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- PDB-4xhs: Crystal structure of human NLRP12 PYD domain and implication in h... -

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Entry
Database: PDB / ID: 4xhs
TitleCrystal structure of human NLRP12 PYD domain and implication in homotypic interaction
ComponentsMaltose-binding periplasmic protein,NACHT, LRR and PYD domains-containing protein 12
KeywordsTRANSPORT PROTEIN / NOD-like receptor / NLRP12 / death domain superfamily / PYD / MBP / homotypic interaction / caspase-1
Function / homology
Function and homology information


regulation of interleukin-18 production / negative regulation of Toll signaling pathway / positive regulation of MHC class I biosynthetic process / regulation of cysteine-type endopeptidase activity involved in apoptotic process / dendritic cell migration / negative regulation of protein autophosphorylation / negative regulation of interleukin-1 production / negative regulation of non-canonical NF-kappaB signal transduction / regulation of canonical NF-kappaB signal transduction / negative regulation of cytokine production ...regulation of interleukin-18 production / negative regulation of Toll signaling pathway / positive regulation of MHC class I biosynthetic process / regulation of cysteine-type endopeptidase activity involved in apoptotic process / dendritic cell migration / negative regulation of protein autophosphorylation / negative regulation of interleukin-1 production / negative regulation of non-canonical NF-kappaB signal transduction / regulation of canonical NF-kappaB signal transduction / negative regulation of cytokine production / detection of maltose stimulus / negative regulation of NF-kappaB transcription factor activity / maltose transport complex / cellular response to cytokine stimulus / carbohydrate transport / cysteine-type endopeptidase activator activity involved in apoptotic process / negative regulation of interleukin-6 production / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / negative regulation of signal transduction / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / negative regulation of canonical NF-kappaB signal transduction / ERK1 and ERK2 cascade / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / positive regulation of interleukin-1 beta production / negative regulation of ERK1 and ERK2 cascade / negative regulation of inflammatory response / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / activation of cysteine-type endopeptidase activity involved in apoptotic process / protein-macromolecule adaptor activity / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / SARS-CoV-2 activates/modulates innate and adaptive immune responses / signal transduction / ATP binding / membrane / cytoplasm / cytosol
Similarity search - Function
NACHT-associated domain / Fish-specific NACHT associated domain / Fish-specific NACHT associated domain / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain ...NACHT-associated domain / Fish-specific NACHT associated domain / Fish-specific NACHT associated domain / NACHT, LRR and PYD domains-containing protein, helical domain HD2 / NLRC4 helical domain HD2 / NOD2, winged helix domain / NOD2 winged helix domain / DAPIN domain / DAPIN domain profile. / PAAD/DAPIN/Pyrin domain / NACHT nucleoside triphosphatase / NACHT domain / NACHT-NTPase domain profile. / PAAD/DAPIN/Pyrin domain / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Leucine-rich repeat profile. / Death-like domain superfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
alpha-maltose / FORMIC ACID / Maltose/maltodextrin-binding periplasmic protein / Maltose/maltodextrin-binding periplasmic protein / NACHT, LRR and PYD domains-containing protein 12
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsJin, T. / Huang, M. / Jiang, J. / Xiao, T.
CitationJournal: To Be Published
Title: Crystal structure of human NLRP12 PYD domain and implication in homotypic interaction
Authors: Jin, T. / Huang, M. / Jiang, J. / Smith, P. / Xiao, T.
History
DepositionJan 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 20, 2016Group: Data collection
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Maltose-binding periplasmic protein,NACHT, LRR and PYD domains-containing protein 12
B: Maltose-binding periplasmic protein,NACHT, LRR and PYD domains-containing protein 12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,58515
Polymers105,5562
Non-polymers1,03013
Water19,4741081
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-71 kcal/mol
Surface area37760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.720, 103.620, 186.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11B-1009-

HOH

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Components

#1: Protein Maltose-binding periplasmic protein,NACHT, LRR and PYD domains-containing protein 12 / MBP / MMBP / Maltodextrin-binding protein / Monarch-1 / PYRIN-containing APAF1-like protein 7 / ...MBP / MMBP / Maltodextrin-binding protein / Monarch-1 / PYRIN-containing APAF1-like protein 7 / Regulated by nitric oxide


Mass: 52777.801 Da / Num. of mol.: 2
Fragment: UNP P0AEY0 residues 27-392, UNP P59046 residues 10-106
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria), (gene. exp.) Homo sapiens (human)
Gene: malE, Z5632, ECs5017, NLRP12, NALP12, PYPAF7, RNO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P0AEY0, UniProt: P59046, UniProt: P0AEX9*PLUS
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1081 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 3.5 M Sodium Formate, 0.1 M Sodium Acetate pH 4.6 / Temp details: RT

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 22, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 110662 / % possible obs: 97.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 22.4
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 3.7 / % possible all: 85.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1683refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VD8, 2L6A

3vd8

2l6a


Resolution: 1.7→46.988 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1901 2000 1.8 %Random selection
Rwork0.1601 ---
obs0.1606 110662 94.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→46.988 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7029 0 65 1081 8175
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067428
X-RAY DIFFRACTIONf_angle_d0.99610113
X-RAY DIFFRACTIONf_dihedral_angle_d12.0772763
X-RAY DIFFRACTIONf_chiral_restr0.0411112
X-RAY DIFFRACTIONf_plane_restr0.0051299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.72080.2334840.25164941X-RAY DIFFRACTION63
1.7208-1.74350.23871050.23075856X-RAY DIFFRACTION74
1.7435-1.76740.2641110.22346176X-RAY DIFFRACTION78
1.7674-1.79260.2581250.21246504X-RAY DIFFRACTION82
1.7926-1.81940.22111280.21476910X-RAY DIFFRACTION86
1.8194-1.84780.20871270.21247051X-RAY DIFFRACTION90
1.8478-1.87810.27081370.1967410X-RAY DIFFRACTION93
1.8781-1.91050.22991420.19597588X-RAY DIFFRACTION96
1.9105-1.94520.22191500.18667901X-RAY DIFFRACTION99
1.9452-1.98260.21671440.17647836X-RAY DIFFRACTION100
1.9826-2.02310.26081490.17687957X-RAY DIFFRACTION100
2.0231-2.06710.18781440.16257865X-RAY DIFFRACTION100
2.0671-2.11520.20221460.16718016X-RAY DIFFRACTION100
2.1152-2.16810.18151440.16657848X-RAY DIFFRACTION100
2.1681-2.22670.2351400.16747906X-RAY DIFFRACTION100
2.2267-2.29220.19281440.16397991X-RAY DIFFRACTION100
2.2922-2.36620.18811470.16687864X-RAY DIFFRACTION100
2.3662-2.45080.20241460.16947878X-RAY DIFFRACTION100
2.4508-2.54890.2061460.16967942X-RAY DIFFRACTION100
2.5489-2.66490.20831500.17047884X-RAY DIFFRACTION100
2.6649-2.80540.21951480.16467933X-RAY DIFFRACTION100
2.8054-2.98110.17541460.1687896X-RAY DIFFRACTION100
2.9811-3.21120.19071470.15887890X-RAY DIFFRACTION100
3.2112-3.53430.18881380.1437946X-RAY DIFFRACTION100
3.5343-4.04540.1391470.12437904X-RAY DIFFRACTION100
4.0454-5.09590.15081470.12357894X-RAY DIFFRACTION100
5.0959-47.00590.17391410.15877904X-RAY DIFFRACTION100

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