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- PDB-1aqd: HLA-DR1 (DRA, DRB1 0101) HUMAN CLASS II HISTOCOMPATIBILITY PROTEI... -

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Basic information

Entry
Database: PDB / ID: 1aqd
TitleHLA-DR1 (DRA, DRB1 0101) HUMAN CLASS II HISTOCOMPATIBILITY PROTEIN (EXTRACELLULAR DOMAIN) COMPLEXED WITH ENDOGENOUS PEPTIDE
Components
  • (HLA-DR1 CLASS II HISTOCOMPATIBILITY PROTEIN) x 2
  • HLA-A2HLA-A*02
KeywordsCOMPLEX (MHC PROTEIN/ANTIGEN) / COMPLEX (MHC PROTEIN-ANTIGEN) / HISTOCOMPATIBILITY ANTIGEN / COMPLEX (MHC PROTEIN-ANTIGEN) complex
Function / homology
Function and homology information


regulation of interleukin-4 production / regulation of interleukin-10 production / 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 / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation ...regulation of interleukin-4 production / regulation of interleukin-10 production / 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 / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / CD4 receptor binding / positive regulation of kinase activity / inflammatory response to antigenic stimulus / intermediate filament / transport vesicle membrane / T-helper 1 type immune response / polysaccharide binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of insulin secretion involved in cellular response to glucose stimulus / humoral immune response / macrophage differentiation / T cell mediated cytotoxicity directed against tumor cell target / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / negative regulation of type II interferon production / positive regulation of memory T cell activation / Generation of second messenger molecules / TAP complex binding / immunological synapse / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / PD-1 signaling / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / epidermis development / endoplasmic reticulum exit site / beta-2-microglobulin binding / TAP binding / negative regulation of T cell proliferation / protection from natural killer cell mediated cytotoxicity / negative regulation of inflammatory response to antigenic stimulus / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / MHC class II antigen presentation / detection of bacterium / T cell receptor binding / trans-Golgi network membrane / Nef mediated downregulation of MHC class I complex cell surface expression / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / protein tetramerization / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / MHC class I peptide loading complex / structural constituent of cytoskeleton / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / cognition / positive regulation of T cell cytokine production / MHC class I protein complex / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / endocytic vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / positive regulation of T cell activation / Interferon alpha/beta signaling / positive regulation of type II interferon production / Downstream TCR signaling / E3 ubiquitin ligases ubiquitinate target proteins / MHC class II protein complex binding / late endosome membrane / ER-Phagosome pathway / antibacterial humoral response / T cell receptor signaling pathway / early endosome membrane / positive regulation of canonical NF-kappaB signal transduction / adaptive immune response / positive regulation of MAPK cascade / positive regulation of viral entry into host cell / lysosome / positive regulation of ERK1 and ERK2 cascade / defense response to Gram-positive bacterium / immune response / positive regulation of protein phosphorylation / lysosomal membrane / external side of plasma membrane / Golgi 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 class I, alpha chain, C-terminal ...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 class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / 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 I histocompatibility antigen, A alpha chain / 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 I histocompatibility antigen, A alpha chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsMurthy, V.L. / Stern, L.J.
Citation
Journal: Structure / Year: 1997
Title: The class II MHC protein HLA-DR1 in complex with an endogenous peptide: implications for the structural basis of the specificity of peptide binding.
Authors: Murthy, V.L. / Stern, L.J.
#1: Journal: Thesis / Year: 1996
Title: Three Dimensional Structure of a Human Class II Mhc Protein Hla-Dr1 Bound to an Endogenous Peptide
Authors: Murthy, V.L.
#2: Journal: Nature / Year: 1994
Title: Crystal Structure of the Human Class II Mhc Protein Hla-Dr1 Complexed with an Influenza Virus Peptide
Authors: Stern, L.J. / Brown, J.H. / Jardetzky, T.S. / Gorga, J.C. / Urban, R.G. / Strominger, J.L. / Wiley, D.C.
#3: Journal: Nature / Year: 1993
Title: Three-Dimensional Structure of the Human Class II Histocompatibility Antigen Hla-Dr1
Authors: Brown, J.H. / Jardetzky, T.S. / Gorga, J.C. / Stern, L.J. / Urban, R.G. / Strominger, J.L. / Wiley, D.C.
History
DepositionJul 28, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Refinement description / Category: 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: HLA-DR1 CLASS II HISTOCOMPATIBILITY PROTEIN
B: HLA-DR1 CLASS II HISTOCOMPATIBILITY PROTEIN
C: HLA-A2
D: HLA-DR1 CLASS II HISTOCOMPATIBILITY PROTEIN
E: HLA-DR1 CLASS II HISTOCOMPATIBILITY PROTEIN
F: HLA-A2
G: HLA-DR1 CLASS II HISTOCOMPATIBILITY PROTEIN
H: HLA-DR1 CLASS II HISTOCOMPATIBILITY PROTEIN
I: HLA-A2
J: HLA-DR1 CLASS II HISTOCOMPATIBILITY PROTEIN
K: HLA-DR1 CLASS II HISTOCOMPATIBILITY PROTEIN
L: HLA-A2


Theoretical massNumber of molelcules
Total (without water)188,14712
Polymers188,14712
Non-polymers00
Water2,738152
1
A: HLA-DR1 CLASS II HISTOCOMPATIBILITY PROTEIN
B: HLA-DR1 CLASS II HISTOCOMPATIBILITY PROTEIN
C: HLA-A2


Theoretical massNumber of molelcules
Total (without water)47,0373
Polymers47,0373
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-35 kcal/mol
Surface area17620 Å2
MethodPISA
2
G: HLA-DR1 CLASS II HISTOCOMPATIBILITY PROTEIN
H: HLA-DR1 CLASS II HISTOCOMPATIBILITY PROTEIN
I: HLA-A2


Theoretical massNumber of molelcules
Total (without water)47,0373
Polymers47,0373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7370 Å2
ΔGint-37 kcal/mol
Surface area17440 Å2
MethodPISA
3
D: HLA-DR1 CLASS II HISTOCOMPATIBILITY PROTEIN
E: HLA-DR1 CLASS II HISTOCOMPATIBILITY PROTEIN
F: HLA-A2


Theoretical massNumber of molelcules
Total (without water)47,0373
Polymers47,0373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-38 kcal/mol
Surface area17340 Å2
MethodPISA
4
J: HLA-DR1 CLASS II HISTOCOMPATIBILITY PROTEIN
K: HLA-DR1 CLASS II HISTOCOMPATIBILITY PROTEIN
L: HLA-A2


Theoretical massNumber of molelcules
Total (without water)47,0373
Polymers47,0373
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7440 Å2
ΔGint-37 kcal/mol
Surface area17470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.514, 134.320, 131.232
Angle α, β, γ (deg.)90.00, 104.82, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
/ NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(-0.79191, 0.53255, 0.29877), (0.51517, 0.32, 0.79511), (0.32783, 0.78358, -0.52777)27.22638, -39.64445, 49.03718
2given(0.00458, -0.99941, -0.03407), (0.9993, 0.00584, -0.03683), (0.037, -0.03388, 0.99874)45.1323, -22.11342, -61.74336
3given(-0.51898, -0.34098, -0.78383), (-0.79916, 0.51896, 0.30336), (0.30334, 0.78384, -0.54183)83.35107, 3.8172, -10.51804
DetailsTHERE ARE FOUR MOLECULES IN THIS COORDINATE SET EACH MOLECULE HAS ONE ALPHA CHAIN : RESIDUES 3-182 EACH MOLECULE HAS ONE BETA CHAIN : RESIDUES 4-190 EACH MOLECULE HAS ONE PEPTIDE CHAIN: RESIDUES 3-14 MOLECULE THREE IS THE MOST WELL DEFINED. MOLECULES 1 - 2 AND 3 - 4 EACH FORM THE SO-CALLED "DIMER OF DIMERS".

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Components

#1: Protein
HLA-DR1 CLASS II HISTOCOMPATIBILITY PROTEIN / DRA / DRB1 01010


Mass: 22222.027 Da / Num. of mol.: 4 / Fragment: SECRETED EXTRACELLULAR DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: LYMPHOID / Cellular location: PLASMA MEMBRANECell membrane / Gene: DRA*0101, DRB1*0101 / Organ: PLASMA / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P01903
#2: Protein
HLA-DR1 CLASS II HISTOCOMPATIBILITY PROTEIN / DRA / DRB1 01010


Mass: 22956.596 Da / Num. of mol.: 4 / Fragment: SECRETED EXTRACELLULAR DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: LYMPHOID / Cellular location: PLASMA MEMBRANECell membrane / Gene: DRA*0101, DRB1*0101 / Organ: PLASMA / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P04229, UniProt: P01911*PLUS
#3: Protein/peptide
HLA-A2 / HLA-A*02


Mass: 1858.045 Da / Num. of mol.: 4 / Fragment: ANTIGENIC PEPTIDE
Source method: isolated from a genetically manipulated source
Details: HLA-DR1 IS A CLASS II MHC PROTEIN, HLA-A2 IS A CLASS I HISTOCOMPATIBILITY ANTIGEN
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P01892, UniProt: P04439*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 3.04 Å3/Da / Density % sol: 56.2 %
Crystal growpH: 3.5
Details: CRYSTALS GREW AS NEEDLES FROM 10MG/ML HLA-DR1 / PEPTIDE COMPLEX, 15% PEG 4000, 100MM GLYCINE, PH 3.5, AT ROOM TEMPERATURE, OVER ONE WEEK.
Temp details: room temp
Crystal
*PLUS
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein11
215 %PEG400011
3100 mMglycine11

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Feb 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.45→20 Å / Num. obs: 73538 / % possible obs: 85 % / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Biso Wilson estimate: 37.2 Å2 / Rsym value: 0.07 / Net I/σ(I): 14.9
Reflection shellResolution: 2.45→2.57 Å / Redundancy: 1.8 % / Mean I/σ(I) obs: 4.4 / Rsym value: 0.331 / % possible all: 70
Reflection
*PLUS
Num. measured all: 157895 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 70 % / Num. unique obs: 7700 / Num. measured obs: 13661 / Rmerge(I) obs: 0.331

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DLH

1dlh


Resolution: 2.45→6 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: REFMAC USED IN LATER STAGES OF REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.279 6884 10 %RANDOM
Rwork0.216 ---
obs0.216 68842 89 %-
Displacement parametersBiso mean: 40.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.27 Å
Refinement stepCycle: LAST / Resolution: 2.45→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11867 0 0 152 12019
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it0.15
X-RAY DIFFRACTIONx_mcangle_it0.2
X-RAY DIFFRACTIONx_scbond_it0.2
X-RAY DIFFRACTIONx_scangle_it0.25
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev Biso (Å2)Rms dev position (Å)
11RESTRAINTS (INTER AND INTRADIMER)X-RAY DIFFRACTION0.10.1
22X-RAY DIFFRACTION0.10.1
33X-RAY DIFFRACTION0.10.1
LS refinement shellResolution: 2.45→2.57 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.354 770 10 %
Rwork0.319 6930 -
obs--70 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAMHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PARAM3_MOD.CHOTOPH3.CHO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26

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