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- PDB-3ecb: Crystal structure of mouse H-2Dd in complex with peptide P18-I10 ... -

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Basic information

Entry
Database: PDB / ID: 3ecb
TitleCrystal structure of mouse H-2Dd in complex with peptide P18-I10 derived from human immunodeficiency virus envelope glycoprotein 120
Components
  • Beta-2 microglobulin
  • H-2 class I histocompatibility antigen, D-D alpha chain
  • Peptide P18-I10 from HIV gp160
KeywordsIMMUNE SYSTEM / class I major histompatibility complex / MHC-I / H-2Dd / Glycoprotein / Immune response / Membrane / MHC I / Phosphoprotein / Transmembrane / Immunoglobulin domain / Secreted / AIDS / Apoptosis / Cell membrane / Cleavage on pair of basic residues / Coiled coil / Envelope protein / Fusion protein / Host-virus interaction / Lipoprotein / Palmitate / Viral immunoevasion / Virion
Function / homology
Function and homology information


Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Dectin-2 family / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Dectin-2 family / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / beta-2-microglobulin binding / cellular defense response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / Neutrophil degranulation / host cell endosome membrane / 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 / lumenal side of endoplasmic reticulum membrane / peptide binding / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / sensory perception of smell / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / clathrin-dependent endocytosis of virus by host cell / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / viral protein processing / immune response / lysosomal membrane / fusion of virus membrane with host plasma membrane / external side of plasma membrane / signaling receptor binding / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / protein-containing complex binding / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / Golgi apparatus / protein homodimerization activity / extracellular space / membrane / plasma membrane / cytosol
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / 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 ...Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-D alpha chain / Envelope glycoprotein gp160 / Beta-2-microglobulin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.698 Å
AuthorsNatarajan, K. / Wang, R. / Margulies, D.H.
CitationJournal: J.Immunol. / Year: 2009
Title: Structural basis of the CD8alphabeta/MHC class i interaction: focused recognition orients CD8beta to a T cell proximal position
Authors: Wang, R. / Natarajan, K. / Margulies, D.H.
History
DepositionAug 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 40 MOLPROBITY STRUCTURE VALIDATION PROGRAMS : MOLPROBITY (KING, REDUCE, AND PROBE) AUTHORS : I.W. ... MOLPROBITY STRUCTURE VALIDATION PROGRAMS : MOLPROBITY (KING, REDUCE, AND PROBE) AUTHORS : I.W.DAVIS,V.B.CHEN, : R.M.IMMORMINO,J.J.HEADD,W.B.ARENDALL,J.M.WORD

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, D-D alpha chain
B: Beta-2 microglobulin
P: Peptide P18-I10 from HIV gp160
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,52910
Polymers45,1333
Non-polymers3977
Water5,675315
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-5 kcal/mol
Surface area18490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.727, 89.452, 109.705
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein H-2 class I histocompatibility antigen, D-D alpha chain / H-2D(D)


Mass: 32265.902 Da / Num. of mol.: 1 / Fragment: UNP residues 26 to 298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/c / Gene: H2-D1 / Plasmid: pET21-b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01900
#2: Protein Beta-2 microglobulin


Mass: 11791.545 Da / Num. of mol.: 1 / Fragment: UNP residues 21 to 119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m, RP23-34E24.5-001 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q91XJ8, UniProt: P01887*PLUS

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Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide Peptide P18-I10 from HIV gp160 / Env polyprotein / Surface protein / SU / Glycoprotein 120 / gp120 / Transmembrane protein / TM / ...Env polyprotein / Surface protein / SU / Glycoprotein 120 / gp120 / Transmembrane protein / TM / Glycoprotein 41 / gp41


Mass: 1075.265 Da / Num. of mol.: 1 / Fragment: UNP residues 309 to 318 / Source method: obtained synthetically
Details: The peptide is chemically synthesized. It is found naturally in Human immunodeficiency virus envelope glycoprotein gp120.
References: UniProt: P19551

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Non-polymers , 3 types, 322 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 315 / Source method: isolated from a natural source / Formula: H2O

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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: 2.58 Å3/Da / Density % sol: 52.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 16% PEG 3350, 0.2M Magnesium formate, , pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorDate: Jul 10, 2008
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 51683 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.06
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1DDH

1ddh


Resolution: 1.698→28.798 Å / SU ML: 0.25 / σ(F): 1.34 / Phase error: 23.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2273 2488 5.08 %
Rwork0.1816 --
obs0.1839 48991 94.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.003 Å2 / ksol: 0.351 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.78 Å20 Å20 Å2
2--2.49 Å20 Å2
3----9.87 Å2
Refinement stepCycle: LAST / Resolution: 1.698→28.798 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3136 0 25 315 3476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053241
X-RAY DIFFRACTIONf_angle_d1.0174384
X-RAY DIFFRACTIONf_dihedral_angle_d17.7631178
X-RAY DIFFRACTIONf_chiral_restr0.072444
X-RAY DIFFRACTIONf_plane_restr0.004573
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.698-1.73070.2396810.17781770X-RAY DIFFRACTION64
1.7307-1.7660.27061080.17241967X-RAY DIFFRACTION75
1.766-1.80440.28391230.17612224X-RAY DIFFRACTION82
1.8044-1.84640.24611280.17032476X-RAY DIFFRACTION93
1.8464-1.89250.27511310.16122636X-RAY DIFFRACTION97
1.8925-1.94370.21981410.15642671X-RAY DIFFRACTION99
1.9437-2.00090.21771600.15612635X-RAY DIFFRACTION99
2.0009-2.06540.21291510.15522674X-RAY DIFFRACTION99
2.0654-2.13920.24361560.15842679X-RAY DIFFRACTION100
2.1392-2.22480.2521470.15932705X-RAY DIFFRACTION99
2.2248-2.32610.22291400.16462686X-RAY DIFFRACTION100
2.3261-2.44860.22581380.17362721X-RAY DIFFRACTION100
2.4486-2.60190.2431370.17892729X-RAY DIFFRACTION100
2.6019-2.80270.25381640.19562706X-RAY DIFFRACTION100
2.8027-3.08440.23081540.19392732X-RAY DIFFRACTION100
3.0844-3.53010.24241340.18892762X-RAY DIFFRACTION100
3.5301-4.44490.19171500.16792787X-RAY DIFFRACTION100
4.4449-28.80210.19781450.18642943X-RAY DIFFRACTION100

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