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- PDB-5jlz: Crystal structure of HLA-DRB1*04:01 in complex with modified alph... -

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Basic information

Entry
Database: PDB / ID: 5jlz
TitleCrystal structure of HLA-DRB1*04:01 in complex with modified alpha-enolase peptide 26-40 with citrulline at the position 32
Components
  • Alpha-enolase
  • HLA class II histocompatibility antigen, DR alpha chain
  • HLA class II histocompatibility antigen, DRB1-4 beta chain
KeywordsIMMUNE SYSTEM / HLA / autoimmune desease / rheumatoid arthritis / MHC class II / citrulline
Function / homology
Function and homology information


Manipulation of host energy metabolism / positive regulation of plasminogen activation / regulation of interleukin-4 production / regulation of interleukin-10 production / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / MHC class II receptor activity / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / myeloid dendritic cell antigen processing and presentation ...Manipulation of host energy metabolism / positive regulation of plasminogen activation / regulation of interleukin-4 production / regulation of interleukin-10 production / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / MHC class II receptor activity / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / 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 / positive regulation of CD4-positive, alpha-beta T cell activation / positive regulation of muscle contraction / positive regulation of kinase activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of T cell mediated immune response to tumor cell / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / inflammatory response to antigenic stimulus / CD4 receptor binding / Gluconeogenesis / M band / canonical glycolysis / Glycolysis / intermediate filament / T-helper 1 type immune response / transport vesicle membrane / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / polysaccharide binding / negative regulation of type II interferon production / positive regulation of ATP biosynthetic process / humoral immune response / nuclear outer membrane / macrophage differentiation / Generation of second messenger molecules / immunological synapse / Co-inhibition by PD-1 / epidermis development / detection of bacterium / positive regulation of insulin secretion involved in cellular response to glucose stimulus / T cell receptor binding / negative regulation of T cell proliferation / MHC class II antigen presentation / transcription corepressor binding / trans-Golgi network membrane / glycolytic process / gluconeogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / 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 / negative regulation of cell growth / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / structural constituent of cytoskeleton / DNA-binding transcription repressor activity, RNA polymerase II-specific / response to virus / cognition / 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 / Interferon gamma signaling / positive regulation of protein phosphorylation / endocytic vesicle membrane / transcription corepressor activity / MHC class II protein complex binding / Downstream TCR signaling / T cell receptor signaling pathway / late endosome membrane / GTPase binding / early endosome membrane / cell cortex / adaptive immune response / positive regulation of viral entry into host cell / positive regulation of canonical NF-kappaB signal transduction / positive regulation of ERK1 and ERK2 cascade / lysosome / positive regulation of MAPK cascade / immune response / cadherin binding / Golgi membrane / external side of plasma membrane / lysosomal membrane / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / magnesium ion binding / cell surface / negative regulation of transcription by RNA polymerase II / signal transduction / protein homodimerization activity / extracellular space / RNA binding
Similarity search - Function
Enolase / Enolase, conserved site / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase signature. / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 ...Enolase / Enolase, conserved site / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase signature. / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / 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 / Enolase-like, N-terminal / Enolase-like, C-terminal domain 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 / Roll / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MALONIC ACID / phosphopyruvate hydratase / HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain / Alpha-enolase / HLA class II histocompatibility antigen, DRB1 beta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsDubnovitsky, A. / Kozhukh, G. / Sandalova, T. / Achour, A.
CitationJournal: Front Immunol / Year: 2016
Title: Functional and Structural Characterization of a Novel HLA-DRB1*04:01-Restricted alpha-Enolase T Cell Epitope in Rheumatoid Arthritis.
Authors: Gerstner, C. / Dubnovitsky, A. / Sandin, C. / Kozhukh, G. / Uchtenhagen, H. / James, E.A. / Ronnelid, J. / Ytterberg, A.J. / Pieper, J. / Reed, E. / Tandre, C. / Rieck, M. / Zubarev, R.A. / ...Authors: Gerstner, C. / Dubnovitsky, A. / Sandin, C. / Kozhukh, G. / Uchtenhagen, H. / James, E.A. / Ronnelid, J. / Ytterberg, A.J. / Pieper, J. / Reed, E. / Tandre, C. / Rieck, M. / Zubarev, R.A. / Ronnblom, L. / Sandalova, T. / Buckner, J.H. / Achour, A. / Malmstrom, V.
History
DepositionApr 28, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ncs_dom_lim
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.1Jan 10, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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, DRB1-4 beta chain
C: HLA class II histocompatibility antigen, DR alpha chain
D: HLA class II histocompatibility antigen, DRB1-4 beta chain
E: Alpha-enolase
F: Alpha-enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,0347
Polymers92,9306
Non-polymers1041
Water6,593366
1
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1-4 beta chain
E: Alpha-enolase


Theoretical massNumber of molelcules
Total (without water)46,4653
Polymers46,4653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7410 Å2
ΔGint-31 kcal/mol
Surface area18990 Å2
MethodPISA
2
C: HLA class II histocompatibility antigen, DR alpha chain
D: HLA class II histocompatibility antigen, DRB1-4 beta chain
F: Alpha-enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5694
Polymers46,4653
Non-polymers1041
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7720 Å2
ΔGint-35 kcal/mol
Surface area18250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.442, 73.782, 145.482
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSGLUGLUAA2 - 1792 - 179
21LYSLYSGLUGLUCC2 - 1792 - 179
12ASPASPALAALABB2 - 1902 - 190
22ASPASPALAALADD2 - 1902 - 190

NCS ensembles :
ID
1
2

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Components

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


Mass: 21911.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Extracellular Domain, UNP residues 26-206 / Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01903
#2: Protein HLA class II histocompatibility antigen, DRB1-4 beta chain / MHC class II antigen DRB1*4 / DR4


Mass: 23102.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Extracellular Domain, UNP residues 30-219 / Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P13760, UniProt: P01911*PLUS
#3: Protein/peptide Alpha-enolase


Mass: 1450.617 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Post-translational modification of Arg32 of human alpha-enolase
Source: (synth.) Homo sapiens (human) / References: UniProt: K7EM90, UniProt: P06733*PLUS
#4: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / Source method: isolated from a natural source / Formula: H2O
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: 2.09 Å3/Da / Density % sol: 41.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 0.1M sodium malonate, 15% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.99→47.76 Å / Num. obs: 51357 / % possible obs: 99.1 % / Redundancy: 5.3 % / Biso Wilson estimate: 38.3 Å2 / CC1/2: 0.994 / Net I/σ(I): 9.9
Reflection shellResolution: 1.99→2.05 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 1.9 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MCY

4mcy


Resolution: 1.99→47.76 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / SU B: 14.329 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.228 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24313 2100 4.1 %RANDOM
Rwork0.20602 ---
obs0.20753 49255 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.751 Å2
Baniso -1Baniso -2Baniso -3
1-1.69 Å20 Å20 Å2
2---3.37 Å20 Å2
3---1.68 Å2
Refinement stepCycle: LAST / Resolution: 1.99→47.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6307 0 7 366 6680
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196528
X-RAY DIFFRACTIONr_bond_other_d0.0060.025949
X-RAY DIFFRACTIONr_angle_refined_deg1.6121.9378882
X-RAY DIFFRACTIONr_angle_other_deg1.295313683
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5535766
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.83523.584346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.117151029
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9171549
X-RAY DIFFRACTIONr_chiral_restr0.1030.2942
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217406
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021626
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2162.0143082
X-RAY DIFFRACTIONr_mcbond_other1.2152.0143081
X-RAY DIFFRACTIONr_mcangle_it2.1533.0123844
X-RAY DIFFRACTIONr_mcangle_other2.1533.0123845
X-RAY DIFFRACTIONr_scbond_it1.2352.1163446
X-RAY DIFFRACTIONr_scbond_other1.2342.1143444
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1263.1225034
X-RAY DIFFRACTIONr_long_range_B_refined6.2316.3427132
X-RAY DIFFRACTIONr_long_range_B_other6.22916.3477133
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A199040.11
12C199040.11
21B204420.1
22D204420.1
LS refinement shellResolution: 1.993→2.045 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 142 -
Rwork0.332 3350 -
obs--93.07 %
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)
10.592-0.911-0.17831.65460.27550.1236-0.17490.1207-0.15020.28970.01550.2410.08760.01770.15950.1232-0.0060.12940.23980.01730.3208-22.1664-1.3895-24.4729
20.2299-0.5288-0.12111.91550.53750.2312-0.20280.151-0.01490.8202-0.09020.39780.297-0.00820.2930.4071-0.03290.31430.19630.07680.4834-24.78273.4812-8.9449
30.2216-0.5739-0.21951.96430.17860.7797-0.1464-0.02690.08280.60510.2093-0.16820.1310.0095-0.06290.39910.0537-0.00620.1795-0.05020.1327-0.876116.2278-7.0731
40.2744-0.4813-0.31451.910.34980.4407-0.02270.02150.05050.15440.0717-0.10060.03880.0291-0.0490.08950.0189-0.01020.2166-0.03620.22721.789712.5042-23.1637
57.0086.032-4.75415.2659-4.16083.3501-0.52020.6704-0.151-0.36740.55120.04440.1992-0.4989-0.0310.227-0.00960.140.2154-0.0690.4454-42.13788.9011-25.5256
62.1108-1.89720.02691.7294-0.04660.95450.0375-0.09180.37460.04050.0669-0.3209-0.17060.0063-0.10440.2181-0.04040.02510.2044-0.07460.31495.025635.5101-16.4103
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 181
2X-RAY DIFFRACTION2B1 - 193
3X-RAY DIFFRACTION3C2 - 180
4X-RAY DIFFRACTION4D2 - 191
5X-RAY DIFFRACTION5E27 - 40
6X-RAY DIFFRACTION6F27 - 40

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