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- PDB-3qxd: F54C HLA-DR1 bound with CLIP peptide -

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Basic information

Entry
Database: PDB / ID: 3qxd
TitleF54C HLA-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 / T cell activation involved in immune response / positive regulation of T cell mediated immune response to tumor cell / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / negative thymic T cell selection / autolysosome membrane / positive regulation of type 2 immune response / T cell selection / regulation of T-helper cell differentiation / positive regulation of prostaglandin biosynthetic process / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / negative regulation of viral entry into host cell / MHC class II receptor activity / MHC class II protein binding / positive regulation of CD4-positive, alpha-beta T cell activation / 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 memory T cell differentiation / positive regulation of monocyte differentiation / CD4 receptor binding / vacuole / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of kinase activity / inflammatory response to antigenic stimulus / positive regulation of neutrophil chemotaxis / cytokine receptor activity / positive regulation of macrophage cytokine production / intermediate filament / prostaglandin biosynthetic process / positive regulation of T cell differentiation / regulation of macrophage activation / transport vesicle membrane / T-helper 1 type immune response / polysaccharide binding / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / cytokine binding / nitric-oxide synthase binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / response to type II interferon / positive regulation of insulin secretion involved in cellular response to glucose stimulus / negative regulation of DNA damage response, signal transduction by p53 class mediator / chaperone cofactor-dependent protein refolding / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / immunoglobulin mediated immune response / Generation of second messenger molecules / immunological synapse / antigen processing and presentation / PD-1 signaling / epidermis development / positive regulation of B cell proliferation / protein folding chaperone / positive regulation of chemokine production / negative regulation of inflammatory response to antigenic stimulus / negative regulation of T cell proliferation / MHC class II antigen presentation / detection of bacterium / T cell receptor binding / multivesicular body / 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 / protein tetramerization / clathrin-coated endocytic vesicle membrane / intracellular protein transport / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cognition / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / positive regulation of interleukin-6 production / MHC class II protein complex / peptide antigen binding / endocytic vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of fibroblast proliferation / Interferon gamma signaling / positive regulation of immune response / positive regulation of T cell activation / positive regulation of peptidyl-tyrosine phosphorylation
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
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)
Homo Sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.302 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
F: HLA class II histocompatibility antigen gamma chain peptide
C: HLA class II histocompatibility antigen gamma chain peptide


Theoretical massNumber of molelcules
Total (without water)89,7376
Polymers89,7376
Non-polymers00
Water8,323462
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)44,8693
Polymers44,8693
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-44 kcal/mol
Surface area17920 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)44,8693
Polymers44,8693
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-42 kcal/mol
Surface area17940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.001, 94.870, 154.090
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: 21111.873 Da / Num. of mol.: 2 / Fragment: UNP residues 26-207 / Mutation: F54C
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 human
Source: (synth.) Homo Sapiens (human) / References: UniProt: P04233
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 462 / 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: 2.65 Å3/Da / Density % sol: 53.54 %
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: Oct 19, 2008
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: 2.3→50 Å / Num. obs: 43039 / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.069 / Χ2: 1.049 / Net I/σ(I): 10.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.347.50.4121030.8171100
2.34-2.387.50.37921310.8131100
2.38-2.437.50.34221010.8351100
2.43-2.487.50.30821320.8321100
2.48-2.537.50.26221060.8181100
2.53-2.597.50.22521300.8511100
2.59-2.667.40.20621220.851100
2.66-2.737.40.17221250.8681100
2.73-2.817.50.14921340.911100
2.81-2.97.50.12221160.8781100
2.9-37.40.10621560.8961100
3-3.127.40.09121300.9291100
3.12-3.267.40.06921590.9231100
3.26-3.447.40.05921460.9861100
3.44-3.657.40.04821581.011100
3.65-3.937.40.04821521.2461100
3.93-4.337.30.05321911.9431100
4.33-4.957.20.05121862.2191100
4.95-6.246.90.03722201.1221100
6.24-506.80.02623411.246199.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 44.65 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å44.01 Å
Translation2.5 Å44.01 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: 2.302→37.185 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8585 / SU ML: 0.32 / σ(F): 0 / Phase error: 20.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.221 1955 4.65 %
Rwork0.1886 --
obs0.1901 42025 97.71 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20 Å2 / ksol: 0.326 e/Å3
Displacement parametersBiso max: 91.81 Å2 / Biso mean: 21.8676 Å2 / Biso min: 0 Å2
Baniso -1Baniso -2Baniso -3
1-15.6096 Å2-0 Å20 Å2
2--10.1078 Å20 Å2
3---16.871 Å2
Refinement stepCycle: LAST / Resolution: 2.302→37.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6230 0 0 462 6692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046456
X-RAY DIFFRACTIONf_angle_d0.8188782
X-RAY DIFFRACTIONf_chiral_restr0.055945
X-RAY DIFFRACTIONf_plane_restr0.0031150
X-RAY DIFFRACTIONf_dihedral_angle_d13.5812384
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.302-2.38430.25381890.21433763395294
2.3843-2.47970.29361870.22333843403095
2.4797-2.59250.21941890.21293904409396
2.5925-2.72920.21731890.20373912410197
2.7292-2.90010.26351960.20473986418298
2.9001-3.12390.25491950.20564007420298
3.1239-3.43810.22591990.20084076427599
3.4381-3.93510.23191990.188541014300100
3.9351-4.9560.1652010.150441584359100
4.956-37.18950.21372110.182843204531100
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)
10.0404-0.00410.01380.03850.00390.00890.0432-0.05250.02510.0333-0.0067-0.07070.03340.02860.0265-0.0903-0.06040.0133-0.02250.01840.065329.26327.6863-0.1775
20.02790.01980.01540.01830.01490.0225-0.00320.05020.0236-0.01140.0327-0.046-0.04140.04450.0640.0081-0.1351-0.20790.06660.001-0.008420.592318.6403-34.9104
30.0061-0.0023-0.00030.00790.00520.00760.01840.0182-0.0068-0.0099-0.0043-0.01840.02110.0056-0.00210.21640.0258-0.1410.0462-0.08120.104514.8871-7.9356-33.1389
40.0410.0614-0.01340.0993-0.02340.01220.0233-0.0586-0.0268-0.01480.02830.09170.0085-0.0541-0.02180.0451-0.0457-0.03660.09140.05320.1165-9.5849-4.3316-23.8591
50.0182-0.00660.00020.0141-0.01080.02110.02030.0192-0.0645-0.0282-0.03190.00270.02320.0123-0.00730.13530.0787-0.09670.0242-0.00790.136620.2924-25.7242-18.2168
60.00330.00090.00130.0032-0.00330.00810.0206-0.037-0.0511-0.0020.0140.04730.0489-0.044-0.00970.0446-0.0434-0.03640.0160.09520.12976.6747-7.2689-7.2156
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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