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- PDB-1es0: CRYSTAL STRUCTURE OF THE MURINE CLASS II ALLELE I-A(G7) COMPLEXED... -

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Basic information

Entry
Database: PDB / ID: 1es0
TitleCRYSTAL STRUCTURE OF THE MURINE CLASS II ALLELE I-A(G7) COMPLEXED WITH THE GLUTAMIC ACID DECARBOXYLASE (GAD65) PEPTIDE 207-220
Components
  • 65 KD GLUTAMIC ACID DECARBOXYLASE+H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN
  • H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN
KeywordsIMMUNE SYSTEM / HISTOCOMPATIBILITY ANTIGEN / CLASS II MHC I-A(G7)
Function / homology
Function and homology information


GABA synthesis / gamma-aminobutyrate shunt / MECP2 regulates transcription of genes involved in GABA signaling / glutamate decarboxylase / glutamate decarboxylase activity / gamma-aminobutyric acid biosynthetic process / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / GABA synthesis, release, reuptake and degradation / antigen processing and presentation of peptide antigen / positive regulation of T cell differentiation ...GABA synthesis / gamma-aminobutyrate shunt / MECP2 regulates transcription of genes involved in GABA signaling / glutamate decarboxylase / glutamate decarboxylase activity / gamma-aminobutyric acid biosynthetic process / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / GABA synthesis, release, reuptake and degradation / antigen processing and presentation of peptide antigen / positive regulation of T cell differentiation / antigen processing and presentation / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / pyridoxal phosphate binding / presynaptic membrane / chemical synaptic transmission / adaptive immune response / lysosome / Golgi membrane / axon / external side of plasma membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Pyridoxal-phosphate binding site / DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site. / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / 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 ...Pyridoxal-phosphate binding site / DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site. / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / 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 / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / 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
: / H-2 class II histocompatibility antigen, A-D alpha chain / Glutamate decarboxylase 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsCorper, A.L. / Teyton, L. / Wilson, I.A.
CitationJournal: Science / Year: 2000
Title: A structural framework for deciphering the link between I-Ag7 and autoimmune diabetes.
Authors: Corper, A.L. / Stratmann, T. / Apostolopoulos, V. / Scott, C.A. / Garcia, K.C. / Kang, A.S. / Wilson, I.A. / Teyton, L.
History
DepositionApr 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN
B: 65 KD GLUTAMIC ACID DECARBOXYLASE+H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN


Theoretical massNumber of molelcules
Total (without water)47,1872
Polymers47,1872
Non-polymers00
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint-28 kcal/mol
Surface area17770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.149, 110.123, 96.084
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN


Mass: 21623.129 Da / Num. of mol.: 1 / Fragment: ALPHA CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: UniProt: P04228
#2: Protein 65 KD GLUTAMIC ACID DECARBOXYLASE+H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN


Mass: 25563.430 Da / Num. of mol.: 1 / Fragment: PEPTIDE (RESIDUES 222-235) + BETA CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: Q05329, GenBank: 387435
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS ENTRY CONTAINS COORDINATES FOR THE EXTRACELLULAR DOMAINS OF THE MURINE MHC CLASS II ALLELE I- ...THIS ENTRY CONTAINS COORDINATES FOR THE EXTRACELLULAR DOMAINS OF THE MURINE MHC CLASS II ALLELE I-A(G7) WITH A FRAGMENT FROM GAD65 (207 - 220) COVALENTLY ATTACHED TO THE FIRST RESIDUE OF THE AMINO TERMINUS OF THE MATURE BETA CHAIN. THE NUMBERING SCHEME FOR THE I-A(G7) RESIDUES IS AS DESCRIBED IN "SEQUENCES OF PROTEINS OF IMMUNOLOGICAL INTEREST" (1991), EDITED BY E.A. KABAT, T.T. WU, H.M. PERRY, K.S. GOTTESMAN AND C. FOELLER. DIMERIZATION OF THE I-A(G7) HETERODIMER WAS FACILITATED BY ADDING A LEUCINE ZIPPER TAIL TO THE CARBOXY TERMINUS OF EACH CHAIN. IN ADDITION, A HEXAHISTIDINE SEQUENCE WAS ENGINEERED TO THE CARBOXY TERMINAL END OF THE LEUCINE ZIPPER. THIS ALLOWED THE SECRETED PROTEIN TO BE PURIFIED BY NI-NTA CHROMATOGRAPHY. A THROMBIN CUT SITE WAS ENGINEERED IN A SPACER SEQUENCE BETWEEN THE CARBOXY TERMINAL RESIDUE OF EACH CHAIN AND THE LEUCINE ZIPPER- HEXAHISTIDINE SEQUENCE SO THAT MOST OF THE ENGINEERED RESIDUES COULD BE REMOVED FOR CRYSTALLIZATION. AFTER THROMBIN DIGESTION, EIGHT ENGINEERED RESIDUES (SSADLVPR) REMAINED ATTACHED TO THE CARBOXY TERMINAL END OF EACH I-A(G7) CHAIN. NO ELECTRON DENSITY WAS VISIBLE FOR 1) THE FIRST 2 RESIDUES OF THE ALPHA CHAIN 2) THE LAST 6 RESIDUES OF THE SPACER SEQUENCE ATTACHED TO THE C-TERMINUS OF THE ALPHA CHAIN, 3) THE 6 RESIDUE (GSGSGS) LINKER BETWEEN GAD65 AND THE BETA CHAIN, 4) THE FIRST 4 RESIDUES OF THE BETA CHAIN, AND 5) THE LAST 7 RESIDUES OF THE SPACER SEQUENCE ATTACHED TO THE C-TERMINUS OF THE BETA CHAIN. SIX ADDITIONAL RESIDUES (GSHSRG) FROM THE SIGNAL SEQUENCE REMAIN CONNECTED TO THE AMINO TERMINUS OF THE GAD65 PEPTIDE; NO DENSITY IS PRESENT FOR THESE RESIDUES. THE RESIDUE NUMBERING FOR THE TWO PROTEIN CHAINS IS: A 1B - A 178 : MHC CLASS II ALPHA CHAIN A 179 - A 186 : SPACER SEQUENCE B 207P - B 220P : RESIDUES 207-220 OF GAD65 B 1 - B 188 : MHC CLASS II BETA CHAIN B 189 - B 196 : SPACER SEQUENCE

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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: 2.9 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 16-18% PEG 4000, 0.2 M LICL (PH 6.6), 1% MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 7.5 / Method: unknown / Details: seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein11
220 mMHEPES11
325 mM11NaCl

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Data collection

DiffractionMean temperature: 96 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 16, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.6→39.96 Å / Num. obs: 15754 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 51.8 Å2 / Rsym value: 0.068 / Net I/σ(I): 15.7
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 4.2 / Rsym value: 0.353 / % possible all: 99.6
Reflection
*PLUS
Num. measured all: 66107 / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
% possible obs: 99.6 % / Rmerge(I) obs: 0.353

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Processing

Software
NameVersionClassification
DENZOdata reduction
TRUNCATEdata reduction
AMoREphasing
CNS0.9refinement
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: I-A(K) - PDB CODE 1IAK

1iak


Resolution: 2.6→39.96 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1541 9.8 %RANDOM
Rwork0.21 ---
obs0.21 15754 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.63 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 36.1 Å2
Baniso -1Baniso -2Baniso -3
1-8 Å20 Å20 Å2
2---3.51 Å20 Å2
3----4.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.6→39.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3012 0 0 76 3088
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.6→2.69 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.344 149 9.6 %
Rwork0.276 1396 -
obs--99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CIS_PEPTIDE.PARAMCIS_PEPTIDE.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81

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