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- PDB-4ov5: Structure of HLA-DR1 with a bound peptide with non-optimal alanin... -

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Basic information

Entry
Database: PDB / ID: 4ov5
TitleStructure of HLA-DR1 with a bound peptide with non-optimal alanine in the P1 pocket
Components
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • HLA class II histocompatibility antigen, DR alpha chain
  • HLA class II histocompatibility antigen, DRB1-1 beta chain
KeywordsIMMUNE SYSTEM / Ig-like domain
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 / protection from natural killer cell mediated cytotoxicity / negative regulation of inflammatory response to antigenic stimulus / negative regulation of T cell proliferation / 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 / protein tetramerization / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / 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 / positive regulation of MAPK cascade / adaptive immune response / 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
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: 2.199 Å
AuthorsTrenh, P. / Yin, L. / Stern, L.J.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Susceptibility to HLA-DM Protein Is Determined by a Dynamic Conformation of Major Histocompatibility Complex Class II Molecule Bound with Peptide.
Authors: Yin, L. / Trenh, P. / Guce, A. / Wieczorek, M. / Lange, S. / Sticht, J. / Jiang, W. / Bylsma, M. / Mellins, E.D. / Freund, C. / Stern, L.J.
History
DepositionFeb 20, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Database references
Revision 1.2Sep 10, 2014Group: Database references
Revision 1.3Sep 20, 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

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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
G: HLA class II histocompatibility antigen, DR alpha chain
H: HLA class II histocompatibility antigen, DRB1-1 beta chain
J: HLA class II histocompatibility antigen, DR alpha chain
K: HLA class II histocompatibility antigen, DRB1-1 beta chain
M: HLA class II histocompatibility antigen, DR alpha chain
N: HLA class II histocompatibility antigen, DRB1-1 beta chain
P: HLA class II histocompatibility antigen, DR alpha chain
Q: HLA class II histocompatibility antigen, DRB1-1 beta chain
C: HLA class I histocompatibility antigen, A-2 alpha chain
F: HLA class I histocompatibility antigen, A-2 alpha chain
I: HLA class I histocompatibility antigen, A-2 alpha chain
L: HLA class I histocompatibility antigen, A-2 alpha chain
O: HLA class I histocompatibility antigen, A-2 alpha chain
R: HLA class I histocompatibility antigen, A-2 alpha chain


Theoretical massNumber of molelcules
Total (without water)269,19218
Polymers269,19218
Non-polymers00
Water11,512639
1
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1-1 beta chain
C: HLA class I histocompatibility antigen, A-2 alpha chain


Theoretical massNumber of molelcules
Total (without water)44,8653
Polymers44,8653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint-36 kcal/mol
Surface area17770 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 I histocompatibility antigen, A-2 alpha chain


Theoretical massNumber of molelcules
Total (without water)44,8653
Polymers44,8653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7300 Å2
ΔGint-38 kcal/mol
Surface area17620 Å2
MethodPISA
3
G: HLA class II histocompatibility antigen, DR alpha chain
H: HLA class II histocompatibility antigen, DRB1-1 beta chain
I: HLA class I histocompatibility antigen, A-2 alpha chain


Theoretical massNumber of molelcules
Total (without water)44,8653
Polymers44,8653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7010 Å2
ΔGint-37 kcal/mol
Surface area17550 Å2
MethodPISA
4
J: HLA class II histocompatibility antigen, DR alpha chain
K: HLA class II histocompatibility antigen, DRB1-1 beta chain
L: HLA class I histocompatibility antigen, A-2 alpha chain


Theoretical massNumber of molelcules
Total (without water)44,8653
Polymers44,8653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7130 Å2
ΔGint-38 kcal/mol
Surface area17610 Å2
MethodPISA
5
M: HLA class II histocompatibility antigen, DR alpha chain
N: HLA class II histocompatibility antigen, DRB1-1 beta chain
O: HLA class I histocompatibility antigen, A-2 alpha chain


Theoretical massNumber of molelcules
Total (without water)44,8653
Polymers44,8653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint-37 kcal/mol
Surface area17420 Å2
MethodPISA
6
P: HLA class II histocompatibility antigen, DR alpha chain
Q: HLA class II histocompatibility antigen, DRB1-1 beta chain
R: HLA class I histocompatibility antigen, A-2 alpha chain


Theoretical massNumber of molelcules
Total (without water)44,8653
Polymers44,8653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7170 Å2
ΔGint-38 kcal/mol
Surface area17590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.955, 173.188, 96.484
Angle α, β, γ (deg.)90.00, 109.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
HLA class II histocompatibility antigen, DR alpha chain / HLA-DR1 / MHC class II antigen DRA


Mass: 21155.904 Da / Num. of mol.: 6
Fragment: Secreted extracellular domain (UNP residues 26-207)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01903
#2: Protein
HLA class II histocompatibility antigen, DRB1-1 beta chain / HLA-DR1 / MHC class II antigen DRB1*1 / DR-1 / DR1


Mass: 22080.664 Da / Num. of mol.: 6
Fragment: Secreted extracellular domain (UNP residues 30-219)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB, HLA-DRB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P04229, UniProt: P01911*PLUS
#3: Protein/peptide
HLA class I histocompatibility antigen, A-2 alpha chain / HLA-A2 / MHC class I antigen A*2


Mass: 1628.811 Da / Num. of mol.: 6 / Fragment: peptide (UNP residues 128-141) / Mutation: W1A, Q9L / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01892, UniProt: P04439*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 639 / 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: 2.8 Å3/Da / Density % sol: 56.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 4% PEG4000, 10% ethylene glycol, 100 mM sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 9, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.199→46 Å / Num. all: 140622 / Num. obs: 140577 / % possible obs: 93.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.44 / Redundancy: 2.5 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 16.09
Reflection shellResolution: 2.199→2.24 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 1.44 / Num. unique all: 6124 / Rsym value: 0.477 / % possible all: 81.8

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AQD

1aqd


Resolution: 2.199→41.511 Å / SU ML: 0.32 / σ(F): 1.39 / Phase error: 26.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2395 7084 5.04 %RANDOM
Rwork0.2052 ---
obs0.2069 140577 93.64 %-
all-140622 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.199→41.511 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18427 0 0 639 19066
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00318983
X-RAY DIFFRACTIONf_angle_d0.77325850
X-RAY DIFFRACTIONf_dihedral_angle_d13.7616767
X-RAY DIFFRACTIONf_chiral_restr0.0532788
X-RAY DIFFRACTIONf_plane_restr0.0033385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.199-2.22360.32291810.2643855X-RAY DIFFRACTION81
2.2236-2.24970.3232050.25083950X-RAY DIFFRACTION83
2.2497-2.27720.28292180.24523908X-RAY DIFFRACTION83
2.2772-2.3060.29462400.24353956X-RAY DIFFRACTION84
2.306-2.33630.32932200.24974051X-RAY DIFFRACTION85
2.3363-2.36830.32012310.26213999X-RAY DIFFRACTION86
2.3683-2.40220.33332030.27034148X-RAY DIFFRACTION86
2.4022-2.4380.34932000.25994159X-RAY DIFFRACTION88
2.438-2.47610.31582170.25224228X-RAY DIFFRACTION88
2.4761-2.51670.30722190.25464236X-RAY DIFFRACTION90
2.5167-2.56010.27872150.2464347X-RAY DIFFRACTION92
2.5601-2.60670.30512390.25214468X-RAY DIFFRACTION93
2.6067-2.65680.29822530.24784409X-RAY DIFFRACTION94
2.6568-2.7110.32672370.24444522X-RAY DIFFRACTION95
2.711-2.76990.2762510.23664510X-RAY DIFFRACTION96
2.7699-2.83440.28562420.22634664X-RAY DIFFRACTION97
2.8344-2.90520.28662840.22494629X-RAY DIFFRACTION98
2.9052-2.98370.27782490.22844659X-RAY DIFFRACTION99
2.9837-3.07150.2672730.22434652X-RAY DIFFRACTION98
3.0715-3.17060.24882080.22364701X-RAY DIFFRACTION98
3.1706-3.28390.272550.22514711X-RAY DIFFRACTION99
3.2839-3.41530.24612320.21584755X-RAY DIFFRACTION99
3.4153-3.57070.22972690.19994689X-RAY DIFFRACTION99
3.5707-3.75880.2222260.19284742X-RAY DIFFRACTION100
3.7588-3.99410.22932440.19644761X-RAY DIFFRACTION99
3.9941-4.30220.19072510.17114728X-RAY DIFFRACTION99
4.3022-4.73460.18322510.15864753X-RAY DIFFRACTION100
4.7346-5.41850.18492380.16614783X-RAY DIFFRACTION100
5.4185-6.82180.22732780.19634742X-RAY DIFFRACTION99
6.8218-41.51840.18092550.18364778X-RAY DIFFRACTION99

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