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- PDB-5t7g: Crystal Structure of Murine MHC-I H-2Dd in complex with Murine Be... -

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Basic information

Entry
Database: PDB / ID: 5t7g
TitleCrystal Structure of Murine MHC-I H-2Dd in complex with Murine Beta2-Microglobulin and a Variant of Peptide (PT9) of HIV gp120 MN Isolate (IGPGRAFYT)
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, D-D alpha chain
  • Peptide (PT9) of HIV gp120 MN isolate (IGPGRAFYT)
KeywordsIMMUNE SYSTEM / MAJOR HISTOMPATIBILITY COMPLEX CLASS I / MHC-I / H2-Dd / H-2Dd / HIV peptide / PVI10 / PV9 / PT9 / GLYCOPROTEIN / IMMUNE RESPONSE
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 / cellular defense response / positive regulation of plasma membrane raft polarization ...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 / cellular defense response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / Neutrophil degranulation / host cell endosome membrane / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / 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 / MHC class I protein complex / 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 / phagocytic vesicle membrane / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / T cell differentiation in thymus / negative regulation of neuron projection development / protein refolding / protein homotetramerization / clathrin-dependent endocytosis of virus by host cell / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / viral protein processing / fusion of virus membrane with host plasma membrane / external side of plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / 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 / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / 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
Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-D alpha chain / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesMus musculus (house mouse)
Human immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.961 Å
AuthorsJiang, J. / Natarajan, K. / Margulies, D.
CitationJournal: J. Immunol. / Year: 2018
Title: Effects of Cross-Presentation, Antigen Processing, and Peptide Binding in HIV Evasion of T Cell Immunity.
Authors: Frey, B.F. / Jiang, J. / Sui, Y. / Boyd, L.F. / Yu, B. / Tatsuno, G. / Billeskov, R. / Solaymani-Mohammadi, S. / Berman, P.W. / Margulies, D.H. / Berzofsky, J.A.
History
DepositionSep 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 28, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 19, 2020Group: Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_struct_assembly ...entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.4Oct 4, 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

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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 (PT9) of HIV gp120 MN isolate (IGPGRAFYT)
C: H-2 class I histocompatibility antigen, D-D alpha chain
D: Beta-2-microglobulin
Q: Peptide (PT9) of HIV gp120 MN isolate (IGPGRAFYT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,30318
Polymers89,5596
Non-polymers74512
Water6,918384
1
A: H-2 class I histocompatibility antigen, D-D alpha chain
B: Beta-2-microglobulin
P: Peptide (PT9) of HIV gp120 MN isolate (IGPGRAFYT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,27611
Polymers44,7793
Non-polymers4978
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint2 kcal/mol
Surface area18500 Å2
MethodPISA
2
C: H-2 class I histocompatibility antigen, D-D alpha chain
D: Beta-2-microglobulin
Q: Peptide (PT9) of HIV gp120 MN isolate (IGPGRAFYT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0287
Polymers44,7793
Non-polymers2484
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-7 kcal/mol
Surface area18410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.243, 120.496, 143.740
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 H-2 class I histocompatibility antigen, D-D alpha chain / H-2D(D)


Mass: 32005.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / 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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01887
#3: Protein/peptide Peptide (PT9) of HIV gp120 MN isolate (IGPGRAFYT)


Mass: 982.115 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 group M subtype B (isolate MN)
Production host: synthetic construct (others) / References: UniProt: P05877*PLUS
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.58 Å3/Da / Density % sol: 49.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 12% PEG 10000, 0.1M MES buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.0333 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 19, 2016
RadiationMonochromator: SI 100 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0333 Å / Relative weight: 1
ReflectionResolution: 1.96→39 Å / Num. obs: 63236 / % possible obs: 99.5 % / Redundancy: 4 % / Biso Wilson estimate: 27.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.9
Reflection shellResolution: 1.96→2.03 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.972 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.546 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KD7

5kd7


Resolution: 1.961→38.966 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 25.09
RfactorNum. reflection% reflection
Rfree0.2379 3077 5.01 %
Rwork0.1947 --
obs0.1969 61427 96.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 38 Å2
Refinement stepCycle: LAST / Resolution: 1.961→38.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6183 0 48 384 6615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096406
X-RAY DIFFRACTIONf_angle_d1.1948691
X-RAY DIFFRACTIONf_dihedral_angle_d17.2823782
X-RAY DIFFRACTIONf_chiral_restr0.068884
X-RAY DIFFRACTIONf_plane_restr0.011134
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.961-1.99110.3621290.3242423X-RAY DIFFRACTION90
1.9911-2.02380.36741320.29712552X-RAY DIFFRACTION94
2.0238-2.05870.28021350.29032531X-RAY DIFFRACTION95
2.0587-2.09610.33151410.26982596X-RAY DIFFRACTION95
2.0961-2.13640.30151350.26232554X-RAY DIFFRACTION96
2.1364-2.180.29511390.24112630X-RAY DIFFRACTION95
2.18-2.22740.25961360.23072563X-RAY DIFFRACTION96
2.2274-2.27920.28781400.22642647X-RAY DIFFRACTION96
2.2792-2.33620.27911330.2282590X-RAY DIFFRACTION96
2.3362-2.39940.27741410.2282635X-RAY DIFFRACTION97
2.3994-2.470.27141390.21212622X-RAY DIFFRACTION97
2.47-2.54970.25541390.21622634X-RAY DIFFRACTION97
2.5497-2.64080.26011390.21112696X-RAY DIFFRACTION98
2.6408-2.74650.24441410.2132652X-RAY DIFFRACTION98
2.7465-2.87150.2771430.19542692X-RAY DIFFRACTION98
2.8715-3.02280.2621410.19812693X-RAY DIFFRACTION98
3.0228-3.21210.20951440.19142703X-RAY DIFFRACTION98
3.2121-3.460.23411430.18492724X-RAY DIFFRACTION99
3.46-3.80790.18721440.16222768X-RAY DIFFRACTION99
3.8079-4.35830.19861450.15412749X-RAY DIFFRACTION99
4.3583-5.48850.18921460.14072811X-RAY DIFFRACTION99
5.4885-38.9660.21361520.18832885X-RAY DIFFRACTION97
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)
12.19590.1987-0.53573.7229-1.23873.342-0.08610.0516-0.1591-0.12070.0936-0.02710.1401-0.0611-0.02030.3514-0.0010.01050.1036-0.02010.193751.56281.8609165.4855
20.90480.5478-0.47645.46910.60210.7825-0.19070.1159-0.1211-0.73090.1179-0.16480.3945-0.01430.08250.6126-0.02130.17990.2151-0.02070.298161.00179.3489148.3901
32.11330.12690.41913.09090.43732.10940.0365-0.02240.1552-0.35710.0796-0.5783-0.0370.2659-0.09770.2045-0.01420.0380.1236-0.01170.198360.90837.65160.3726
41.7751-0.32610.0432.889-0.16022.5064-0.0464-0.08730.0015-0.3584-0.07410.56840.1197-0.32430.01810.2874-0.0287-0.08040.1375-0.02540.186740.676926.6091160.6423
52.4826-1.01390.76064.5568-0.53192.1724-0.0721-0.22630.0615-0.11110.05430.5134-0.0089-0.33540.06140.2755-0.0114-0.00680.2075-0.04920.162641.274727.232163.0014
60.41310.0314-0.25980.3663-0.24541.3093-0.10470.0452-0.0983-0.22170.06650.04530.04050.1846-0.02940.5479-0.06590.03050.1911-0.02610.285352.087-5.3794166.8948
73.17880.16071.30144.3926-1.05955.7171-0.0836-0.59440.07830.5410.15360.0595-0.1836-0.1626-0.03850.28790.04290.01760.2629-0.00670.249550.607733.5507198.4991
84.0045-0.25460.99213.6437-0.34534.3776-0.30050.09940.1172-0.294-0.0058-0.8301-0.01010.73270.20910.249-0.00470.04910.25850.03270.344161.853936.9466185.8764
91.5477-0.86280.3690.8047-0.9591.6594-0.3947-0.21040.23940.76060.3031-0.384-0.2860.20210.13710.24840.1193-0.13950.39390.10750.241365.29114.2736204.2541
101.34440.24940.3971.98180.78761.18150.1569-0.1223-0.02040.058-0.1149-0.8941-0.35880.5940.0361-0.17830.2231-0.07230.25940.13870.365267.15580.9774196.5648
112.73730.6727-0.96563.939-0.56563.57240.0385-0.1869-0.01150.22240.04330.1879-0.1817-0.1385-0.06160.13570.0493-0.01980.19340.01770.199445.81549.5367201.1708
123.13670.2674-0.35654.5919-0.64761.51860.0114-0.0113-0.0828-0.1056-0.03320.32580.0224-0.03980.03210.14680.0424-0.02650.17070.01890.181145.99838.969198.6617
134.45420.1757-1.39865.6882-2.31037.4055-0.2581-0.3369-0.01840.27860.1024-0.4336-0.43560.7275-0.07060.27650.0216-0.07420.156-0.06340.25254.654141.9662192.3334
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 162 )
2X-RAY DIFFRACTION2chain 'A' and (resid 163 through 185 )
3X-RAY DIFFRACTION3chain 'A' and (resid 186 through 274 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 51 )
5X-RAY DIFFRACTION5chain 'B' and (resid 52 through 99 )
6X-RAY DIFFRACTION6chain 'P' and (resid 1 through 9 )
7X-RAY DIFFRACTION7chain 'C' and (resid 2 through 103 )
8X-RAY DIFFRACTION8chain 'C' and (resid 104 through 162 )
9X-RAY DIFFRACTION9chain 'C' and (resid 163 through 198 )
10X-RAY DIFFRACTION10chain 'C' and (resid 199 through 274 )
11X-RAY DIFFRACTION11chain 'D' and (resid 1 through 51 )
12X-RAY DIFFRACTION12chain 'D' and (resid 52 through 99 )
13X-RAY DIFFRACTION13chain 'Q' and (resid 1 through 9 )

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