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- PDB-7kei: DQA1*01:02/DQB1*06:02 in complex with a hemagglutinin peptide fro... -

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Basic information

Entry
Database: PDB / ID: 7kei
TitleDQA1*01:02/DQB1*06:02 in complex with a hemagglutinin peptide from the H1N1 pandemic flu virus.
Components
  • HA peptide from 2009 H1N1 pandemic flu virus.
  • HLA class II histocompatibility antigen, DQ beta 1 chain
  • MHC class II HLA-DQ-alpha chain
KeywordsIMMUNE SYSTEM / MHC class II / antigen presentation / flu virus / peptide.
Function / homology
Function and homology information


antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / MHC class II protein complex / adaptive immune response / endosome membrane / lysosomal membrane
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 ...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
MHC class II HLA-DQ-alpha chain / MHC class II antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
H1N1 subtype (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsBirtley, J.R. / Stern, L.J. / Mellins, E.D. / Jiang, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5 U01 AI101990 United States
CitationJournal: To Be Published
Title: Crystal structure of DQA1*01:02/DQB1*06:02 in complex with a flu peptide.
Authors: Birtley, J.R. / Stern, L.J. / Mellins, E.D. / Jiang, W.
History
DepositionOct 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: 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: MHC class II HLA-DQ-alpha chain
B: HLA class II histocompatibility antigen, DQ beta 1 chain
C: HA peptide from 2009 H1N1 pandemic flu virus.
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9216
Polymers49,5433
Non-polymers1,3783
Water10,359575
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Assembly confirmed by gel filtration.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9180 Å2
ΔGint-13 kcal/mol
Surface area18700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.310, 58.255, 67.507
Angle α, β, γ (deg.)90.000, 96.080, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein MHC class II HLA-DQ-alpha chain


Mass: 23106.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQA1 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q30066
#2: Protein HLA class II histocompatibility antigen, DQ beta 1 chain / MHC class II antigen


Mass: 24075.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQB1 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q5SU54

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Protein/peptide / Non-polymers , 2 types, 576 molecules C

#3: Protein/peptide HA peptide from 2009 H1N1 pandemic flu virus.


Mass: 2360.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) H1N1 subtype (virus) / Production host: Drosophila melanogaster (fruit fly)
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 575 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 3 types, 3 molecules

#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#6: 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

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Details

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: 2.34 Å3/Da / Density % sol: 47.45 % / Description: Thick rods.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 35% PEG MME 550, 0.2M MgCl2, 0.1M MES pH 6.5.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Feb 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.75→27.93 Å / Num. obs: 46303 / % possible obs: 99.42 % / Redundancy: 3.7 % / Biso Wilson estimate: 16.04 Å2 / Rmerge(I) obs: 0.08291 / Net I/σ(I): 8.41
Reflection shellResolution: 1.75→1.813 Å / Num. unique obs: 4600 / CC1/2: 0.924

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UVQ

1uvq


Resolution: 1.75→27.93 Å / SU ML: 0.2269 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.7072
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2333 2427 5.27 %
Rwork0.2031 43640 -
obs0.2047 46067 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.89 Å2
Refinement stepCycle: LAST / Resolution: 1.75→27.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3061 0 91 575 3727
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01253274
X-RAY DIFFRACTIONf_angle_d0.94034466
X-RAY DIFFRACTIONf_chiral_restr0.0678500
X-RAY DIFFRACTIONf_plane_restr0.0071576
X-RAY DIFFRACTIONf_dihedral_angle_d10.5663477
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.790.31681440.31472528X-RAY DIFFRACTION98.63
1.79-1.820.32811600.2942499X-RAY DIFFRACTION98.59
1.82-1.870.3131480.30552538X-RAY DIFFRACTION98.68
1.87-1.910.37141610.31222511X-RAY DIFFRACTION99.4
1.91-1.970.30651430.25572555X-RAY DIFFRACTION99.63
1.97-2.020.2731370.23462585X-RAY DIFFRACTION99.96
2.02-2.090.25111270.21892574X-RAY DIFFRACTION99.96
2.09-2.160.26011070.21722611X-RAY DIFFRACTION99.96
2.16-2.250.25181290.21832593X-RAY DIFFRACTION99.71
2.25-2.350.27311560.23662524X-RAY DIFFRACTION99.22
2.35-2.480.28891550.22742538X-RAY DIFFRACTION99.08
2.48-2.630.25571200.20862600X-RAY DIFFRACTION99.52
2.63-2.830.23091360.19982590X-RAY DIFFRACTION99.67
2.83-3.120.21911170.18332596X-RAY DIFFRACTION99.93
3.12-3.570.19741490.14982604X-RAY DIFFRACTION99.96
3.57-4.490.16081820.14612579X-RAY DIFFRACTION99.78
4.49-27.930.19371560.18482615X-RAY DIFFRACTION99.07
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)
10.2461861980140.391242169397-0.1058533399040.252178680785-0.06701720599720.06909004280450.0167449930523-0.0997185380788-0.0627316864302-0.0344356112691-0.0214936520133-0.0266499140452-0.01679371754760.0463085489762-0.001002352087090.1020002093110.01097391523230.01409869673250.0698897973210.002805307357920.084878934769-13.5175765057-67.4315253114147.753315488
20.3702217639060.200412407523-0.1319566721170.2923848398390.1634392958070.1338959195080.01147534615980.000457966538015-0.097726997604-0.0724559348017-0.0564756283707-0.09158969118350.1080912394680.0734601321828-0.01231748176140.1316440763910.00368898635737-0.004376372558530.03706640021150.03252024329710.0770232328595-13.6919871686-73.0194295109142.601358199
30.1183214482430.01742282487330.05517838297840.210367445058-0.06084892859520.4214141593-0.00656040912681-0.0379515341189-0.00759790701133-0.00795934947599-0.075853945448-0.0008828818299160.02766098864720.0902299170887-0.1030134531870.0728552274650.003917434343410.01241771124850.09986510108750.03156869376350.1247572225422.51864562506-59.680602123145.2571386
40.121326705180.00967400726923-0.1356494661220.09890881290930.01757853649030.1291428908220.0214764854880.0906016021014-0.150668995779-0.160266618856-0.103897159117-0.0337390072839-0.008915708028130.550102153388-0.04084056905340.0163754024635-0.04722560606120.05527727861850.2452137187870.0886133886050.1351940583038.81969034114-57.1417313894141.500615199
50.3732123772680.212496281782-0.0007242278108230.426239455533-0.1229079516160.2519015876740.0487797324911-0.0107180361940.0355909522455-0.0864479303159-0.04134908317190.09055865003650.0114424564199-0.06264212475490.02825292068460.07732489560970.02210065503930.004631531285580.0683603366762-0.01278101413320.0969308472208-26.1941215631-64.9392195161142.427787623
60.01631327291860.0100008225469-0.001825644679350.0174733513903-0.02445326234990.02651235172790.0612068320412-0.1211040207640.0216442519272-0.1009156822390.07545567751630.1439839036680.201804638057-0.05092680892880.005832180993040.114934342801-0.02834240914840.01635887997160.1478320676790.02176086789020.157674959895-32.8075562754-73.9138598957151.350414226
70.0335951249677-0.04492683439310.02715492223270.07483169463850.0266189598108-0.01900900335680.0703121434717-0.164512415810.02701128778560.148099505885-0.05836380690680.01422772761270.0581438090856-0.0297333840104-0.00186392679530.163943437277-0.02618297879240.009459725946020.195475710585-0.004741424504130.083029888181-14.8432026409-65.0199695483164.46154869
80.162386244607-0.02056264114360.03933999373750.1495405929370.2560796343730.193352867878-0.00791643061967-0.05410608783170.033610372982-0.03258318213210.0168913095395-0.0117334949217-0.01592720959990.0622034168998-0.006438719581860.126714796966-0.02675312909460.001886448941460.153465045314-0.01609456706730.1003927379570.832723090478-42.1240912587162.640324695
90.0008359841497090.02097730462570.00521498320266-0.0004009386208150.01295599993550.0425227244535-0.0279966656327-0.05118201627380.02142385521680.3673753707760.167318680405-0.1582233860340.2351191477570.2953820390410.001499434857850.20633008169-0.0191532035835-0.007224179385580.234349653575-0.06171045129960.1631643119722.36141426922-45.0684437426171.819979778
100.0057257311246-0.00252997565191-0.000389267612280.00311171233861-0.01007600810110.00677031763384-0.00877565539545-0.0299369710111-0.06759066123050.1463060802610.0283293303341-0.04868212613630.0414461565107-0.009024949783210.0009751855455330.12057239317-0.0323100830653-0.008765756492540.1887815386760.1152653608280.0783524872388-17.8690247329-76.9363981801158.06620399
110.004329531322910.0118228818301-0.003063798328460.0336573146879-0.008695894929040.002718748624490.136283130569-0.00768722110837-0.02842399477830.0026557979553-0.01337281053330.164990844281-0.0571160235660.00991442196560.04793791258450.242864112533-0.0300944714407-0.0133115012717-0.114653896071-0.20513678525-0.108702242071-25.3833900554-75.1167862526143.321225812
121.77752411774E-5-2.11347036437E-60.006050387618440.003363228108310.004827551401880.0672792662584-0.0830772264242-0.0236069744770.0113809432647-0.00935188953109-0.0310486066768-0.013484829141-0.03586383711660.0169698416803-2.4603243421E-50.178443441415-0.0194646556352-0.03401247834790.200574990157-0.0382352521370.205053138896-30.2198633632-75.6307886214130.558502416
130.04034105864540.00464540154220.002014517752780.0210233276207-0.01088065435560.01137021479340.0336038578478-0.0150474496872-0.05165523336860.02310288241960.0115934609982-0.02172979234470.05677839777980.04015455969690.0151620041370.399885592268-0.0453124381042-0.1089726898550.4119367965540.01425773345140.0565933518047-23.78551021-69.42815539118.345173969
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 38 )AA2 - 381 - 40
22chain 'A' and (resid 39 through 90 )AA39 - 9041 - 92
33chain 'A' and (resid 91 through 149 )AA91 - 14993 - 156
44chain 'A' and (resid 150 through 183 )AA150 - 183157 - 190
55chain 'B' and (resid 2 through 64 )BB2 - 641 - 63
66chain 'B' and (resid 65 through 77 )BB65 - 7764 - 76
77chain 'B' and (resid 78 through 97 )BB78 - 9777 - 99
88chain 'B' and (resid 98 through 177 )BB98 - 177100 - 174
99chain 'B' and (resid 178 through 189 )BB178 - 189175 - 186
1010chain 'C' and (resid 3 through 7 )CC3 - 71 - 5
1111chain 'C' and (resid 8 through 12 )CC8 - 126 - 10
1212chain 'C' and (resid 13 through 17 )CC13 - 1711 - 15
1313chain 'C' and (resid 18 through 22 )CC18 - 2216 - 20

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