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- PDB-3cup: Crystal structure of the MHC class II molecule I-Ag7 in complex w... -

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Basic information

Entry
Database: PDB / ID: 3cup
TitleCrystal structure of the MHC class II molecule I-Ag7 in complex with the peptide GAD221-235
Components
  • H-2 class II histocompatibility antigen, A-D alpha chain
  • MHC class II H2-IA-beta chain linked to GAD221-235 peptide
KeywordsIMMUNE SYSTEM / Histocompatability antigen / MHC class II / I-Ag7 / Glycoprotein / Immune response / Membrane / MHC II / Transmembrane
Function / homology
Function and homology information


: / GABA synthesis / glutamate decarboxylation to succinate / glutamate decarboxylase / glutamate decarboxylase activity / : / GABA synthesis, release, reuptake and degradation / inhibitory synapse / response to xenobiotic stimulus => GO:0009410 / antigen processing and presentation of peptide antigen ...: / GABA synthesis / glutamate decarboxylation to succinate / glutamate decarboxylase / glutamate decarboxylase activity / : / GABA synthesis, release, reuptake and degradation / inhibitory synapse / response to xenobiotic stimulus => GO:0009410 / antigen processing and presentation of peptide antigen / carboxy-lyase activity / glutamate binding / positive regulation of T cell differentiation / carboxylic acid metabolic process / antigen processing and presentation / negative regulation of T cell proliferation / multivesicular body / synaptic vesicle membrane / 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 / pyridoxal phosphate binding / presynaptic membrane / MHC class II protein complex binding / late endosome membrane / chemical synaptic transmission / cytoplasmic vesicle / adaptive immune response / lysosome / early endosome / lysosomal membrane / axon / external side of plasma membrane / Golgi membrane / synapse / protein-containing complex binding / perinuclear region of cytoplasm / Golgi apparatus / cell surface / plasma membrane / cytosol / cytoplasm
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 / 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 ...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 / 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 / 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 / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
H-2 class II histocompatibility antigen, A-D alpha chain / Glutamate decarboxylase 2 / H2-Ab1 protein / 65 kDa glutamate decarboxylase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.09 Å
AuthorsCorper, A.L. / Yoshida, K. / Teyton, L. / Wilson, I.A.
CitationJournal: To be Published
Title: Crystal structure of the MHC class II molecule I-Ag7 in complex with the peptide GAD221-235
Authors: Yoshida, K. / Corper, A.L. / Puckett, C. / Sim, J. / Valerie, M.-D. / Jabri, B. / Wilson, I.A. / Teyton, L.
History
DepositionApr 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jun 28, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation_author / entity_src_gen / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / software / struct_conf / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / 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_seq_id / _atom_site.pdbx_PDB_ins_code / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_PDB_ins_code / _atom_site_anisotrop.pdbx_auth_seq_id / _citation_author.name / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Jul 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_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Aug 30, 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

Downloads & links

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Assembly

Deposited unit
A: H-2 class II histocompatibility antigen, A-D alpha chain
B: MHC class II H2-IA-beta chain linked to GAD221-235 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6224
Polymers47,1632
Non-polymers4602
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6580 Å2
ΔGint-19.6 kcal/mol
Surface area17680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.832, 55.832, 338.834
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein H-2 class II histocompatibility antigen, A-D alpha chain


Mass: 21623.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Aa / Plasmid: pRMHa-3 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 cells / References: UniProt: P04228
#2: Protein MHC class II H2-IA-beta chain linked to GAD221-235 peptide


Mass: 25539.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pRMHa-3 / Gene: H2-Ab1 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): S2 cells
References: UniProt: Q6LDA5, UniProt: Q31135, UniProt: Q05683*PLUS
#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.: 1
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-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
Sequence detailsTHE SYNTHETIC MURINE GAD65 PEPTIDE (RESIDUES 221-235) IN CHAIN B IS LINKED TO THE N-TERMINUS OF THE ...THE SYNTHETIC MURINE GAD65 PEPTIDE (RESIDUES 221-235) IN CHAIN B IS LINKED TO THE N-TERMINUS OF THE MHC CLASS II H2-IA(G7)-BETA CHAIN BY GSGSGS LINKER RESIDUES. KABAT NUMBERING IS USED FOR I-A(G7) RESIDUES.

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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: 2.8 Å3/Da / Density % sol: 56.06 %
Crystal growTemperature: 295 K / pH: 7.5
Details: 0.1M Hepes pH 7.5, 28% PEG 8000, 2% Jeffamine 900, VAPOR DIFFUSION, SITTING DROP, temperature 295K, pH 7.50

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Data collection

DiffractionMean temperature: 96 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 10, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.088→38.449 Å / Num. obs: 10586 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 60.07 Å2 / Rsym value: 0.128 / Net I/σ(I): 10.6
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.682 / % possible all: 99.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ES0

1es0


Resolution: 3.09→38.45 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.286 563 5.32 %RANDOM
Rwork0.232 ---
obs0.235 10586 98.7 %-
all-10729 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 73.44 Å2
Baniso -1Baniso -2Baniso -3
1-5.361 Å20 Å2-0 Å2
2--5.361 Å20 Å2
3----25.103 Å2
Refinement stepCycle: LAST / Resolution: 3.09→38.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2924 0 29 0 2953
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033035
X-RAY DIFFRACTIONf_angle_d0.6384117
X-RAY DIFFRACTIONf_dihedral_angle_d14.7211086
X-RAY DIFFRACTIONf_chiral_restr0.039444
X-RAY DIFFRACTIONf_plane_restr0.002523
LS refinement shellResolution: 3.09→3.4 Å / Total num. of bins used: 4
RfactorNum. reflection% reflection
Rfree0.312 108 -
Rwork0.287 2455 -
obs--99 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.75890.065-0.47321.8576-0.58964.9111-0.03420.1838-0.3171-0.1477-0.1332-0.22480.68160.20220.00010.4667-0.02390.02080.6249-0.02330.615958.07431.561548.9693
22.2797-0.5698-0.31771.1922-0.44724.655-0.1408-0.0692-0.58980.268-0.07590.30740.5476-0.621200.6013-0.20140.07120.6847-0.01080.642440.52320.879370.9108
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 82
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION1B4 - 93
4X-RAY DIFFRACTION1B222 - 236
5X-RAY DIFFRACTION2A83 - 181
6X-RAY DIFFRACTION2A302
7X-RAY DIFFRACTION2B94 - 188

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