q: LYSOZYME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,61512
Polymers89,2886
Non-polymers1,3276
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18090 Å2
ΔGint-38 kcal/mol
Surface area36750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.540, 109.540, 176.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11D-1005-

HOH

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Components

#1: Protein H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN


Mass: 20792.258 Da / Num. of mol.: 2 / Fragment: A-D ALPHA CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P04228
#2: Protein MHC CLASS II NOD


Mass: 22179.779 Da / Num. of mol.: 2 / Fragment: BETA CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q31135
#3: Protein/peptide LYSOZYME C


Mass: 1671.880 Da / Num. of mol.: 2
Fragment: RESIDUES 11-24, CORRESPOND TO BINDING SITES P-3 TO P11
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P00698
#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 / 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / 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-Ag7 WITH PEPTIDE FROM HEN EGG WHITE LYSOZYME (11 - 24). THE COMPLEX WAS PRODUCED AS A CHIMERIC MOLECULE WITH THE PEPTIDE COVALENTLY ATTACHED TO THE I-AK BETA CHAIN VIA A POLYPEPTIDE LINKER. MODIFIED LEUCINE ZIPPER TAILS WERE ATTACHED TO THE ALPHA AND BETA CHAIN TERMINI. THROMBIN TREATMENT RELEASED THE ZIPPER TAILS AND CUT THE PEPTIDE LINKER.

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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: 2.96 Å3/Da / Density % sol: 58.46 %
Crystal growpH: 4.4 / Details: pH 4.4
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 %PEG5000 MME1reservoir
2100 mMsodium acetate1reservoir
310 %ethylene glycol1reservoir
420 mMHEPES1drop
50.02 %sodium azide1drop
610 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: YALE MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. obs: 18859 / % possible obs: 93.7 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 39.1 Å2 / Rmerge(I) obs: 0.129 / Net I/σ(I): 6
Reflection shellResolution: 3.1→3.29 Å / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 2.3 / % possible all: 98.8
Reflection
*PLUS
Num. measured all: 102791
Reflection shell
*PLUS
% possible obs: 98.8 % / Num. unique obs: 3524 / Num. measured obs: 15897

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4data reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IAK

1iak


Resolution: 3.1→19.82 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 285984.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.299 781 4.8 %RANDOM
Rwork0.221 ---
obs0.221 16107 80.2 %-
Displacement parametersBiso mean: 36.4 Å2
Baniso -1Baniso -2Baniso -3
1-4.07 Å20 Å20 Å2
2--4.07 Å20 Å2
3----8.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.9 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 3.1→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6308 0 84 72 6464
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.391.5
X-RAY DIFFRACTIONc_mcangle_it2.512
X-RAY DIFFRACTIONc_scbond_it1.432
X-RAY DIFFRACTIONc_scangle_it2.462.5
LS refinement shellResolution: 3.1→3.29 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.363 112 5 %
Rwork0.285 2143 -
obs--69 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.1 Å / σ(F): 3 / % reflection Rfree: 4.8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 36.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.86
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.363 / % reflection Rfree: 5 % / Rfactor Rwork: 0.285 / Rfactor obs: 0.285

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