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- PDB-5lax: Crystal structure of HLA_DRB1*04:01 in complex with alpha-enolase... -

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Basic information

Entry
Database: PDB / ID: 5lax
TitleCrystal structure of HLA_DRB1*04:01 in complex with alpha-enolase peptide 26-40
Components
  • HLA class II histocompatibility antigen, DR alpha chain
  • HLA class II histocompatibility antigen, DRB1-4 beta chain
  • alpha-enolase peptideTSKGLFRAAVPSGAS
KeywordsIMMUNE SYSTEM / HLA / autoimmune desease / rheumathoid arthritis / MHC class II
Function / homology
Function and homology information


Manipulation of host energy metabolism / positive regulation of plasminogen activation / regulation of interleukin-4 production / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / regulation of interleukin-10 production / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II ...Manipulation of host energy metabolism / positive regulation of plasminogen activation / regulation of interleukin-4 production / negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / 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 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 / positive regulation of muscle contraction / 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 kinase activity / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / Gluconeogenesis / inflammatory response to antigenic stimulus / CD4 receptor binding / canonical glycolysis / M band / 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 / nuclear outer membrane / positive regulation of ATP biosynthetic process / negative regulation of type II interferon production / humoral immune response / macrophage differentiation / Generation of second messenger molecules / immunological synapse / Co-inhibition by PD-1 / epidermis development / positive regulation of insulin secretion involved in cellular response to glucose stimulus / detection of bacterium / T cell receptor binding / negative regulation of T cell proliferation / MHC class II antigen presentation / trans-Golgi network membrane / transcription corepressor binding / glycolytic process / gluconeogenesis / lumenal side of endoplasmic reticulum membrane / RNA polymerase II transcription regulatory region sequence-specific DNA binding / protein tetramerization / peptide antigen assembly with MHC class II protein complex / negative regulation of inflammatory response to antigenic stimulus / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / negative regulation of cell growth / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / peptide antigen binding / structural constituent of cytoskeleton / positive regulation of T cell mediated cytotoxicity / response to virus / DNA-binding transcription repressor activity, RNA polymerase II-specific / cognition / positive regulation of protein phosphorylation / Interferon gamma signaling / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / transcription corepressor activity / Downstream TCR signaling / T cell receptor signaling pathway / GTPase binding / early endosome membrane / cell cortex / adaptive immune response / positive regulation of viral entry into host cell / positive regulation of ERK1 and ERK2 cascade / lysosome / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / immune response / cadherin binding / Golgi membrane / lysosomal membrane / external side of plasma 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 / 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: 2.6 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
DepositionJun 15, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1.2Nov 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 peptideTSKGLFRAAVPSGAS
F: alpha-enolase peptideTSKGLFRAAVPSGAS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,0347
Polymers92,9306
Non-polymers1041
Water4,792266
1
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen, DRB1-4 beta chain
E: alpha-enolase peptideTSKGLFRAAVPSGAS


Theoretical massNumber of molelcules
Total (without water)46,4653
Polymers46,4653
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7060 Å2
ΔGint-38 kcal/mol
Surface area18820 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 peptideTSKGLFRAAVPSGAS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5694
Polymers46,4653
Non-polymers1041
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7340 Å2
ΔGint-39 kcal/mol
Surface area18320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.176, 73.450, 144.600
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
13E
23F

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
12ARGARGALAALABB4 - 1904 - 190
22ARGARGALAALADD4 - 1904 - 190
13SERSERSERSEREE27 - 402 - 15
23SERSERSERSERFF27 - 402 - 15

NCS ensembles :
ID
1
2
3

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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. ADLVPR ARE A PART OF EXPRESSION TAG
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / Variant (production host): Star / 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 26-206. ADLVPR ARE A PART OF EXPRESSION TAG
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Production host: Escherichia coli / Strain (production host): BL21 (DE3) / Variant (production host): Star / References: UniProt: P13760, UniProt: P01911*PLUS
#3: Protein/peptide alpha-enolase peptideTSKGLFRAAVPSGAS


Mass: 1450.640 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: synthetic construct (others) / References: 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.: 266 / 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: 1.98 Å3/Da / Density % sol: 37.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 100 mM sodium malonate, pH 4.0, 12 to 18 percent (vol/vol) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 13, 2016
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.6→48.2 Å / Num. obs: 138347 / % possible obs: 99.6 % / Redundancy: 5.9 % / Biso Wilson estimate: 38.6 Å2 / CC1/2: 0.989 / Net I/σ(I): 7.8
Reflection shellResolution: 2.6→2.75 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1.8 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDS13.14.0data reduction
XDS13.14.0data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JLZ

5jlz


Resolution: 2.6→47.56 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.877 / SU B: 31.692 / SU ML: 0.341 / Cross valid method: THROUGHOUT / ESU R Free: 0.389 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26965 1167 5 %RANDOM
Rwork0.19101 ---
obs0.19491 22161 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 44.247 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2---2.11 Å20 Å2
3---1.97 Å2
Refinement stepCycle: 1 / Resolution: 2.6→47.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6302 0 7 266 6575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196494
X-RAY DIFFRACTIONr_bond_other_d0.0060.025926
X-RAY DIFFRACTIONr_angle_refined_deg1.6141.9338829
X-RAY DIFFRACTIONr_angle_other_deg1.341313623
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4435763
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.86723.526346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.541151031
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8871550
X-RAY DIFFRACTIONr_chiral_restr0.0890.2935
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217357
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021617
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_it0.8091.9153070
X-RAY DIFFRACTIONr_mcbond_other0.8051.9143069
X-RAY DIFFRACTIONr_mcangle_it1.4242.8633827
X-RAY DIFFRACTIONr_mcangle_other1.4242.8643828
X-RAY DIFFRACTIONr_scbond_it0.7131.9373424
X-RAY DIFFRACTIONr_scbond_other0.6991.9343422
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2542.8755002
X-RAY DIFFRACTIONr_long_range_B_refined3.67914.987027
X-RAY DIFFRACTIONr_long_range_B_other3.62314.8376968
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)
11A194260.12
12C194260.12
21B204840.11
22D204840.11
31E8120.17
32F8120.17
LS refinement shellResolution: 2.597→2.665 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 84 -
Rwork0.314 1592 -
obs--97.39 %
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)
14.10790.3256-2.45044.4731-1.20383.1124-0.26420.3213-0.4003-0.1165-0.03440.78670.0967-0.26520.29860.0421-0.01690.02910.1181-0.07410.3018-31.44726.2188-27.5437
21.5565-0.58390.71047.5427-0.61650.4514-0.16840.0137-0.17520.41490.14640.0940.05090.00140.0220.22360.02480.1560.1749-0.00940.1205-14.3989-7.5517-21.5577
33.5256-0.4522-2.74682.62280.17133.6995-0.19380.06160.12970.2148-0.01420.3635-0.0313-0.08890.20790.056-0.01660.02210.1233-0.01980.258-33.506717.0207-21.0528
46.7436-1.29063.49692.7771-1.89454.3806-0.0973-0.7439-0.2981.0890.0994-0.15580.0922-0.132-0.00210.96830.09280.20750.16520.05440.295-15.7099-10.10193.5682
54.36180.0841-1.09753.8990.15621.88590.1944-0.52970.09550.7490.0273-0.2132-0.18670.0629-0.22160.2633-0.0228-0.04140.1291-0.04880.0802-0.962527.8287-10.889
64.1233-2.66281.15823.9166-0.52632.347-0.2382-0.3587-0.0981.05540.2711-0.18810.35350.1727-0.03290.55440.0262-0.03680.1795-0.03730.136-0.85686.6375-3.7245
72.5018-0.7879-0.56323.83070.57891.70340.12370.08670.1954-0.09350.0136-0.0511-0.1872-0.1274-0.13720.04140.01910.02470.0783-0.01180.0648-4.823431.265-23.0889
83.2986-0.4058-0.35745.98221.18262.59-0.2725-0.0351-0.19490.33880.2355-0.44650.47120.15760.0370.10510.0558-0.0020.1662-0.04860.12888.7306-6.8085-23.3057
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 83
2X-RAY DIFFRACTION2A84 - 182
3X-RAY DIFFRACTION3B1 - 94
4X-RAY DIFFRACTION4B95 - 192
5X-RAY DIFFRACTION5C1 - 83
6X-RAY DIFFRACTION6C84 - 182
7X-RAY DIFFRACTION7D1 - 94
8X-RAY DIFFRACTION8D95 - 191

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