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- PDB-2idh: Crystal Structure of human FE65 WW domain -

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Basic information

Entry
Database: PDB / ID: 2idh
TitleCrystal Structure of human FE65 WW domain
ComponentsAmyloid beta A4 protein-binding family B member 1
KeywordsPROTEIN BINDING / WW domain / FE65
Function / homology
Function and homology information


negative regulation of cell cycle G1/S phase transition / proline-rich region binding / low-density lipoprotein particle receptor binding / smooth muscle contraction / axonogenesis / positive regulation of protein secretion / positive regulation of neuron projection development / lamellipodium / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization ...negative regulation of cell cycle G1/S phase transition / proline-rich region binding / low-density lipoprotein particle receptor binding / smooth muscle contraction / axonogenesis / positive regulation of protein secretion / positive regulation of neuron projection development / lamellipodium / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / amyloid-beta binding / growth cone / histone binding / transcription coactivator activity / molecular adaptor activity / nuclear speck / positive regulation of apoptotic process / synapse / apoptotic process / DNA damage response / ubiquitin protein ligase binding / chromatin binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Amyloid beta precursor protein binding family B member 1/2/3 / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues ...Amyloid beta precursor protein binding family B member 1/2/3 / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / PH-like domain superfamily
Similarity search - Domain/homology
Amyloid beta precursor protein binding family B member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.28 Å
AuthorsMeiyappan, M. / Birrane, G. / Ladias, J.A.A.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural Basis for Polyproline Recognition by the FE65 WW Domain.
Authors: Meiyappan, M. / Birrane, G. / Ladias, J.A.
History
DepositionSep 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2007Provider: repository / Type: Initial release
Revision 1.1Sep 17, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
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.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN ATOMS MISSING FROM TETRAETHYLENE GLYCOL, PG4, WERE NOT MODELED DUE TO LACK OF ELECTRON DENSITY.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amyloid beta A4 protein-binding family B member 1
B: Amyloid beta A4 protein-binding family B member 1
C: Amyloid beta A4 protein-binding family B member 1
D: Amyloid beta A4 protein-binding family B member 1
E: Amyloid beta A4 protein-binding family B member 1
F: Amyloid beta A4 protein-binding family B member 1
G: Amyloid beta A4 protein-binding family B member 1
H: Amyloid beta A4 protein-binding family B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,10817
Polymers33,5568
Non-polymers1,5529
Water2,144119
1
A: Amyloid beta A4 protein-binding family B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,4853
Polymers4,1951
Non-polymers2902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Amyloid beta A4 protein-binding family B member 1


Theoretical massNumber of molelcules
Total (without water)4,1951
Polymers4,1951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Amyloid beta A4 protein-binding family B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,3892
Polymers4,1951
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Amyloid beta A4 protein-binding family B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,4853
Polymers4,1951
Non-polymers2902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Amyloid beta A4 protein-binding family B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,3892
Polymers4,1951
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Amyloid beta A4 protein-binding family B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,3892
Polymers4,1951
Non-polymers1941
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Amyloid beta A4 protein-binding family B member 1


Theoretical massNumber of molelcules
Total (without water)4,1951
Polymers4,1951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Amyloid beta A4 protein-binding family B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,5833
Polymers4,1951
Non-polymers3882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.610, 75.610, 226.489
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11H-312-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21G
31F
12E
22H
32C
13A
23B
14C
24D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: TRP / Beg label comp-ID: TRP / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: 5 / Auth seq-ID: 259 - 279 / Label seq-ID: 8 - 28

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21GG
31FF
12EE
22HH
32CC
13AA
23BB
14CC
24DD

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein/peptide
Amyloid beta A4 protein-binding family B member 1 / Fe65 protein


Mass: 4194.533 Da / Num. of mol.: 8 / Fragment: WW domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APBB1, FE65 / Plasmid: pGEX-KT / Production host: Escherichia coli (E. coli) / References: UniProt: O00213
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.78 Å3/Da / Density % sol: 55.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.2M Ammonium Sulfate, 0.1M hepes 7.5, 2% PEG400, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X12C10.975
SYNCHROTRONNSLS X12C20.9789
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDJun 29, 2005
ADSC QUANTUM 2102CCDJun 28, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9751
20.97891
ReflectionResolution: 2.19→50 Å / Num. all: 20708 / Num. obs: 20584 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.2 % / Rmerge(I) obs: 0.045 / Rsym value: 0.036 / Net I/σ(I): 43.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.28→37.29 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.901 / SU B: 6.124 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.257 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28185 924 5 %RANDOM
Rwork0.2167 ---
all0.244 18339 --
obs0.21976 17415 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.28→37.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2036 0 62 119 2217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0212191
X-RAY DIFFRACTIONr_bond_other_d0.0050.021452
X-RAY DIFFRACTIONr_angle_refined_deg1.9251.923012
X-RAY DIFFRACTIONr_angle_other_deg1.02533513
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.1815245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86323.06198
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.14515259
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.0291510
X-RAY DIFFRACTIONr_chiral_restr0.1260.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022375
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02451
X-RAY DIFFRACTIONr_nbd_refined0.2410.2353
X-RAY DIFFRACTIONr_nbd_other0.2230.21331
X-RAY DIFFRACTIONr_nbtor_refined0.2040.2968
X-RAY DIFFRACTIONr_nbtor_other0.0960.21049
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2122
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.230.260
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.210
X-RAY DIFFRACTIONr_mcbond_it1.5741.51333
X-RAY DIFFRACTIONr_mcbond_other0.3691.5490
X-RAY DIFFRACTIONr_mcangle_it1.89322042
X-RAY DIFFRACTIONr_scbond_it2.55231159
X-RAY DIFFRACTIONr_scangle_it3.2244.5968
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A121medium positional0.170.5
12G121medium positional0.180.5
13F121medium positional0.310.5
21E121medium positional0.710.5
22H121medium positional0.560.5
23C121medium positional0.440.5
31A123medium positional0.340.5
41C121medium positional0.580.5
11A164loose positional0.425
12G164loose positional0.645
13F164loose positional0.645
21E154loose positional0.885
22H154loose positional0.795
23C154loose positional0.845
31A172loose positional0.895
41C154loose positional1.025
11A121medium thermal2.832
12G121medium thermal3.292
13F121medium thermal1.352
21E121medium thermal1.72
22H121medium thermal4.132
23C121medium thermal2.682
31A123medium thermal2.692
41C121medium thermal2.922
11A164loose thermal3.6410
12G164loose thermal3.9210
13F164loose thermal2.3910
21E154loose thermal2.5310
22H154loose thermal5.7910
23C154loose thermal3.7910
31A172loose thermal2.5110
41C154loose thermal3.7910
LS refinement shellResolution: 2.28→2.339 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 73 -
Rwork0.222 1256 -
obs--99.7 %

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