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- PDB-6t3y: Improved High Resolution Structure of MHC Class II complex -

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Basic information

Entry
Database: PDB / ID: 6t3y
TitleImproved High Resolution Structure of MHC Class II complex
Components
  • MHC class II alpha chain
  • MHC class II beta chain 2
KeywordsIMMUNE SYSTEM / MHC II / Immune Synapse
Function / homology
Function and homology information


antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / antigen processing and presentation / MHC class II protein complex / adaptive immune response / immune response
Similarity search - Function
MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / 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
ACETATE ION / MHC class II beta chain 2 / MHC class II alpha chain
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHalabi, S. / Moncrieffe, M.C. / Kaufman, J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust110106/Z/15/Z United Kingdom
CitationJournal: Plos Biol. / Year: 2021
Title: The dominantly expressed class II molecule from a resistant MHC haplotype presents only a few Marek's disease virus peptides by using an unprecedented binding motif.
Authors: Halabi, S. / Ghosh, M. / Stevanovic, S. / Rammensee, H.G. / Bertzbach, L.D. / Kaufer, B.B. / Moncrieffe, M.C. / Kaspers, B. / Hartle, S. / Kaufman, J.
History
DepositionOct 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2021Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class II alpha chain
B: MHC class II beta chain 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2486
Polymers45,9132
Non-polymers3354
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-35 kcal/mol
Surface area17830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.153, 60.002, 51.713
Angle α, β, γ (deg.)90.000, 108.750, 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
Components on special symmetry positions
IDModelComponents
11A-336-

HOH

21A-447-

HOH

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Components

#1: Protein MHC class II alpha chain / MHC class II antigen alpha chain


Mass: 21033.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: B-LA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q4U5Z6
#2: Protein MHC class II beta chain 2


Mass: 24879.623 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: BLB2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: B5BSA0
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 317 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.47 Å3/Da / Density % sol: 50.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2 M Na Acetate 0.1 M TRIS 30 %w/v PEG 4K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.7→26.85 Å / Num. obs: 294236 / % possible obs: 99.75 % / Redundancy: 6 % / Biso Wilson estimate: 21.85 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.023 / Rrim(I) all: 0.057 / Net I/σ(I): 18.4
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 6 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 29547 / CC1/2: 0.88 / Rpim(I) all: 0.31 / Rrim(I) all: 0.78 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.17rc4_3626refinement
PHENIX1.17rc4_3626refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4x5w

4x5w


Resolution: 1.7→26.85 Å / SU ML: 0.1669 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.7665
RfactorNum. reflection% reflection
Rfree0.2021 4990 10.1 %
Rwork0.1715 --
obs0.1747 49389 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 35.61 Å2
Refinement stepCycle: LAST / Resolution: 1.7→26.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3027 0 22 317 3366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01273129
X-RAY DIFFRACTIONf_angle_d1.12174253
X-RAY DIFFRACTIONf_chiral_restr0.0759444
X-RAY DIFFRACTIONf_plane_restr0.0085560
X-RAY DIFFRACTIONf_dihedral_angle_d6.6887420
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.35351580.30831391X-RAY DIFFRACTION92.31
1.72-1.740.3141660.27471443X-RAY DIFFRACTION99.69
1.74-1.760.2991500.26351485X-RAY DIFFRACTION99.33
1.76-1.780.27431520.24421473X-RAY DIFFRACTION99.82
1.78-1.80.23541570.24111508X-RAY DIFFRACTION99.82
1.8-1.830.26281800.22071438X-RAY DIFFRACTION99.63
1.83-1.850.26451500.22641530X-RAY DIFFRACTION99.76
1.85-1.880.23791730.20781454X-RAY DIFFRACTION99.94
1.88-1.910.23791640.20371456X-RAY DIFFRACTION99.57
1.91-1.940.23271770.18791476X-RAY DIFFRACTION99.94
1.94-1.980.24431800.18611458X-RAY DIFFRACTION99.45
1.98-2.010.17462010.1721421X-RAY DIFFRACTION99.57
2.01-2.050.1971660.17121464X-RAY DIFFRACTION99.63
2.05-2.090.22041840.16251469X-RAY DIFFRACTION99.7
2.09-2.140.19761840.16221491X-RAY DIFFRACTION99.94
2.14-2.190.19431670.15771463X-RAY DIFFRACTION99.94
2.19-2.240.19251390.16011515X-RAY DIFFRACTION99.7
2.24-2.30.2141630.16581462X-RAY DIFFRACTION99.82
2.3-2.370.23241690.16741491X-RAY DIFFRACTION99.88
2.37-2.450.22731630.17771485X-RAY DIFFRACTION99.94
2.45-2.530.21881480.16711503X-RAY DIFFRACTION99.88
2.53-2.630.2041460.17421504X-RAY DIFFRACTION99.88
2.63-2.750.21071650.16811505X-RAY DIFFRACTION100
2.75-2.90.19121610.1721489X-RAY DIFFRACTION99.94
2.9-3.080.22221500.17211500X-RAY DIFFRACTION99.88
3.08-3.320.18141570.16651517X-RAY DIFFRACTION99.88
3.32-3.650.16471820.14991464X-RAY DIFFRACTION99.88
3.65-4.180.16241640.14381512X-RAY DIFFRACTION99.76
4.18-5.260.15511930.14131495X-RAY DIFFRACTION99.88
5.26-26.850.24481810.19371537X-RAY DIFFRACTION99.65
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)
11.17386371001-0.413845592194-0.3095349689433.22222261007-0.08063242346330.760185505721-0.0468953099270.01445353338560.104294738602-0.0223371668350.06776132235610.051523563608-0.0266109272443-0.0757855234945-0.08296205980360.183616505467-0.0165852315248-0.002956723217540.2726908194540.01913447575040.16346275996714.408766790112.5203153229-10.6063361061
22.01691283806-0.8150480451190.5367108016570.9185661249990.380642497771.878504614090.06483942206140.2306096165470.0481209682292-0.13308532267-0.02862341176-0.0354636623136-0.01896278999290.413011296821-0.02580323460.158973924903-0.01058020581830.007582768972130.2975057798520.01717873529020.16581886228824.26734155942.80191234174-13.4397366964
31.5926607502-1.62304275811-0.9336433941791.98894936021.142848958980.8495864975550.01105485062260.06280918999530.0607036172214-0.09716994602820.06599820382920.00958251314624-0.1138342656260.00856809774601-0.02271650027770.2070940550690.000968148833434-0.02016112673480.3907857209520.01028038371780.2169273303847.7815279094715.4182994496-19.7717916688
42.647936240950.02549778178050.5318374404392.0214336805-0.6763361056671.67185834807-0.114744690352-0.383037121347-0.002751629039920.1822875921870.1472407681420.0601767970872-0.177279856569-0.144066700541-0.0624252213020.225574300522-0.0202908554369-0.02502723398030.312458140517-0.06701215419080.21431698204722.800604551617.76898305152.31997515431
50.9304658303120.637342997420.6102899671450.5719958525130.1781439936750.758115950794-0.10785941370.07507526543070.02212330644540.04126516470520.0961505684299-0.126194853011-0.09791730057030.1186738148630.01462816663130.189283410477-0.0242040750301-0.009753902797060.329348280732-0.01073631271430.23560620186426.269609628416.6878152699-1.03408522097
62.570653672580.6369332498990.7229954528511.013968195160.5017435316831.0749256005-0.0138484917722-0.188240974060.02288356501340.09895820877180.0150004144739-0.0454282937415-0.08705162446260.2439846837760.03290411825390.199359828634-0.044376882806-0.02770044821720.351052610205-0.01730633270630.25882945457435.317180349217.30474990983.35647485699
73.86011854601-1.132561384111.704551173261.37944545978-0.02930470809762.05742333765-0.795884616601-0.8083984049360.896150072890.4440345450340.127243082603-0.401188322052-0.478048366374-0.468212481640.4672091376020.291790635172-0.0173156055921-0.05195241086140.415903406666-0.06548079211460.35005576492229.847459695422.94840234316.30414822763
81.4178580189-0.01331015805750.1103033441041.494293645840.2528731996161.01496105821-0.0186010260697-0.0251325916908-0.05381020345810.138022142535-0.1039689799250.155311355260.0206210808819-0.1533490692160.09325096584720.167709248102-0.002424735641520.003018736420290.302446328367-0.008933126803620.1729855637646.351531371895.5203123572-10.5686779021
91.10808763123-0.4467667197670.1830627142070.6873115756480.0008321620463490.867222499358-0.0109149799089-0.0842803442669-0.062150119750.0514976875321-0.05015562281480.04243737525490.0918210074725-0.1226584642170.05326405645960.207830707514-0.03685034015690.02369608428550.3392602902520.006332380322510.2285631933038.24030489851.52755544265-5.91580592672
100.8138910626910.3211686436110.6673515809451.95325636844-0.3119936661722.66807309938-0.0635434965287-0.657745816586-0.1195381735550.608268434351-0.0442165096999-0.1921540204040.2292897502310.04237191708040.06469474590950.4275744611470.0684770269316-0.0371874171310.6471824048450.06628421604840.26321875757929.0394318362-2.4191995410517.8767053977
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 60 )
3X-RAY DIFFRACTION3chain 'A' and (resid 61 through 81 )
4X-RAY DIFFRACTION4chain 'A' and (resid 82 through 106 )
5X-RAY DIFFRACTION5chain 'A' and (resid 107 through 151 )
6X-RAY DIFFRACTION6chain 'A' and (resid 152 through 172 )
7X-RAY DIFFRACTION7chain 'A' and (resid 173 through 186 )
8X-RAY DIFFRACTION8chain 'B' and (resid 6 through 67 )
9X-RAY DIFFRACTION9chain 'B' and (resid 68 through 148 )
10X-RAY DIFFRACTION10chain 'B' and (resid 149 through 224 )

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