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- PDB-1qqd: CRYSTAL STRUCTURE OF HLA-CW4, A LIGAND FOR THE KIR2D NATURAL KILL... -

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Basic information

Entry
Database: PDB / ID: 1qqd
TitleCRYSTAL STRUCTURE OF HLA-CW4, A LIGAND FOR THE KIR2D NATURAL KILLER CELL INHIBITORY RECEPTOR
Components
  • BETA-2 MICROGLOBULIN
  • HISTOCOMPATIBILITY LEUKOCYTE ANTIGEN (HLA)-CW4 (HEAVY CHAIN)
  • HLA-CW4 SPECIFIC PEPTIDE
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN (IG)-LIKE DOMAIN / ALPHA HELIX / BETA SHEET
Function / homology
Function and homology information


TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / secretory granule membrane / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion ...TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / secretory granule membrane / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily ...MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class I histocompatibility antigen, C alpha chain / HLA class I histocompatibility antigen, C alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsFan, Q.R. / Wiley, D.C.
CitationJournal: J.Exp.Med. / Year: 1999
Title: Structure of human histocompatibility leukocyte antigen (HLA)-Cw4, a ligand for the KIR2D natural killer cell inhibitory receptor
Authors: Fan, Q.R. / Wiley, D.C.
History
DepositionJun 3, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HISTOCOMPATIBILITY LEUKOCYTE ANTIGEN (HLA)-CW4 (HEAVY CHAIN)
B: BETA-2 MICROGLOBULIN
C: HLA-CW4 SPECIFIC PEPTIDE


Theoretical massNumber of molelcules
Total (without water)44,6223
Polymers44,6223
Non-polymers00
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-17 kcal/mol
Surface area19200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.960, 77.490, 108.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HISTOCOMPATIBILITY LEUKOCYTE ANTIGEN (HLA)-CW4 (HEAVY CHAIN)


Mass: 31830.947 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PLM-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P30504, UniProt: P10321*PLUS
#2: Protein BETA-2 MICROGLOBULIN


Mass: 11676.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PLM-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide HLA-CW4 SPECIFIC PEPTIDE


Mass: 1115.213 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The nonameric peptide contains the consensus peptide-binding motif for HLA-Cw4, which was determined by pool sequencing.
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.59 Å3/Da / Density % sol: 52.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, calcium acetate, sodium cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K
Crystal grow
*PLUS
Method: unknown
Details: seeding using 12% PEG8000, 0.2 M Ca acetate, and 0.1M Na cacodylate
Components of the solutions
*PLUS
IDConc.UnitCommon nameCrystal-IDSol-ID
118 %PEG80001reservoir
2MCa-acetate1reservoir
3MNa cacodylate1reservoir

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: May 31, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 2.7→22 Å / Num. all: 12895 / Num. obs: 12895 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 60.2 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 5.4
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3 % / Rmerge(I) obs: 0.504 / Num. unique all: 1175 / % possible all: 90.5
Reflection shell
*PLUS
% possible obs: 90.5 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.4refinement
RefinementResolution: 2.7→22 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2295736.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1330 10.3 %random
Rwork0.223 ---
all0.223 12895 --
obs0.223 12895 97.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.12 Å2 / ksol: 0.382 e/Å3
Displacement parametersBiso mean: 52.9 Å2
Baniso -1Baniso -2Baniso -3
1-19.88 Å20 Å20 Å2
2--1.96 Å20 Å2
3----21.83 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.7→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3144 0 0 35 3179
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d0.76
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.374 204 10.1 %
Rwork0.332 1822 -
obs--93.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76

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