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- PDB-3qxa: HLA-DR1 bound with CLIP peptide -

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Basic information

Entry
Database: PDB / ID: 3qxa
TitleHLA-DR1 bound with CLIP peptide
Components
  • HLA class II histocompatibility antigen gamma chain peptide
  • HLA class II histocompatibility antigen, DR alpha chain
  • HLA class II histocompatibility antigen, DRB1-1 beta chain
KeywordsIMMUNE SYSTEM / MHC class II
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 / regulation of interleukin-4 production / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / T cell activation involved in immune response / autolysosome membrane / positive regulation of prostaglandin biosynthetic process / regulation of T-helper cell differentiation / T cell selection / positive regulation of type 2 immune response / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / host-mediated suppression of symbiont invasion / MHC class II receptor activity / negative thymic T cell selection / positive regulation of CD4-positive, alpha-beta T cell activation / 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 regulation of T cell mediated immune response to tumor cell / positive regulation of kinase activity / positive regulation of memory T cell differentiation / CD4 receptor binding / positive regulation of monocyte differentiation / inflammatory response to antigenic stimulus / positive thymic T cell selection / vacuole / cytokine receptor activity / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of neutrophil chemotaxis / prostaglandin biosynthetic process / intermediate filament / positive regulation of macrophage cytokine production / positive regulation of T cell differentiation / T-helper 1 type immune response / regulation of macrophage activation / nitric-oxide synthase binding / transport vesicle membrane / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / antigen processing and presentation / Translocation of ZAP-70 to Immunological synapse / cytokine binding / Phosphorylation of CD3 and TCR zeta chains / negative regulation of DNA damage response, signal transduction by p53 class mediator / polysaccharide binding / negative regulation of type II interferon production / humoral immune response / immunoglobulin mediated immune response / macrophage differentiation / positive regulation of insulin secretion involved in cellular response to glucose stimulus / : / Generation of second messenger molecules / immunological synapse / response to type II interferon / Co-inhibition by PD-1 / epidermis development / detection of bacterium / T cell receptor binding / positive regulation of chemokine production / negative regulation of T cell proliferation / positive regulation of B cell proliferation / multivesicular body / protein folding chaperone / MHC class II antigen presentation / lysosomal lumen / negative regulation of cell migration / 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 / protein tetramerization / peptide antigen assembly with MHC class II protein complex / negative regulation of inflammatory response to antigenic stimulus / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / structural constituent of cytoskeleton / positive regulation of T cell mediated cytotoxicity / positive regulation of interleukin-6 production / positive regulation of T cell activation / cognition / positive regulation of fibroblast proliferation / Interferon gamma signaling / MHC class II protein complex binding / endocytic vesicle membrane
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 ...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 / Roll / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain / HLA class II histocompatibility antigen, DRB1 beta chain / HLA class II histocompatibility antigen gamma chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.712 Å
AuthorsPainter, C.A. / Stern, L.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Conformational lability in the class II MHC 310 helix and adjacent extended strand dictate HLA-DM susceptibility and peptide exchange.
Authors: Painter, C.A. / Negroni, M.P. / Kellersberger, K.A. / Zavala-Ruiz, Z. / Evans, J.E. / Stern, L.J.
History
DepositionMar 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2011Group: Database references
Revision 1.2Dec 14, 2011Group: Database references
Revision 1.3Sep 13, 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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1-1 beta chain
D: HLA class II histocompatibility antigen, DR alpha chain
E: HLA class II histocompatibility antigen, DRB1-1 beta chain
C: HLA class II histocompatibility antigen gamma chain peptide
F: HLA class II histocompatibility antigen gamma chain peptide


Theoretical massNumber of molelcules
Total (without water)89,8256
Polymers89,8256
Non-polymers00
Water2,774154
1
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1-1 beta chain
C: HLA class II histocompatibility antigen gamma chain peptide


Theoretical massNumber of molelcules
Total (without water)44,9133
Polymers44,9133
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7200 Å2
ΔGint-43 kcal/mol
Surface area18130 Å2
MethodPISA
2
D: HLA class II histocompatibility antigen, DR alpha chain
E: HLA class II histocompatibility antigen, DRB1-1 beta chain
F: HLA class II histocompatibility antigen gamma chain peptide


Theoretical massNumber of molelcules
Total (without water)44,9133
Polymers44,9133
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-41 kcal/mol
Surface area17880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.296, 95.887, 151.573
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HLA class II histocompatibility antigen, DR alpha chain / MHC class II antigen DRA


Mass: 21155.904 Da / Num. of mol.: 2 / Fragment: UNP residues 26-207
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DR1, HLA-DRA, HLA-DRA1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P01903
#2: Protein HLA class II histocompatibility antigen, DRB1-1 beta chain / MHC class II antigen DRB1*1 / DR-1 / DR1


Mass: 22080.664 Da / Num. of mol.: 2 / Fragment: UNP residues 30-219
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DR1, HLA-DRB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P04229, UniProt: P01911*PLUS
#3: Protein/peptide HLA class II histocompatibility antigen gamma chain peptide / HLA-DR antigens-associated invariant chain / Ia antigen-associated invariant chain / Ii / p33


Mass: 1676.118 Da / Num. of mol.: 2 / Fragment: CLIP region / Source method: obtained synthetically
Details: This chemically synthesized sequence occurs naturally in Humans
Source: (synth.) Homo sapiens (human) / References: UniProt: P04233
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
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: 2.64 Å3/Da / Density % sol: 53.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 4000, 10% Glycerol, 100mM Sodium Acetate pH 5.6, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 21, 2009
Details: vertically focusing mirror and horizontally focusing monochromator
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 26368 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.125 / Χ2: 3.134 / Net I/σ(I): 10.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.7-2.756.80.40212911.261199.5
2.75-2.86.90.34212811.38199.7
2.8-2.856.90.31112791.288199.7
2.85-2.916.90.26812881.351199.8
2.91-2.976.80.25513221.456199.8
2.97-3.046.90.2312861.541199.9
3.04-3.126.90.19613091.587199.9
3.12-3.270.17513001.8271100
3.2-3.36.90.14713112.057199.9
3.3-3.470.13913002.2631100
3.4-3.5270.17912954.4581100
3.52-3.667.10.14113324.0151100
3.66-3.837.10.10713023.051100
3.83-4.037.10.14213115.5771100
4.03-4.297.20.09613214.3741100
4.29-4.627.10.0913394.8711100
4.62-5.087.10.09113265.0061100
5.08-5.816.90.08913494.071100
5.81-7.326.90.09213763.9921100
7.32-506.70.08114506.354199.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 43.39 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.71 Å37.45 Å
Translation2.71 Å37.45 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SJE

1sje


Resolution: 2.712→37.447 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8437 / SU ML: 0.36 / σ(F): 0 / Phase error: 21.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2349 1223 4.77 %
Rwork0.193 --
obs0.1949 25637 96.79 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20 Å2 / ksol: 0.354 e/Å3
Displacement parametersBiso max: 97.98 Å2 / Biso mean: 24.8573 Å2 / Biso min: 0 Å2
Baniso -1Baniso -2Baniso -3
1-4.7268 Å20 Å20 Å2
2--4.1297 Å2-0 Å2
3---16.9643 Å2
Refinement stepCycle: LAST / Resolution: 2.712→37.447 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6253 0 0 154 6407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026429
X-RAY DIFFRACTIONf_angle_d0.6278735
X-RAY DIFFRACTIONf_chiral_restr0.041939
X-RAY DIFFRACTIONf_plane_restr0.0021143
X-RAY DIFFRACTIONf_dihedral_angle_d14.3252358
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7124-2.82090.31841200.24592410253088
2.8209-2.94930.2591290.22572599272894
2.9493-3.10470.30961270.21012643277096
3.1047-3.29910.23521240.19632724284897
3.2991-3.55370.2451320.18432727285999
3.5537-3.91090.20261330.17922766289999
3.9109-4.47610.19641620.1682761292399
4.4761-5.63630.20251530.16972816296999
5.6363-37.45060.27361430.22329683111100
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)
10.07650.0096-0.03790.1077-0.00010.0903-0.01060.14830.0087-0.1292-0.04520.05850.0291-0.0655-0.10790.06770.0212-0.04790.03460.0315-0.0127-30.2467.7583-0.3464
20.1135-0.09680.09860.1409-0.05060.1270.0149-0.1447-0.00590.05090.0650.0939-0.034-0.07080.0785-0.02630.0234-0.10590.0748-0.02950.0486-21.293518.691433.9843
30.0022-0.0040.00020.0612-0.05650.08240.04330.0084-0.0894-0.0290.05570.05540.0822-0.02450.11090.0358-0.0107-0.19120.04680.02720.1084-14.1693-7.999132.1143
40.0696-0.0739-0.01670.0790.02840.02990.04930.0958-0.0635-0.04020.0301-0.14590.05530.0922-0.0083-0.01370.087-0.01510.136-0.09780.17619.6433-3.247323.2027
50.00970.014-0.00470.02440.00190.01960.0507-0.0251-0.0990.00840.0151-0.02710.0626-0.00380.00730.1678-0.0088-0.11070.08170.01290.1817-19.8333-25.712717.1241
60.0508-0.0076-0.04270.0555-0.04620.08610.00190.0513-0.0428-0.0320.0163-0.05620.07970.03810.00990.05060.0286-0.01320.1107-0.04290.0864-7.0822-6.38516.5981
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and ((resseq 4:78))) or (chain 'C' and ((resseq 87:101))) or (chain 'B' and ((resseq 1:92)))A0
2X-RAY DIFFRACTION2(chain 'E' and ((resseq 1:92))) or (chain 'D' and ((resseq 4:80))) or (chain 'F' and ((resseq 87:101)))E0
3X-RAY DIFFRACTION3chain 'D' and ((resseq 83:182))D0
4X-RAY DIFFRACTION4chain 'E' and ((resseq 93:190))E0
5X-RAY DIFFRACTION5chain 'B' and ((resseq 94:190))B0
6X-RAY DIFFRACTION6chain 'A' and ((resseq 83:182))A0

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