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- PDB-4i0p: HLA-DO in complex with HLA-DM -

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Basic information

Entry
Database: PDB / ID: 4i0p
TitleHLA-DO in complex with HLA-DM
Components
  • (HLA class II histocompatibility antigen, DO ...) x 2
  • HLA class II histocompatibility antigen, DM beta chain
  • HLA-DMA protein
KeywordsIMMUNE SYSTEM / HLA-DM / HLA-DO / HLA-DR / peptide loading / inhibitor / enzyme HLA-DM
Function / homology
Function and homology information


negative regulation of antigen processing and presentation of peptide antigen via MHC class II / MHC class II protein complex assembly / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / MHC class II receptor activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / regulation of T cell differentiation / positive regulation of T cell proliferation / MHC class II antigen presentation / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex ...negative regulation of antigen processing and presentation of peptide antigen via MHC class II / MHC class II protein complex assembly / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / MHC class II receptor activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / regulation of T cell differentiation / positive regulation of T cell proliferation / MHC class II antigen presentation / 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 / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / adaptive immune response / lysosome / membrane => GO:0016020 / endosome membrane / lysosomal membrane / intracellular membrane-bounded organelle / plasma 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
ACETATE ION / TRIETHYLENE GLYCOL / HLA class II histocompatibility antigen, DO alpha chain / HLA class II histocompatibility antigen, DO beta chain / HLA class II histocompatibility antigen, DM beta chain / HLA-DMA protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsGuce, A.I. / Mortimer, S.E. / Stern, L.J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: HLA-DO acts as a substrate mimic to inhibit HLA-DM by a competitive mechanism.
Authors: Guce, A.I. / Mortimer, S.E. / Yoon, T. / Painter, C.A. / Jiang, W. / Mellins, E.D. / Stern, L.J.
History
DepositionNov 18, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionDec 26, 2012ID: 3USA
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_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 1.3Sep 20, 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: HLA-DMA protein
B: HLA class II histocompatibility antigen, DM beta chain
C: HLA class II histocompatibility antigen, DO alpha chain
D: HLA class II histocompatibility antigen, DO beta chain
E: HLA-DMA protein
F: HLA class II histocompatibility antigen, DM beta chain
G: HLA class II histocompatibility antigen, DO alpha chain
H: HLA class II histocompatibility antigen, DO beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,08020
Polymers170,0468
Non-polymers2,03412
Water1086
1
A: HLA-DMA protein
B: HLA class II histocompatibility antigen, DM beta chain
C: HLA class II histocompatibility antigen, DO alpha chain
D: HLA class II histocompatibility antigen, DO beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7798
Polymers85,0234
Non-polymers7564
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14530 Å2
ΔGint-65 kcal/mol
Surface area33660 Å2
MethodPISA
2
E: HLA-DMA protein
F: HLA class II histocompatibility antigen, DM beta chain
G: HLA class II histocompatibility antigen, DO alpha chain
H: HLA class II histocompatibility antigen, DO beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,30112
Polymers85,0234
Non-polymers1,2788
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15400 Å2
ΔGint-61 kcal/mol
Surface area34040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.260, 147.100, 95.959
Angle α, β, γ (deg.)90.00, 106.49, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
15
25
16
26

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111(CHAIN A AND RESSEQ 15:90) OR (CHAIN B AND RESSEQ 5:90)
211(CHAIN E AND RESSEQ 15:90) OR (CHAIN E AND RESSEQ 5:90)
112CHAIN A AND RESSEQ 91:197
212CHAIN E AND RESSEQ 91:197
113(CHAIN B AND RESSEQ 91:138) OR (CHAIN B AND RESSEQ 147:176)
213(CHAIN F AND RESSEQ 91:138) OR (CHAIN F AND RESSEQ 147:176)
114(CHAIN C AND RESSEQ 5:75) OR (CHAIN D AND RESSEQ 6:90)
214(CHAIN G AND RESSEQ 5:75) OR (CHAIN H AND RESSEQ 6:90)
115CHAIN C AND RESSEQ 91:150
215CHAIN G AND RESSEQ 91:150
116CHAIN D AND RESSEQ 91:170
216CHAIN H AND RESSEQ 91:170

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 2 types, 4 molecules AEBF

#1: Protein HLA-DMA protein


Mass: 21303.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: Homo sapiensHuman / Gene: 3108, HLA-DMA / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): Schneider-2 / References: UniProt: Q6ICR9
#2: Protein HLA class II histocompatibility antigen, DM beta chain / MHC class II antigen DMB / Really interesting new gene 7 protein


Mass: 21507.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: Homo sapiensHuman / Gene: 3109, DMB, HLA-DMB, RING7 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): Schneider-2 / References: UniProt: P28068

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HLA class II histocompatibility antigen, DO ... , 2 types, 4 molecules CGDH

#3: Protein HLA class II histocompatibility antigen, DO alpha chain / MHC DN-alpha / MHC DZ alpha / MHC class II antigen DOA


Mass: 20577.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: Homo sapiensHuman / Gene: 3111, HLA-DNA, HLA-DOA, HLA-DZA / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): Schneider-2 / References: UniProt: P06340
#4: Protein HLA class II histocompatibility antigen, DO beta chain / MHC class II antigen DOB


Mass: 21634.520 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: Homo sapiensHuman / Gene: 3112, HLA-DOB / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): Schneider-2 / References: UniProt: P13765

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Sugars , 1 types, 7 molecules

#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.: 7
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 , 4 types, 11 molecules

#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 3.31 Å3/Da / Density % sol: 62.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 100 mM Na acetate, 8% PEG 4K, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2010
Details: Pt-coated toroidal Si mirror for horizontal and vertical focussing followed by double flat Si crystal monochromator
RadiationMonochromator: Si-111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 36565 / % possible obs: 93.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 49 Å2 / Rmerge(I) obs: 0.683 / Rsym value: 0.683 / Net I/σ(I): 5.4
Reflection shellResolution: 3.2→3.3143 Å / Rmerge(I) obs: 0.683 / Mean I/σ(I) obs: 5.4 / Rsym value: 0.683 / % possible all: 94

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2BC4 (DM), 1KLU (DR1)

2bc4

1klu


Resolution: 3.2→43.909 Å / SU ML: 0.46 / σ(F): 0 / Phase error: 25.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2419 1856 5.4 %
Rwork0.1877 --
obs0.1906 34364 93.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→43.909 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11928 0 130 6 12064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312506
X-RAY DIFFRACTIONf_angle_d0.85317035
X-RAY DIFFRACTIONf_dihedral_angle_d14.3884510
X-RAY DIFFRACTIONf_chiral_restr0.0481851
X-RAY DIFFRACTIONf_plane_restr0.0042204
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A623X-RAY DIFFRACTIONPOSITIONAL
12E623X-RAY DIFFRACTIONPOSITIONAL0.012
21A847X-RAY DIFFRACTIONPOSITIONAL
22E847X-RAY DIFFRACTIONPOSITIONAL0.012
31B621X-RAY DIFFRACTIONPOSITIONAL
32F621X-RAY DIFFRACTIONPOSITIONAL0.014
41C1262X-RAY DIFFRACTIONPOSITIONAL
42G1262X-RAY DIFFRACTIONPOSITIONAL0.011
51C489X-RAY DIFFRACTIONPOSITIONAL
52G489X-RAY DIFFRACTIONPOSITIONAL0.011
61D639X-RAY DIFFRACTIONPOSITIONAL
62H639X-RAY DIFFRACTIONPOSITIONAL0.012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.28650.35112240.26332241X-RAY DIFFRACTION89
3.2865-3.38321000000000.24442480X-RAY DIFFRACTION89
3.3832-3.49230.31051980.24022274X-RAY DIFFRACTION88
3.4923-3.61710.28321820.21542306X-RAY DIFFRACTION89
3.6171-3.76181000000000.20732541X-RAY DIFFRACTION90
3.7618-3.93290.27541680.20982353X-RAY DIFFRACTION91
3.9329-4.14020.25631590.18442490X-RAY DIFFRACTION93
4.1402-4.39930.18211370.16092571X-RAY DIFFRACTION97
4.3993-4.73860.19351350.14322644X-RAY DIFFRACTION99
4.7386-5.21480.19652240.13922575X-RAY DIFFRACTION99
5.2148-5.96780.2634890.17392715X-RAY DIFFRACTION99
5.9678-7.51270.23561770.19462608X-RAY DIFFRACTION99
7.5127-43.91280.2051630.18452710X-RAY DIFFRACTION100

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