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- PDB-5b3z: Crystal structure of hPin1 WW domain (5-39) fused with maltose-bi... -

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Basic information

Entry
Database: PDB / ID: 5b3z
TitleCrystal structure of hPin1 WW domain (5-39) fused with maltose-binding protein
ComponentsPeptidyl-prolyl cis-trans isomerase NIMA-interacting 1,Maltose-binding periplasmic protein
KeywordsISOMERASE / SUGAR BINDING PROTEIN
Function / homology
Function and homology information


cis-trans isomerase activity / phosphothreonine residue binding / negative regulation of cell motility / ubiquitin ligase activator activity / regulation of protein localization to nucleus / GTPase activating protein binding / mitogen-activated protein kinase kinase binding / protein targeting to mitochondrion / protein peptidyl-prolyl isomerization / regulation of mitotic nuclear division ...cis-trans isomerase activity / phosphothreonine residue binding / negative regulation of cell motility / ubiquitin ligase activator activity / regulation of protein localization to nucleus / GTPase activating protein binding / mitogen-activated protein kinase kinase binding / protein targeting to mitochondrion / protein peptidyl-prolyl isomerization / regulation of mitotic nuclear division / detection of maltose stimulus / maltose transport complex / negative regulation of SMAD protein signal transduction / PI5P Regulates TP53 Acetylation / negative regulation of amyloid-beta formation / carbohydrate transport / cytoskeletal motor activity / carbohydrate transmembrane transporter activity / RHO GTPases Activate NADPH Oxidases / maltose binding / phosphoserine residue binding / maltose transport / maltodextrin transmembrane transport / postsynaptic cytosol / negative regulation of protein binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / Rho protein signal transduction / ATP-binding cassette (ABC) transporter complex / regulation of cytokinesis / cell chemotaxis / peptidylprolyl isomerase / Negative regulators of DDX58/IFIH1 signaling / peptidyl-prolyl cis-trans isomerase activity / phosphoprotein binding / negative regulation of transforming growth factor beta receptor signaling pathway / beta-catenin binding / synapse organization / negative regulation of protein catabolic process / regulation of protein stability / negative regulation of ERK1 and ERK2 cascade / ISG15 antiviral mechanism / tau protein binding / positive regulation of protein phosphorylation / neuron differentiation / positive regulation of canonical Wnt signaling pathway / outer membrane-bounded periplasmic space / regulation of gene expression / midbody / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / response to hypoxia / periplasmic space / protein stabilization / nuclear speck / ciliary basal body / DNA damage response / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
: / Peptidyl-prolyl cis-trans isomerase, PpiC-type, conserved site / PpiC-type peptidyl-prolyl cis-trans isomerase signature. / PPIC-type PPIASE domain / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. ...: / Peptidyl-prolyl cis-trans isomerase, PpiC-type, conserved site / PpiC-type peptidyl-prolyl cis-trans isomerase signature. / PPIC-type PPIASE domain / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / 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 / Peptidyl-prolyl cis-trans isomerase domain superfamily / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein / Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHanazono, Y. / Takeda, K. / Miki, K.
CitationJournal: Sci Rep / Year: 2016
Title: Structural studies of the N-terminal fragments of the WW domain: Insights into co-translational folding of a beta-sheet protein
Authors: Hanazono, Y. / Takeda, K. / Miki, K.
History
DepositionMar 17, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Derived calculations / Category: diffrn_source / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
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 / struct_conn / 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_atom_id / _atom_site.label_comp_id / _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.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 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

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1,Maltose-binding periplasmic protein
B: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1,Maltose-binding periplasmic protein
C: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1,Maltose-binding periplasmic protein
D: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1,Maltose-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,9278
Polymers178,5584
Non-polymers1,3694
Water20,1231117
1
A: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1,Maltose-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9822
Polymers44,6391
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint2 kcal/mol
Surface area17190 Å2
MethodPISA
2
B: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1,Maltose-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9822
Polymers44,6391
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint1 kcal/mol
Surface area17410 Å2
MethodPISA
3
C: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1,Maltose-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9822
Polymers44,6391
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area630 Å2
ΔGint2 kcal/mol
Surface area17430 Å2
MethodPISA
4
D: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1,Maltose-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9822
Polymers44,6391
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint2 kcal/mol
Surface area16740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.514, 120.433, 110.670
Angle α, β, γ (deg.)90.00, 97.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1,Maltose-binding periplasmic protein


Mass: 44639.414 Da / Num. of mol.: 4 / Fragment: UNP(Q13526) 5-39,UNP(P0AEX9) residues 27-393 / Mutation: R403N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli K-12 (bacteria)
Gene: PIN1, malE / Strain: K-12 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13526, UniProt: P0AEX9
#2: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1117 / 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: 3.13 Å3/Da / Density % sol: 60.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.6M ammonium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 92792 / % possible obs: 95.4 % / Redundancy: 2.7 % / Rsym value: 0.097 / Net I/σ(I): 10.3
Reflection shellResolution: 2.3→2.34 Å / Mean I/σ(I) obs: 1.9 / % possible all: 89.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ANF

1anf


Resolution: 2.3→49.014 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 21.78
RfactorNum. reflection% reflectionSelection details
Rfree0.2241 4661 5.02 %Random selection
Rwork0.1812 ---
obs0.1834 92768 95.28 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→49.014 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12523 0 92 1117 13732
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00412939
X-RAY DIFFRACTIONf_angle_d0.83417568
X-RAY DIFFRACTIONf_dihedral_angle_d12.8054770
X-RAY DIFFRACTIONf_chiral_restr0.0561893
X-RAY DIFFRACTIONf_plane_restr0.0042264
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3004-2.32650.29971400.26312568X-RAY DIFFRACTION84
2.3265-2.35390.34631490.27832774X-RAY DIFFRACTION90
2.3539-2.38260.28761450.26382720X-RAY DIFFRACTION90
2.3826-2.41270.33261770.25892854X-RAY DIFFRACTION91
2.4127-2.44450.2891230.25592747X-RAY DIFFRACTION91
2.4445-2.4780.2741550.25382810X-RAY DIFFRACTION91
2.478-2.51340.34141150.25342858X-RAY DIFFRACTION92
2.5134-2.55090.31871740.25772850X-RAY DIFFRACTION93
2.5509-2.59070.30151370.23842827X-RAY DIFFRACTION93
2.5907-2.63320.27431610.22492877X-RAY DIFFRACTION93
2.6332-2.67860.28531700.21862848X-RAY DIFFRACTION94
2.6786-2.72730.27581470.20832949X-RAY DIFFRACTION95
2.7273-2.77980.271490.20522889X-RAY DIFFRACTION94
2.7798-2.83650.24441750.20972897X-RAY DIFFRACTION96
2.8365-2.89820.26141340.19142977X-RAY DIFFRACTION96
2.8982-2.96560.22471430.19722947X-RAY DIFFRACTION96
2.9656-3.03970.24241590.18783002X-RAY DIFFRACTION97
3.0397-3.12190.2211650.18152972X-RAY DIFFRACTION97
3.1219-3.21380.23381320.19123026X-RAY DIFFRACTION98
3.2138-3.31750.23221900.17582976X-RAY DIFFRACTION98
3.3175-3.4360.21611470.17253033X-RAY DIFFRACTION98
3.436-3.57350.21591390.15173067X-RAY DIFFRACTION99
3.5735-3.73610.17051550.14463057X-RAY DIFFRACTION99
3.7361-3.9330.17641420.14363099X-RAY DIFFRACTION99
3.933-4.17930.1921700.13583069X-RAY DIFFRACTION100
4.1793-4.50180.18831700.13933073X-RAY DIFFRACTION99
4.5018-4.95440.15271610.1323091X-RAY DIFFRACTION100
4.9544-5.67040.1981700.15513073X-RAY DIFFRACTION99
5.6704-7.14060.20071740.18163079X-RAY DIFFRACTION99
7.1406-49.02530.17991930.16333098X-RAY DIFFRACTION98

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