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- PDB-5ksv: Crystal structure of HLA-DQ2.5-CLIP2 -

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Basic information

Entry
Database: PDB / ID: 5ksv
TitleCrystal structure of HLA-DQ2.5-CLIP2
Components
  • HLA class II histocompatibility antigen gamma chain
  • MHC class II HLA-DQ-alpha chain
  • MHC class II HLA-DQ-beta-1
KeywordsIMMUNE SYSTEM / HLA-DQ2.5 / CLIP2
Function / homology
Function and homology information


negative regulation of peptide secretion / macrophage migration inhibitory factor signaling pathway / NOS2-CD74 complex / MHC class II protein binding, via antigen binding groove / antigen processing and presentation of endogenous antigen / positive regulation of dendritic cell antigen processing and presentation / negative regulation of T cell differentiation / macrophage migration inhibitory factor binding / positive regulation of macrophage migration inhibitory factor signaling pathway / protein trimerization ...negative regulation of peptide secretion / macrophage migration inhibitory factor signaling pathway / NOS2-CD74 complex / MHC class II protein binding, via antigen binding groove / antigen processing and presentation of endogenous antigen / positive regulation of dendritic cell antigen processing and presentation / negative regulation of T cell differentiation / macrophage migration inhibitory factor binding / positive regulation of macrophage migration inhibitory factor signaling pathway / protein trimerization / macrophage migration inhibitory factor receptor complex / positive regulation of cytokine-mediated signaling pathway / T cell activation involved in immune response / positive regulation of type 2 immune response / T cell selection / negative thymic T cell selection / positive regulation of prostaglandin biosynthetic process / negative regulation of viral entry into host cell / MHC class II receptor activity / MHC class II protein binding / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / negative regulation of mature B cell apoptotic process / positive thymic T cell selection / positive regulation of monocyte differentiation / CD4 receptor binding / positive regulation of kinase activity / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of neutrophil chemotaxis / vacuole / positive regulation of macrophage cytokine production / prostaglandin biosynthetic process / positive regulation of T cell differentiation / cytokine receptor activity / regulation of macrophage activation / transport vesicle membrane / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / nitric-oxide synthase binding / cytokine binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / response to type II interferon / antigen processing and presentation / negative regulation of DNA damage response, signal transduction by p53 class mediator / chaperone cofactor-dependent protein refolding / Generation of second messenger molecules / PD-1 signaling / immunoglobulin mediated immune response / positive regulation of chemokine production / positive regulation of B cell proliferation / protein folding chaperone / MHC class II antigen presentation / multivesicular body / negative regulation of cell migration / lysosomal lumen / trans-Golgi network membrane / positive regulation of interleukin-8 production / lumenal side of endoplasmic reticulum membrane / Cell surface interactions at the vascular wall / intracellular protein transport / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / endocytic vesicle membrane / positive regulation of interleukin-6 production / positive regulation of peptidyl-tyrosine phosphorylation / Interferon gamma signaling / positive regulation of immune response / positive regulation of fibroblast proliferation / late endosome / Downstream TCR signaling / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / amyloid-beta binding / protein-containing complex assembly / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / positive regulation of viral entry into host cell / positive regulation of ERK1 and ERK2 cascade / lysosome / protein stabilization / endosome membrane / positive regulation of protein phosphorylation / immune response / lysosomal membrane / external side of plasma membrane / Golgi membrane / positive regulation of gene expression / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / cell surface / protein-containing complex / extracellular exosome / identical protein binding / membrane / nucleus
Similarity search - Function
MHC class II-associated invariant chain, trimerisation / MHC class II-associated invariant chain/CLIP, MHC II-interacting / MHC class II-associated invariant chain / MHC class II-associated invariant chain, trimerisation domain superfamily / HLA class II histocompatibility antigen, gamma subunit / Class II MHC-associated invariant chain trimerisation domain / CLIP, MHC2 interacting / Thyroglobulin type-1 repeat signature. / Thyroglobulin type-1 / Thyroglobulin type-1 superfamily ...MHC class II-associated invariant chain, trimerisation / MHC class II-associated invariant chain/CLIP, MHC II-interacting / MHC class II-associated invariant chain / MHC class II-associated invariant chain, trimerisation domain superfamily / HLA class II histocompatibility antigen, gamma subunit / Class II MHC-associated invariant chain trimerisation domain / CLIP, MHC2 interacting / Thyroglobulin type-1 repeat signature. / Thyroglobulin type-1 / Thyroglobulin type-1 superfamily / Thyroglobulin type-1 repeat / Thyroglobulin type-1 domain profile. / Thyroglobulin type I repeats. / 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 / MHC class II HLA-DQ-beta-1 / HLA class II histocompatibility antigen, DQ alpha 1 chain / HLA class II histocompatibility antigen gamma chain / HLA class II histocompatibility antigen DQ beta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.195 Å
AuthorsNguyen, T.B. / Jayaraman, P. / Bergseng, E. / Madhusudhan, M.S. / Kim, C.-Y. / Sollid, L.M.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Unraveling the structural basis for the unusually rich association of human leukocyte antigen DQ2.5 with class-II-associated invariant chain peptides.
Authors: Nguyen, T.B. / Jayaraman, P. / Bergseng, E. / Madhusudhan, M.S. / Kim, C.Y. / Sollid, L.M.
History
DepositionJul 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 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

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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: MHC class II HLA-DQ-beta-1
C: HLA class II histocompatibility antigen gamma chain


Theoretical massNumber of molelcules
Total (without water)47,7663
Polymers47,7663
Non-polymers00
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-43 kcal/mol
Surface area17530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.014, 137.014, 137.014
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11B-386-

HOH

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Components

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


Mass: 22423.109 Da / Num. of mol.: 1 / Fragment: UNP residues 1-193
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQA1 / Production host: unidentified baculovirus / References: UniProt: O19705, UniProt: P01909*PLUS
#2: Protein MHC class II HLA-DQ-beta-1


Mass: 23784.760 Da / Num. of mol.: 1 / Fragment: UNP residues 1-198
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DQB1 / Production host: unidentified baculovirus / References: UniProt: O19712, UniProt: Q5Y7D3*PLUS
#3: Protein/peptide HLA class II histocompatibility antigen gamma chain


Mass: 1557.981 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: unidentified baculovirus / References: UniProt: P04233*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.24 Å3/Da / Density % sol: 45.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M BIS-TRIS, pH 5.5, 22% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 25, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.195→36.62 Å / Num. obs: 21943 / % possible obs: 99.7 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 12.7
Reflection shellResolution: 2.195→2.25 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.037 / Num. measured obs: 1589 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIXdev_1137refinement
HKL-2000data reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S9V

1s9v


Resolution: 2.195→36.619 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.63
RfactorNum. reflection% reflection
Rfree0.2096 1125 5.13 %
Rwork0.1699 --
obs0.172 21938 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.195→36.619 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3003 0 0 175 3178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073082
X-RAY DIFFRACTIONf_angle_d1.1174193
X-RAY DIFFRACTIONf_dihedral_angle_d14.5261123
X-RAY DIFFRACTIONf_chiral_restr0.073470
X-RAY DIFFRACTIONf_plane_restr0.005538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1951-2.2950.29591330.232547X-RAY DIFFRACTION98
2.295-2.4160.29031250.21032597X-RAY DIFFRACTION100
2.416-2.56730.25661410.20562566X-RAY DIFFRACTION100
2.5673-2.76550.29081380.19042599X-RAY DIFFRACTION100
2.7655-3.04360.2591410.18262597X-RAY DIFFRACTION100
3.0436-3.48380.21631510.16232595X-RAY DIFFRACTION100
3.4838-4.3880.1571440.14062616X-RAY DIFFRACTION100
4.388-36.62360.171520.16072696X-RAY DIFFRACTION100
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)
12.23180.6815-0.30331.40350.80161.3025-0.0083-0.0503-0.28950.2039-0.0444-0.29140.28330.2545-0.01260.1620.02860.00490.15990.02880.160914.648347.460517.2593
26.39482.4185-5.43072.3711-2.28527.0204-0.3332-0.92240.02110.4533-0.305-0.35860.21630.96840.37550.14790.0086-0.04860.31220.00740.205325.110954.333621.9086
35.20192.15221.86632.73810.99311.9530.2359-0.520.29020.4602-0.08650.5930.1045-0.4088-0.10260.21240.01830.04980.24880.06590.21553.157342.233526.3873
44.0371-1.838-5.19691.1761.62648.2194-0.23640.3018-0.127-0.31430.19080.08880.2989-0.4205-0.19550.3269-0.19460.24030.077-0.05050.6001-2.019534.05449.8079
52.6371-0.4656-2.24180.78850.68141.9936-0.01950.0606-0.5104-0.1706-0.158-0.09460.360.20320.08090.2790.08650.06910.23550.01360.302120.039737.97523.0503
62.7223-0.22570.06770.614-0.80451.0425-0.38070.5842-0.9073-0.51480.0661-0.18390.55460.13020.20340.45730.06150.16510.3178-0.08940.51621.821931.9941-1.1367
72.19780.2647-0.41630.7615-0.27781.3447-0.0473-0.1592-0.093-0.1715-0.01910.13170.01660.01190.08320.10080.0190.02410.13280.0240.15710.640852.682415.2236
84.36562.42641.61164.67081.97793.0260.2631-1.52550.10770.7695-0.7302-0.06760.2074-0.25640.08720.1698-0.06050.04250.37380.08840.1856-9.390351.219625.284
99.3132.7865-4.14662.5447-1.09495.03160.0864-1.5930.1740.4525-0.30780.0269-0.38320.34480.13780.2886-0.0091-0.04330.4064-0.06720.22951.291462.167127.023
101.2197-0.6294-1.0940.36950.96933.03820.0108-0.11220.0522-0.01340.0681-0.1155-0.05550.3794-0.04220.151-0.0060.02820.15350.00790.149622.656259.85367.0819
111.7041-0.16830.11651.07060.00385.6542-0.08780.0517-0.16840.0402-0.06280.1263-0.04520.42210.13390.08810.00280.03070.15390.02670.187123.086856.1952-11.2696
122.93061.2218-0.77021.7003-0.01910.46720.23650.27150.513-0.1407-0.28350.0826-0.57230.05140.090.21980.00670.01940.39390.0580.295118.73859.7472-21.4826
131.89720.51-0.0980.5204-0.83476.47920.24660.115-0.193-0.01660.1849-0.0090.88140.2378-0.14020.15250.00650.03660.1250.02720.132920.49750.671-6.1005
142.18280.62110.08282.4034-1.68911.2882-0.00780.7280.0858-0.63750.211-0.1408-0.2371-0.57450.01870.2506-0.0009-0.01760.35540.0420.154426.359158.3158-22.0631
152.26710.483-2.00481.4119-1.69586.5210.62280.09330.33110.47950.3410.1235-1.24170.6751.14790.1131-0.13710.12380.35090.02350.143630.471460.7862-13.5865
165.2091.4041-0.7253.2163-0.73041.1267-0.0562-0.2945-0.2240.6124-0.1567-0.274-0.13280.31150.1440.19380.02840.00410.26170.01960.1169.350554.722525.9917
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 46 )
2X-RAY DIFFRACTION2chain 'A' and (resid 47 through 55 )
3X-RAY DIFFRACTION3chain 'A' and (resid 56 through 76 )
4X-RAY DIFFRACTION4chain 'A' and (resid 77 through 87 )
5X-RAY DIFFRACTION5chain 'A' and (resid 88 through 146 )
6X-RAY DIFFRACTION6chain 'A' and (resid 147 through 180 )
7X-RAY DIFFRACTION7chain 'B' and (resid 3 through 51 )
8X-RAY DIFFRACTION8chain 'B' and (resid 52 through 64 )
9X-RAY DIFFRACTION9chain 'B' and (resid 65 through 77 )
10X-RAY DIFFRACTION10chain 'B' and (resid 78 through 104 )
11X-RAY DIFFRACTION11chain 'B' and (resid 113 through 133 )
12X-RAY DIFFRACTION12chain 'B' and (resid 134 through 144 )
13X-RAY DIFFRACTION13chain 'B' and (resid 145 through 163 )
14X-RAY DIFFRACTION14chain 'B' and (resid 164 through 177 )
15X-RAY DIFFRACTION15chain 'B' and (resid 178 through 190 )
16X-RAY DIFFRACTION16chain 'C' and (resid -3 through 9 )

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