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- PDB-7lfl: MODEL OF MHC CLASS Ib H2-M3 WITH MOUSE ND1 N-TERMINAL HEPTAPEPTID... -

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Basic information

Entry
Database: PDB / ID: 7lfl
TitleMODEL OF MHC CLASS Ib H2-M3 WITH MOUSE ND1 N-TERMINAL HEPTAPEPTIDE, VAL MUTANT, MONOCLINIC CELL, REFINED AT 1.60 ANGSTROMS RESOLUTION
Components
  • Beta-2-microglobulin
  • Heptapeptide from NADH-ubiquinone oxidoreductase chain 1
  • Histocompatibility 2, M region locus 3
KeywordsIMMUNE SYSTEM / HISTOCOMPATIBILITY ANTIGEN/PEPTIDE / HISTOCOMPATIBILITY ANTIGEN-PEPTIDE COMPLEX
Function / homology
Function and homology information


alpha-beta T cell activation involved in immune response / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / Complex I biogenesis / Respiratory electron transport / positive regulation of natural killer cell mediated cytotoxicity / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway ...alpha-beta T cell activation involved in immune response / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / Complex I biogenesis / Respiratory electron transport / positive regulation of natural killer cell mediated cytotoxicity / 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 / response to hydroperoxide / NADH:ubiquinone reductase (H+-translocating) / antigen processing and presentation of peptide antigen via MHC class I / mitochondrial respiratory chain complex I assembly / mitochondrial electron transport, NADH to ubiquinone / proton motive force-driven mitochondrial ATP synthesis / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / respiratory chain complex I / NADH dehydrogenase (ubiquinone) activity / cellular defense response / Neutrophil degranulation / nitric oxide biosynthetic process / aerobic respiration / 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 / 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 / positive regulation of type II interferon production / phagocytic vesicle membrane / negative regulation of epithelial cell proliferation / positive regulation of nitric oxide biosynthetic process / sensory perception of smell / positive regulation of cellular senescence / T cell differentiation in thymus / negative regulation of neuron projection development / protein refolding / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / response to hypoxia / mitochondrial inner membrane / defense response to bacterium / response to xenobiotic stimulus / external side of plasma membrane / neuronal cell body / dendrite / structural molecule activity / Golgi apparatus / protein homodimerization activity / mitochondrion / extracellular space / cytosol
Similarity search - Function
NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / 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 ...NADH:ubiquinone oxidoreductase, subunit 1, conserved site / Respiratory-chain NADH dehydrogenase subunit 1 signature 1. / Respiratory-chain NADH dehydrogenase subunit 1 signature 2. / NADH:ubiquinone oxidoreductase, subunit 1/F420H2 oxidoreductase subunit H / NADH dehydrogenase / 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
Similarity search - Domain/homology
Beta-2-microglobulin / NADH-ubiquinone oxidoreductase chain 1 / Histocompatibility 2, M region locus 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsTomchick, D.R. / Deisenhofer, J. / Shen, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM079383 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30-DA035778 United States
Citation
Journal: J.Biomol.Struct.Dyn. / Year: 2022
Title: Structure and dynamics of major histocompatibility class Ib molecule H2-M3 complexed with mitochondrial-derived peptides.
Authors: Strand, A. / Shen, S.T. / Tomchick, D.R. / Wang, J. / Wang, C.R. / Deisenhofer, J.
#1: Journal: Cell / Year: 1995
Title: Nonclassical binding of formylated peptide in crystal structure of the MHC Class IB molecule H2-M3
Authors: Wang, C.R. / Castano, A.R. / Peterson, P.A. / Slaughter, C. / Lindahl, K.F. / Deisenhofer, J.
#2: Journal: Cell / Year: 1991
Title: H2-M3 encodes the MHC Class I molecule presenting the maternally transmitted antigen of the mouse
Authors: Wang, C.R. / Loveland, B.E. / Lindahl, K.F.
History
DepositionJan 17, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histocompatibility 2, M region locus 3
B: Beta-2-microglobulin
C: Heptapeptide from NADH-ubiquinone oxidoreductase chain 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4874
Polymers45,2663
Non-polymers2211
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-23 kcal/mol
Surface area19460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.376, 66.009, 55.216
Angle α, β, γ (deg.)90.000, 113.334, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Histocompatibility 2, M region locus 3 / MHC Class Ib Antigen H2-M3 / MHC class I antigen H-2M3


Mass: 32650.650 Da / Num. of mol.: 1 / Mutation: G299 deletion
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-M3, H-2M3 / Plasmid: pRMHa-3 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q31093
#2: Protein Beta-2-microglobulin


Mass: 11704.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: pRMHa-3 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01887
#3: Protein/peptide Heptapeptide from NADH-ubiquinone oxidoreductase chain 1 / NADH dehydrogenase subunit 1


Mass: 911.118 Da / Num. of mol.: 1 / Fragment: First seven amino-terminal residues / Mutation: I6V / Source method: obtained synthetically / Details: The N-terminal methionine is N-Formylmethionine / Source: (synth.) Mus musculus (house mouse)
References: UniProt: P03888, NADH:ubiquinone reductase (H+-translocating)
#4: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.15 Å3/Da / Density % sol: 42.82 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Hepes, 20% (w/v) PEG 4000, 30% (v/v) ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Jan 4, 1999 / Details: monochromator
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 1.6→22.65 Å / Num. obs: 48328 / % possible obs: 95.4 % / Redundancy: 5.3 % / Biso Wilson estimate: 22.07 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 16
Reflection shellResolution: 1.6→1.68 Å / Rmerge(I) obs: 0.677 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 5624 / % possible all: 80

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Processing

Software
NameVersionClassification
PHENIX1.18.2-3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.6→22.65 Å / SU ML: 0.188 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.4461
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2394 973 2.01 %
Rwork0.1999 47355 -
obs0.2006 48328 95.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.2 Å2
Refinement stepCycle: LAST / Resolution: 1.6→22.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3101 0 14 190 3305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00283209
X-RAY DIFFRACTIONf_angle_d0.68964354
X-RAY DIFFRACTIONf_chiral_restr0.0469455
X-RAY DIFFRACTIONf_plane_restr0.004565
X-RAY DIFFRACTIONf_dihedral_angle_d16.50091201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.680.28151240.285624X-RAY DIFFRACTION79.88
1.68-1.790.31091320.24246766X-RAY DIFFRACTION95.81
1.79-1.930.25221420.22047052X-RAY DIFFRACTION99.92
1.93-2.120.24841500.19017075X-RAY DIFFRACTION99.97
2.12-2.430.22481410.18827090X-RAY DIFFRACTION99.93
2.43-3.060.23411450.20237115X-RAY DIFFRACTION99.74
3.06-22.650.22981390.19086633X-RAY DIFFRACTION92.24
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)
15.268087959530.2395947513051.817144263381.90764046074-0.3354086459254.926780365420.170459064658-0.151578601668-0.425265433239-0.130102623916-0.1222803198130.006533465495310.4313350000040.0156856432125-0.0679847178260.180467012422-0.0366247302940.01866948760290.133280861696-0.0123383462330.17175155321112.6351113894-9.0983765435521.3152054359
28.17883150609-6.012848683376.528325916728.42962403326-6.21170352198.194394345590.177305375135-0.381324820749-0.422343601654-0.1782829823060.01526091940070.7107361954180.215343679935-0.575710788908-0.3991775830620.181179354793-0.06605034922070.0212782394350.272352595266-0.08641206288660.2710520512560.226995700714-7.4696854213822.4539041839
32.48050159585-0.5698541469741.155667580352.10808501472-0.7604001510734.0625495593-0.137637604825-0.1063578866970.7394532828370.0413347765537-0.2540456881290.3394374447-0.5184596205950.05700749410130.3122079281140.243516169446-0.0478431422182-0.02342473889490.227887550331-0.1078535763190.3927158049766.740184716117.120038312523.136649633
44.10476177076-1.639042659861.625222078033.55737149505-0.9450154872864.37455016909-0.155716804082-0.5646230692740.8454529831550.222379528146-0.1584450137060.350022201403-0.43003169171-0.5482072318890.312247341810.29370726232-0.02624959836660.03256322790930.415685938271-0.2495118467340.533338677557-0.8973311480698.4578634821129.8379303192
54.576302521011.49637526419-1.912287807061.74091499224-0.730019933963.207943258310.0619628265501-0.1504290163860.161810235783-0.058901132614-0.0496723914021-0.0145461736668-0.015822535830.06586254926360.06419766503520.154053199572-0.00586307114575-0.03007052404850.0986158649604-0.01680603000360.13680133214934.75875285164.2873779442818.7018118294
64.96584096161.83656073578-0.2292666482472.58803614775-0.2713590365034.92836118556-0.0167613647861-0.0533412049170.37705212954-0.0766185904071-0.00684062672797-0.110475909474-0.3076232796980.5338312535720.03801030957070.1475881753180.004697176149130.007160764498380.125286994967-0.00330482424010.19411908122444.247853910910.571934799515.5467499711
72.01049968560.7167704884383.904750012034.8597360678-1.250167573289.12878666996-0.5061590824520.5455243291870.271516884423-0.07289704263910.6128198665210.341079500223-0.795929681104-0.4454045326660.02593749224020.315746375436-0.08104045028140.008044400605550.2999671235760.07866033581210.23966264504125.20140166810.9621040708095.14628597317
80.347368822999-1.46677692755-0.9381841940436.481142501855.033027514976.93944415586-0.277470449856-0.670616603106-1.258309037380.70715168850.507103097729-1.258119026591.347179361771.63242958956-0.1597195456770.3554539296530.0938799760088-0.01131634703940.353537948295-0.07500735047760.59181952329841.865976445-10.10954162168.99443610344
93.17640638343-4.014963279641.519224550445.71489947832-2.048790532164.138974580570.1266143447780.451974654204-0.158002754502-0.434183754579-0.127304695658-0.08421960973970.1151031607940.0211526983360.006178869573490.181553251484-0.07332437069440.0198420270770.18833299086-0.0145090844780.22075711164927.1440698406-4.598172646768.11970483057
102.58118294497-4.47222661128-4.61172195029.421843046757.079924333569.35095941101-0.05639883618160.610045199115-0.0413661397083-0.4849753571530.0551211644302-0.0259701333143-0.0735054598648-0.4122017315620.3197449940410.281702004672-0.104017272558-0.009639678114430.30718741585-0.02080215177560.21626366230318.5738274184-6.650115322562.1056365632
114.59463708723-1.01310511077-3.384474238436.26071793357-4.666700020957.347321119380.1721609385090.927565951259-0.552409989619-1.179636229030.437351019481-0.02861281510860.575699851842-0.3177704795950.1689060577230.472910749835-0.0730770443378-0.02240422590730.476467911478-0.2163222077830.34126143801228.1415943828-14.4076559089-5.18064134847
124.26190853914-3.5114677318-0.4696476376675.805707224164.053779108344.70153415536-0.2772060138510.140799083567-1.30909153195-0.3164802856430.3225131294520.1551133804370.6392625778040.256790949862-0.3115804184390.414018284454-0.1020029990330.04419512816180.293016042109-0.02590469992820.48365158387524.4227773007-15.72644405765.99843113656
138.72527249477-3.42088506214-2.669358156873.669142165171.386506577933.03074976315-0.2278234637610.0363632499350.0376208210049-0.04105595525250.229613665225-0.3535468964050.2440942589480.134106539216-0.1044210558080.208722162887-0.0618914130764-0.00975516738990.14652292471-0.004641824637560.1632261549525.2684424404-5.62822055718.78850290553
143.53444939446-2.103852129943.303237608193.05532929104-2.633082167743.649665611760.04423737529540.984297548927-0.373349082656-0.6688740651610.2719851590510.3861844521010.174514837194-0.382406519102-0.1174110646460.375198873134-0.0964160366127-0.03957080446670.5079833672320.02947858936150.21435547071719.5487175068-3.01193095758-2.93064046612
153.293150742912.471972100693.678397839324.35000358217-0.08320129003047.76527215832-0.4680886596270.754340397742-0.280767423317-0.5429791405940.68491146608-0.235934005544-0.1092097622880.554460119285-0.1197248184030.358510705374-0.09817580784110.109084016560.303151472887-0.07257272473980.18794055031834.1466812921-1.82341766947-0.116944588221
167.80700977339-2.486228629753.803957149557.65594401309-1.038223011711.87295789562-0.0337764580677-0.2119839616340.692663622161-0.125906925742-0.2300023541060.720560516169-0.396065622767-0.459244141826-0.05052181056230.210381753599-0.03178440545930.07669946172650.37576476496-0.1280359368360.2248554914250.2396355879250.73550698461825.1341609345
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 56 )AA1 - 561 - 58
22chain 'A' and (resid 57 through 84 )AA57 - 8459 - 86
33chain 'A' and (resid 85 through 137 )AA85 - 13787 - 139
44chain 'A' and (resid 138 through 162 )AA138 - 162140 - 164
55chain 'A' and (resid 163 through 240 )AA163 - 240165 - 242
66chain 'A' and (resid 241 through 275 )AA241 - 275243 - 277
77chain 'B' and (resid 3 through 11 )BC3 - 111 - 9
88chain 'B' and (resid 12 through 19 )BC12 - 1910 - 17
99chain 'B' and (resid 20 through 30 )BC20 - 3018 - 28
1010chain 'B' and (resid 31 through 41 )BC31 - 4129 - 39
1111chain 'B' and (resid 42 through 46 )BC42 - 4640 - 44
1212chain 'B' and (resid 47 through 51 )BC47 - 5145 - 49
1313chain 'B' and (resid 52 through 77 )BC52 - 7750 - 75
1414chain 'B' and (resid 78 through 90 )BC78 - 9076 - 88
1515chain 'B' and (resid 91 through 99 )BC91 - 9989 - 97
1616chain 'C' and (resid 1 through 7 )CD1 - 71 - 7

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