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- PDB-5nig: Crystal structure of HLA-DRB1*04:01 with modified alpha-enolase p... -

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Basic information

Entry
Database: PDB / ID: 5nig
TitleCrystal structure of HLA-DRB1*04:01 with modified alpha-enolase peptide 326-340 (arginine 327 to citrulline)
Components
  • (HLA class II histocompatibility antigen, ...) x 2
  • Alpha-enolase
KeywordsIMMUNE SYSTEM / HLA-DR / enolase / arthritis / citrulline
Function / homology
Function and homology information


negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / Manipulation of host energy metabolism / positive regulation of muscle contraction / positive regulation of plasminogen activation / regulation of interleukin-4 production / regulation of interleukin-10 production / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / positive regulation of T cell mediated immune response to tumor cell ...negative regulation of hypoxia-induced intrinsic apoptotic signaling pathway / Manipulation of host energy metabolism / positive regulation of muscle contraction / positive regulation of plasminogen activation / regulation of interleukin-4 production / regulation of interleukin-10 production / phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / 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 / Gluconeogenesis / nuclear outer membrane / positive regulation of kinase activity / inflammatory response to antigenic stimulus / M band / canonical glycolysis / Glycolysis / transport vesicle membrane / intermediate filament / polysaccharide binding / T-helper 1 type immune response / positive regulation of ATP biosynthetic process / 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 / negative regulation of type II interferon production / Generation of second messenger molecules / immunological synapse / PD-1 signaling / epidermis development / detection of bacterium / T cell receptor binding / negative regulation of T cell proliferation / negative regulation of inflammatory response to antigenic stimulus / MHC class II antigen presentation / transcription corepressor binding / trans-Golgi network membrane / gluconeogenesis / lumenal side of endoplasmic reticulum membrane / glycolytic process / protein tetramerization / RNA polymerase II transcription regulatory region sequence-specific DNA binding / clathrin-coated endocytic vesicle membrane / response to virus / ER to Golgi transport vesicle membrane / negative regulation of cell growth / structural constituent of cytoskeleton / cognition / DNA-binding transcription repressor activity, RNA polymerase II-specific / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / peptide antigen binding / transcription corepressor activity / endocytic vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / Interferon gamma signaling / positive regulation of immune response / positive regulation of T cell activation / Downstream TCR signaling / GTPase binding / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / cell cortex / 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 / cadherin binding / immune response / positive regulation of protein phosphorylation / lysosomal membrane / external side of plasma membrane / Golgi membrane / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / magnesium ion binding / cell surface / 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 / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / UREA / 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: 1.35 Å
AuthorsGerstner, C. / Dubnovitsky, A.
CitationJournal: J. Autoimmun. / Year: 2018
Title: Memory T cells specific to citrullinated alpha-enolase are enriched in the rheumatic joint.
Authors: Pieper, J. / Dubnovitsky, A. / Gerstner, C. / James, E.A. / Rieck, M. / Kozhukh, G. / Tandre, K. / Pellegrino, S. / Gebe, J.A. / Ronnblom, L. / Sandalova, T. / Kwok, W.W. / Klareskog, L. / ...Authors: Pieper, J. / Dubnovitsky, A. / Gerstner, C. / James, E.A. / Rieck, M. / Kozhukh, G. / Tandre, K. / Pellegrino, S. / Gebe, J.A. / Ronnblom, L. / Sandalova, T. / Kwok, W.W. / Klareskog, L. / Buckner, J.H. / Achour, A. / Malmstrom, V.
History
DepositionMar 24, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
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
Revision 2.1Jan 17, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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, DRB1-4 beta chain
C: Alpha-enolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2608
Polymers46,6953
Non-polymers5655
Water7,458414
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8730 Å2
ΔGint-46 kcal/mol
Surface area18630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.606, 128.319, 53.521
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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HLA class II histocompatibility antigen, ... , 2 types, 2 molecules AB

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


Mass: 21911.750 Da / Num. of mol.: 1
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, DRB1-4 beta chain / MHC class II antigen DRB1*4 / DR4


Mass: 23102.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1 / Production host: Escherichia coli (E. coli) / References: UniProt: P13760, UniProt: P01911*PLUS

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Alpha-enolase / / 2-phospho-D-glycerate hydro-lyase / C-myc promoter-binding protein / Enolase 1 / MBP-1 / MPB-1 / ...2-phospho-D-glycerate hydro-lyase / C-myc promoter-binding protein / Enolase 1 / MBP-1 / MPB-1 / Non-neural enolase / NNE / Phosphopyruvate hydratase / Plasminogen-binding protein


Mass: 1681.010 Da / Num. of mol.: 1 / Fragment: UNP Residues 326-340 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P06733, phosphopyruvate hydratase

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Non-polymers , 4 types, 419 molecules

#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-URE / UREA / Urea


Mass: 60.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4N2O
#6: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 2.52 Å3/Da / Density % sol: 51.24 % / Description: rod-like big crystals
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES pH 6.5 10% (vol/vol) MPD 15% (vol/vol) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.35→46.86 Å / Num. obs: 103630 / % possible obs: 98.9 % / Redundancy: 4.4 % / Biso Wilson estimate: 23.5 Å2 / CC1/2: 0.996 / Net I/σ(I): 9.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NI9

5ni9


Resolution: 1.35→46.86 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.062 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.047 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1808 2100 2 %RANDOM
Rwork0.14201 ---
obs0.14281 101530 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 22.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å20 Å2
2---1.18 Å20 Å2
3---0.45 Å2
Refinement stepCycle: 1 / Resolution: 1.35→46.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3217 0 38 414 3669
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193448
X-RAY DIFFRACTIONr_bond_other_d0.0020.023212
X-RAY DIFFRACTIONr_angle_refined_deg1.551.9494710
X-RAY DIFFRACTIONr_angle_other_deg0.92437401
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7965420
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0723.846182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.40115564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7761525
X-RAY DIFFRACTIONr_chiral_restr0.0990.2508
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213899
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02849
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_it1.7161.9231600
X-RAY DIFFRACTIONr_mcbond_other1.7151.9191598
X-RAY DIFFRACTIONr_mcangle_it2.1612.8862002
X-RAY DIFFRACTIONr_mcangle_other2.162.8882003
X-RAY DIFFRACTIONr_scbond_it2.1942.2621848
X-RAY DIFFRACTIONr_scbond_other2.1922.2621848
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6873.2732692
X-RAY DIFFRACTIONr_long_range_B_refined3.54324.093812
X-RAY DIFFRACTIONr_long_range_B_other3.54224.093813
X-RAY DIFFRACTIONr_rigid_bond_restr2.17836660
X-RAY DIFFRACTIONr_sphericity_free25.5525256
X-RAY DIFFRACTIONr_sphericity_bonded9.52556714
LS refinement shellResolution: 1.348→1.383 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 149 -
Rwork0.267 7183 -
obs--95.87 %

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