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- PDB-1b3j: STRUCTURE OF THE MHC CLASS I HOMOLOG MIC-A, A GAMMADELTA T CELL LIGAND -

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Basic information

Entry
Database: PDB / ID: 1b3j
TitleSTRUCTURE OF THE MHC CLASS I HOMOLOG MIC-A, A GAMMADELTA T CELL LIGAND
ComponentsMHC CLASS I HOMOLOG MIC-A
KeywordsIMMUNE SYSTEM / HC I HOMOLOG / HUMAN MICA / MICA / IMMUNOLOGY / MHC / GAMMA-DELTA-TCR / GLYCOPROTEIN / SIGNA IMMUNOGLOBULIN FOLD / T-CELL
Function / homology
Function and homology information


immune response to tumor cell / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / gamma-delta T cell activation / negative regulation of natural killer cell mediated cytotoxicity / natural killer cell mediated cytotoxicity / T cell mediated cytotoxicity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / response to heat / defense response to virus ...immune response to tumor cell / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / gamma-delta T cell activation / negative regulation of natural killer cell mediated cytotoxicity / natural killer cell mediated cytotoxicity / T cell mediated cytotoxicity / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / response to heat / defense response to virus / killing of cells of another organism / defense response to bacterium / immune response / receptor ligand activity / external side of plasma membrane / DNA damage response / cell surface / extracellular space / plasma membrane / cytoplasm
Similarity search - Function
MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Class I Histocompatibility antigen, domains alpha 1 and 2 / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / Class I Histocompatibility antigen, domains alpha 1 and 2 / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / MHC class I polypeptide-related sequence A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MIR / Resolution: 3 Å
AuthorsLi, P. / Willie, S. / Bauer, S. / Morris, D. / Spies, T. / Strong, R.
Citation
Journal: Immunity / Year: 1999
Title: Crystal structure of the MHC class I homolog MIC-A, a gammadelta T cell ligand.
Authors: Li, P. / Willie, S.T. / Bauer, S. / Morris, D.L. / Spies, T. / Strong, R.K.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Expression, Purification, Crystallization and Cryst Graphic Charatterization of the Human Mhc Class I R Protein Mica
Authors: Bauer, S. / Willie, S.T. / Spies, T. / Strong, R.K.
History
DepositionDec 11, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Jul 9, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _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 / _pdbx_struct_special_symmetry.label_asym_id / _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_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC CLASS I HOMOLOG MIC-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0252
Polymers31,6001
Non-polymers4241
Water93752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)261.500, 261.500, 261.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number210
Space group name H-MF4132
Components on special symmetry positions
IDModelComponents
11A-313-

HOH

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Components

#1: Protein MHC CLASS I HOMOLOG MIC-A / MICA / MIC / PERB11


Mass: 31600.236 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 1 - 274
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: EXTRACELLULAR / Gene: MICA-001 / Cell line (production host): Hi5 / Gene (production host): MICA-001 / Production host: Trichoplusia ni (cabbage looper) / References: GenBank: 1708676, UniProt: Q29983*PLUS
#2: 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.: 1
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 5.3 Å3/Da / Density % sol: 80 %
Crystal growpH: 5.5 / Details: pH 5.50
Components of the solutions
IDNameCrystal-IDSol-ID
1(NH4)2SO411
2CITRATE BUFFER11
3(NH4)2SO412
Crystal grow
*PLUS
Temperature: 291 K / Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150-55 %satammonium sulfate1reservoir
250-100 mMsodium citrate1reservoir
31

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS VI / Detector: IMAGE PLATE / Date: May 1, 1998 / Details: YALE MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→25 Å / Num. obs: 15536 / % possible obs: 97.9 % / Redundancy: 4 % / Biso Wilson estimate: 70.1 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 23.5
Reflection shellResolution: 3→3.05 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.356 / % possible all: 96.6
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 19368 / % possible obs: 99.7 % / Num. measured all: 130489 / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 5.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
X-PLOR3.851refinement
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 3→15 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED BULK SOLVENT MODELING. METHOD USED: FLAT MODEL KSOL: 0.30 BSOL: 50.0 (A**2)
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1473 10.2 %RANDOM
Rwork0.246 ---
obs0.246 14483 92.1 %-
all-14483 --
Solvent computationBsol: 50 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 46.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2116 0 28 52 2196
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.6
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.7
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.392 219 9.7 %
Rwork0.367 2039 -
obs--88.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM3.CHOTOPH3.CHO
X-RAY DIFFRACTION3PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 9999 Å / Num. reflection obs: 18416 / Rfactor obs: 0.253 / Rfactor Rfree: 0.293
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.9
X-RAY DIFFRACTIONx_improper_angle_d
LS refinement shell
*PLUS

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