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- PDB-3pgc: Crystal Structure of HLA-DR1 with CLIP106-120, flipped peptide or... -

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Basic information

Entry
Database: PDB / ID: 3pgc
TitleCrystal Structure of HLA-DR1 with CLIP106-120, flipped peptide orientation
Components
  • (HLA class II histocompatibility antigen, ...) x 2
  • HLA class II histocompatibility antigen gamma chain
KeywordsIMMUNE SYSTEM / MHC class II / MHC II / self antigen / invariant chain / CLIP
Function / homology
Function and homology information


antigen processing and presentation of endogenous antigen / macrophage migration inhibitory factor signaling pathway / NOS2-CD74 complex / MHC class II protein binding, via antigen binding groove / negative regulation of peptide secretion / positive regulation of cytokine-mediated signaling pathway / positive regulation of dendritic cell antigen processing and presentation / positive regulation of macrophage migration inhibitory factor signaling pathway / protein trimerization / macrophage migration inhibitory factor receptor complex ...antigen processing and presentation of endogenous antigen / macrophage migration inhibitory factor signaling pathway / NOS2-CD74 complex / MHC class II protein binding, via antigen binding groove / negative regulation of peptide secretion / positive regulation of cytokine-mediated signaling pathway / positive regulation of dendritic cell antigen processing and presentation / positive regulation of macrophage migration inhibitory factor signaling pathway / protein trimerization / macrophage migration inhibitory factor receptor complex / macrophage migration inhibitory factor binding / positive regulation of type 2 immune response / T cell activation involved in immune response / positive regulation of macrophage cytokine production / 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 / autolysosome membrane / regulation of macrophage activation / T cell selection / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / regulation of T-helper cell differentiation / positive regulation of prostaglandin biosynthetic process / positive regulation of CD4-positive, alpha-beta T cell activation / T-helper 1 type immune response / MHC class II protein binding / host-mediated suppression of symbiont invasion / negative regulation of mature B cell apoptotic process / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / inflammatory response to antigenic stimulus / positive regulation of T cell mediated immune response to tumor cell / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / CD4 receptor binding / prostaglandin biosynthetic process / positive regulation of chemokine (C-X-C motif) ligand 2 production / vacuole / cytokine receptor activity / positive regulation of neutrophil chemotaxis / antigen processing and presentation / intermediate filament / immunoglobulin mediated immune response / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / transport vesicle membrane / humoral immune response / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / epidermis development / negative regulation of DNA damage response, signal transduction by p53 class mediator / cytokine binding / polysaccharide binding / negative regulation of type II interferon production / macrophage differentiation / Generation of second messenger molecules / nitric-oxide synthase binding / immunological synapse / Co-inhibition by PD-1 / positive regulation of B cell proliferation / negative regulation of T cell proliferation / detection of bacterium / positive regulation of chemokine production / T cell receptor binding / multivesicular body / response to type II interferon / MHC class II antigen presentation / lysosomal lumen / protein folding chaperone / negative regulation of cell migration / positive regulation of fibroblast proliferation / positive regulation of T cell mediated cytotoxicity / Cell surface interactions at the vascular wall / positive regulation of insulin secretion involved in cellular response to glucose stimulus / trans-Golgi network membrane / positive regulation of interleukin-8 production / Developmental Lineage of Pancreatic Ductal Cells / lumenal side of endoplasmic reticulum membrane / protein tetramerization / negative regulation of inflammatory response to antigenic stimulus / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / intracellular protein transport / peptide antigen assembly with MHC class II protein complex / positive regulation of interleukin-6 production / MHC class II protein complex / cognition / positive regulation of immune response / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / T cell receptor signaling pathway / positive regulation of T cell activation / Interferon gamma signaling / structural constituent of cytoskeleton / endocytic vesicle membrane / MHC class II protein complex binding / late endosome / Downstream TCR signaling / late endosome membrane / amyloid-beta binding / protein-containing complex assembly
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
DI(HYDROXYETHYL)ETHER / 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: 2.66 Å
AuthorsGunther, S. / Schlundt, A. / Sticht, J. / Roske, Y. / Heinemann, U. / Wiesmuller, K.-H. / Jung, G. / Falk, K. / Rotzschke, O. / Freund, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Bidirectional binding of invariant chain peptides to an MHC class II molecule.
Authors: Gunther, S. / Schlundt, A. / Sticht, J. / Roske, Y. / Heinemann, U. / Wiesmuller, K.H. / Jung, G. / Falk, K. / Rotzschke, O. / Freund, C.
History
DepositionNov 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
C: HLA class II histocompatibility antigen gamma 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,5498
Polymers94,3516
Non-polymers1982
Water2,072115
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


Theoretical massNumber of molelcules
Total (without water)47,1753
Polymers47,1753
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7280 Å2
ΔGint-47 kcal/mol
Surface area17560 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3735
Polymers47,1753
Non-polymers1982
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7850 Å2
ΔGint-45 kcal/mol
Surface area17520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.146, 138.146, 104.520
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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HLA class II histocompatibility antigen, ... , 2 types, 4 molecules ADBE

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


Mass: 22353.223 Da / Num. of mol.: 2 / Fragment: UNP residues 26-217
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01903
#2: Protein HLA class II histocompatibility antigen, DRB1-1 beta chain / MHC class II antigen DRB1*1 / DR-1 / DR1


Mass: 23087.791 Da / Num. of mol.: 2 / Fragment: UNP residues 30-227
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P04229, UniProt: P01911*PLUS

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Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide HLA class II histocompatibility antigen gamma chain / HLA-DR antigens-associated invariant chain / Ia antigen-associated invariant chain / Ii / p33


Mass: 1734.263 Da / Num. of mol.: 2 / Fragment: UNP residues 106-120 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P04233

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Non-polymers , 3 types, 117 molecules

#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.05 Å3/Da / Density % sol: 59.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG 1500, MIB buffer, pH 6.0, vapor diffusion, sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: Rayonix / Detector: CCD / Date: Nov 3, 2009
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.66→34.537 Å / Num. all: 33425 / Num. obs: 33394 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 57.689 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 17.96
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.66-2.730.6793182072417100
2.73-2.80.5363.7181702407100
2.8-2.890.4344.6175992335100
2.89-2.970.3435.7166712216100
2.97-3.070.2876.9167602224100
3.07-3.180.2139.3157092092100
3.18-3.30.16511.7152652033100
3.3-3.430.1314.6148211985100
3.43-3.590.10118.6138911876100
3.59-3.760.0921.2133971824100
3.76-3.970.07923.4125581718100
3.97-4.210.06327.511877164299.9
4.21-4.50.05432.510812153299.9
4.5-4.860.04835.9100051430100
4.86-5.320.04635.893551333100
5.32-5.950.04634.486621216100
5.95-6.870.04335.476741073100
6.87-8.410.03539.56451914100
8.41-11.90.02843.84948730100
11.9-34.5370.02542.8246339793.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 42.46 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.66 Å34.54 Å
Translation2.66 Å34.54 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.66→34.537 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.37 / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2501 1669 5 %random
Rwork0.1983 ---
obs0.2009 33390 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.316 Å2 / ksol: 0.288 e/Å3
Displacement parametersBiso max: 114.71 Å2 / Biso mean: 53.3584 Å2 / Biso min: 24.53 Å2
Baniso -1Baniso -2Baniso -3
1-3.6444 Å20 Å2-0 Å2
2--3.6444 Å2-0 Å2
3----7.2887 Å2
Refinement stepCycle: LAST / Resolution: 2.66→34.537 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6052 0 13 115 6180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086233
X-RAY DIFFRACTIONf_angle_d1.1328472
X-RAY DIFFRACTIONf_chiral_restr0.071922
X-RAY DIFFRACTIONf_plane_restr0.0051100
X-RAY DIFFRACTIONf_dihedral_angle_d19.3142230
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.66-2.7550.33041660.24231543320
2.755-2.86530.29741630.245330963259
2.8653-2.99560.33751670.258231793346
2.9956-3.15350.33381640.249631163280
3.1535-3.35090.31341650.227531423307
3.3509-3.60940.2511680.196931743342
3.6094-3.97210.24261660.187131623328
3.9721-4.54580.21351680.159831823350
4.5458-5.7230.16831680.151232093377
5.723-34.5370.23841740.192533073481

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