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- PDB-6dig: Crystal structure of DQA1*01:02/DQB1*06:02 in complex with a hypo... -

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Basic information

Entry
Database: PDB / ID: 6dig
TitleCrystal structure of DQA1*01:02/DQB1*06:02 in complex with a hypocretin peptide
Components
  • 13-mer peptide: ALA-GLY-ASN-HIS-ALA-ALA-GLY-ILE-LEU-THR-LEU-GLY-LYS
  • HLA class II histocompatibility antigen, DQ beta 1 chain
  • MHC class II HLA-DQ-alpha chain
KeywordsIMMUNE SYSTEM / MHC Class II HLA
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
Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / 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 ...Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / 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 / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MHC class II HLA-DQ-alpha chain / HLA class II histocompatibility antigen, DQ beta 1 chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBirtley, J.R. / Stern, L.J. / Mellins, E.D. / Jiang, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)5 U01 AI101990 United States
CitationJournal: Nat Commun / Year: 2019
Title: In vivo clonal expansion and phenotypes of hypocretin-specific CD4+T cells in narcolepsy patients and controls.
Authors: Jiang, W. / Birtley, J.R. / Hung, S.C. / Wang, W. / Chiou, S.H. / Macaubas, C. / Kornum, B. / Tian, L. / Huang, H. / Adler, L. / Weaver, G. / Lu, L. / Ilstad-Minnihan, A. / Somasundaram, S. ...Authors: Jiang, W. / Birtley, J.R. / Hung, S.C. / Wang, W. / Chiou, S.H. / Macaubas, C. / Kornum, B. / Tian, L. / Huang, H. / Adler, L. / Weaver, G. / Lu, L. / Ilstad-Minnihan, A. / Somasundaram, S. / Ayyangar, S. / Davis, M.M. / Stern, L.J. / Mellins, E.D.
History
DepositionMay 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _struct.title
Revision 1.2Dec 4, 2019Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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 HLA-DQ-alpha chain
B: HLA class II histocompatibility antigen, DQ beta 1 chain
C: 13-mer peptide: ALA-GLY-ASN-HIS-ALA-ALA-GLY-ILE-LEU-THR-LEU-GLY-LYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8107
Polymers48,8213
Non-polymers9894
Water4,900272
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8380 Å2
ΔGint-22 kcal/mol
Surface area18350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.666, 89.596, 90.928
Angle α, β, γ (deg.)90.000, 99.517, 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

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Protein , 2 types, 2 molecules AB

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


Mass: 23205.865 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: 24391.131 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 , 1 types, 1 molecules C

#3: Protein/peptide 13-mer peptide: ALA-GLY-ASN-HIS-ALA-ALA-GLY-ILE-LEU-THR-LEU-GLY-LYS


Mass: 1224.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Drosophila melanogaster (fruit fly)

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Sugars , 2 types, 3 molecules

#4: 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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
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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Non-polymers , 2 types, 273 molecules

#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 2.62 Å3/Da / Density % sol: 53.04 % / Description: Series of long thin plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Protein at 10mg/ml in PBS pH 7.4 mixed 50/50 mix (v/v) with16% PEG8K, 0.1M Mg Acetate, 0.1M glycine pH 4.5

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Data collection

DiffractionMean temperature: 100 K
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: 2→45 Å / Num. obs: 33906 / % possible obs: 99.52 % / Redundancy: 3.8 % / Biso Wilson estimate: 26.49 Å2 / CC1/2: 0.994 / Rrim(I) all: 0.069 / Net I/σ(I): 5.68
Reflection shellResolution: 2→2.072 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 1.22 / Num. unique obs: 12012 / CC1/2: 0.813 / Rrim(I) all: 0.596 / % possible all: 98.88

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Processing

Software
NameVersionClassification
phenix.refine1.13_2998refinement
PHENIX1.13_2998refinement
xia2data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UVQ

1uvq


Resolution: 2→44.84 Å / SU ML: 0.3068 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.6223 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2546 1711 5.05 %
Rwork0.2159 32195 -
obs0.2178 33906 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.25 Å2
Refinement stepCycle: LAST / Resolution: 2→44.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3022 0 64 272 3358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01163190
X-RAY DIFFRACTIONf_angle_d1.34784352
X-RAY DIFFRACTIONf_chiral_restr0.0615477
X-RAY DIFFRACTIONf_plane_restr0.0121561
X-RAY DIFFRACTIONf_dihedral_angle_d5.40472191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.39111300.3772671X-RAY DIFFRACTION99.01
2.06-2.130.36351740.35622661X-RAY DIFFRACTION99.13
2.13-2.20.39231440.31792661X-RAY DIFFRACTION99.61
2.2-2.290.37681410.34482660X-RAY DIFFRACTION99.01
2.29-2.390.31371420.29132661X-RAY DIFFRACTION99.86
2.39-2.520.31841320.2652672X-RAY DIFFRACTION99.61
2.52-2.680.31041300.24072701X-RAY DIFFRACTION99.68
2.68-2.880.29511520.2322676X-RAY DIFFRACTION99.82
2.88-3.170.24931490.20882685X-RAY DIFFRACTION99.86
3.17-3.630.20781410.17772706X-RAY DIFFRACTION99.96
3.63-4.580.19011440.14282718X-RAY DIFFRACTION99.93
4.58-44.850.1741320.15712723X-RAY DIFFRACTION98.99
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)
12.500048028762.239710242330.692288466165.90787214421.129450289695.068428342280.04928816064170.179597605898-0.02447710786690.0356312575695-0.0135157292282-0.222769814996-0.1609367024270.381881039196-0.05483601021380.2384312176340.00886329710987-0.06641680355370.1803613314570.03489553065610.186808792504-26.14650621444.7493228311317.0769451277
23.97526156933-1.21761865236-1.535401371971.474690002491.386528507638.154646603160.01944744791570.188144566433-0.171916730125-0.19371188025-0.250846025950.218754715276-0.0600690796708-0.3023867901050.2533492407410.236790799268-0.038000955981-0.07281649503640.146616035711-0.001600802429930.214725854352-32.5618212683.1628430303211.8900481382
32.9204766542-0.850909621693-1.774178325581.763505846391.070696084756.678113788160.449488901182-0.279373761172-0.215795110251-0.191370474093-0.336300868092-0.1316167423560.2666260429790.485817577062-0.008802234116110.197116475110.130736141612-0.02258361470060.1430556545460.0427741812470.263382435269-20.8640156096-5.7572966175129.5407180483
42.650947715060.0956915011297-0.03798214706551.34832887514-0.5544238325592.62627507505-0.068219754826-0.208602040037-0.344881686832-0.0124578735762-0.06896405775870.01265154230170.6907882387420.2912389015930.1506641615160.3585615691680.0507556331368-0.03420420497680.171305520160.03547674855210.23290361366-25.9568141517-8.4210690944632.4146447267
52.347758556770.675252488678-0.2357259347362.171214345680.914743744474.81962361085-0.1319617086950.137764238310.1034934480560.172338274187-0.000158495549399-0.293750241007-0.4195948258571.033323994970.0662939461380.289674307647-0.0714052690566-0.0844150411520.4558599780790.05418188757840.219196133647-16.62507351077.597070059399.98051426229
64.49830611154-0.570944572641.407046435352.133302615941.35462362091.582839180170.03146241149130.375788639193-0.129692958135-0.180000566314-0.102233908847-0.356665191134-0.05927115011591.483624602230.2165957387580.23108926063-0.05559054111640.01422441699640.713302515070.07900895805710.260530030976-14.42373099675.53211925338-4.11287706829
75.82749449167-0.952781523813-5.163706159633.768484419672.555415761117.558587263640.08047238862420.3472845494670.245819899249-0.342441101609-0.216877797279-0.147718245674-1.60735168393-0.0572392141958-0.03444310198410.670983286317-0.152774015345-0.1440605660340.3293492863510.1076875168110.309954628387-23.238902399817.7262259420.720388958032
81.04761913881-0.7323082260291.046848796631.69210776752-2.018712231732.4585851799-0.247873219132-0.184262627620.470021161670.1170361466680.0912525863496-0.140256749293-1.71308799001-0.0638942451950.06843406913470.695671746275-0.0180040928442-0.1348298361250.21426137196-0.02354144060780.365701286845-28.360976931720.115535546723.7861093942
99.4101124151.031324384314.685204979854.058801424011.613714000252.6573317316-0.309886397856-0.691394767528-0.158708404750.2470267071550.175250470705-0.380573473087-0.353613344111-0.2808144554680.1349590783860.3381874194750.0449316268176-0.04501479399340.260255202794-0.06405582311940.234817090658-18.464021583511.203508157547.15102904
100.810543483038-1.28363984013-1.147334601782.065074406151.817124877331.62589673073-0.410640401304-0.8431782229011.063961386880.0249367576434-0.1475150286910.137807698479-1.29478755958-0.9077482002960.385266075380.6514825824390.114766806736-0.2091569456780.439229208738-0.1821878480840.478057711082-8.0256366137614.028320223152.1182790933
115.73275034722.055018881973.322492414561.638404296942.388930568745.045593548410.389779439189-0.177593046286-0.2381509094360.372033966949-0.0297344962211-0.3266369250790.5976458518730.035704235651-0.2721357671740.2787979321940.00973853575664-0.04895404095370.160544778042-0.03398328127960.20423238527-19.74827791796.7817977221639.0979573117
122.632316743541.404535896411.541266613111.497184701670.01148207087155.31170974997-0.0917393085415-1.000028446080.3044620757570.934405851396-0.111387858205-0.2530670114360.03975599789510.4627006774890.04705334938730.7722888088160.128036392791-0.1624611983560.665309398617-0.156062449390.380985623245-13.923317537513.963556977456.6308727872
134.73410578528-0.989293652091.007152015182.49255991844-1.884357543463.10422039369-0.377747710571-0.6112156184110.2363905796250.7942644336830.0923322050108-0.0938020850796-1.070691472530.1324511266340.2650205921830.5748624689470.051353552813-0.05196835612990.374591930485-0.116001507710.23971257005-21.545586705618.249590806151.4584065062
141.841674180021.775609233060.8680833891754.09961187023-0.001544718526925.58331555068-0.02679692678120.4314155763620.1710927968470.293614633735-0.0613203128145-0.202960427875-0.3532898992290.4064430702360.1794639506340.2312688920320.0210580277739-0.1064975826670.2607335881260.05277985343950.203841308614-27.15967997738.438913914154.53448199662
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 79 )
3X-RAY DIFFRACTION3chain 'A' and (resid 80 through 104 )
4X-RAY DIFFRACTION4chain 'A' and (resid 105 through 183 )
5X-RAY DIFFRACTION5chain 'B' and (resid 3 through 51 )
6X-RAY DIFFRACTION6chain 'B' and (resid 52 through 64 )
7X-RAY DIFFRACTION7chain 'B' and (resid 65 through 77 )
8X-RAY DIFFRACTION8chain 'B' and (resid 78 through 97 )
9X-RAY DIFFRACTION9chain 'B' and (resid 98 through 133 )
10X-RAY DIFFRACTION10chain 'B' and (resid 134 through 144 )
11X-RAY DIFFRACTION11chain 'B' and (resid 145 through 162 )
12X-RAY DIFFRACTION12chain 'B' and (resid 163 through 177 )
13X-RAY DIFFRACTION13chain 'B' and (resid 178 through 190 )
14X-RAY DIFFRACTION14chain 'C' and (resid 1 through 13 )

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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