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- PDB-3d8d: Crystal structure of the human Fe65-PTB1 domain -

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Basic information

Entry
Database: PDB / ID: 3d8d
TitleCrystal structure of the human Fe65-PTB1 domain
ComponentsAmyloid beta A4 precursor protein-binding family B member 1
KeywordsPROTEIN BINDING / alpha-beta structure / phosphotyrosine binding domain
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 / amyloid-beta binding ...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 / amyloid-beta binding / chromatin organization / growth cone / histone binding / molecular adaptor activity / transcription coactivator activity / nuclear speck / positive regulation of apoptotic process / apoptotic process / synapse / ubiquitin protein ligase binding / DNA damage response / chromatin binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / 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. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / WW domain superfamily / WW/rsp5/WWP domain profile. ...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. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
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: 2.2 Å
AuthorsRadzimanowski, J. / Ravaud, S. / Sinning, I. / Wild, K.
Citation
Journal: J.Biol.Chem. / Year: 2008
Title: Crystal structure of the human Fe65-PTB1 domain.
Authors: Radzimanowski, J. / Ravaud, S. / Schlesinger, S. / Koch, J. / Beyreuther, K. / Sinning, I. / Wild, K.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Mercury-induced crystallization and SAD phasing of the human Fe65-PTB1 domain.
Authors: Radzimanowski, J. / Ravaud, S. / Beyreuther, K. / Sinning, I. / Wild, K.
History
DepositionMay 23, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 10, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amyloid beta A4 precursor protein-binding family B member 1
B: Amyloid beta A4 precursor protein-binding family B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8309
Polymers33,5642
Non-polymers1,2667
Water2,342130
1
A: Amyloid beta A4 precursor protein-binding family B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4465
Polymers16,7821
Non-polymers6644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Amyloid beta A4 precursor protein-binding family B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3844
Polymers16,7821
Non-polymers6023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
B: Amyloid beta A4 precursor protein-binding family B member 1
hetero molecules

A: Amyloid beta A4 precursor protein-binding family B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8309
Polymers33,5642
Non-polymers1,2667
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_466x-1/2,-y+3/2,-z+11
Buried area1670 Å2
ΔGint-128 kcal/mol
Surface area16060 Å2
MethodPISA
4
B: Amyloid beta A4 precursor protein-binding family B member 1
hetero molecules

A: Amyloid beta A4 precursor protein-binding family B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8309
Polymers33,5642
Non-polymers1,2667
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x+1/2,-y+1,z+1/21
Buried area2400 Å2
ΔGint-112 kcal/mol
Surface area15330 Å2
MethodPISA
5
B: Amyloid beta A4 precursor protein-binding family B member 1
hetero molecules

A: Amyloid beta A4 precursor protein-binding family B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8309
Polymers33,5642
Non-polymers1,2667
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-x,y-1/2,-z+1/21
Buried area2500 Å2
ΔGint-112 kcal/mol
Surface area15230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.756, 79.574, 83.974
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Amyloid beta A4 precursor protein-binding family B member 1 / Fe65-PTB1 / Fe65 protein


Mass: 16782.211 Da / Num. of mol.: 2 / Fragment: Fe65-PTB1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APBB1, FE65, RIR / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O00213
#2: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.18 Å3/Da / Density % sol: 43.52 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5
Details: 100mM HEPES, 5% (v/v) ethylene glycol, 8% (w/v) PEG 3350, 1mM CH3HgCl, pH 7.5, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0073 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0073 Å / Relative weight: 1
ReflectionResolution: 2.2→83.9 Å / Num. obs: 15508 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 19.2
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 4.6 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→42 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.92 / SU B: 5.935 / SU ML: 0.154 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.296 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.252 782 5.1 %RANDOM
Rwork0.202 ---
obs0.204 15458 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.469 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å20 Å2
2---0.07 Å20 Å2
3----0.28 Å2
Refine analyzeLuzzati sigma a obs: 0.267 Å
Refinement stepCycle: LAST / Resolution: 2.2→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2180 0 10 130 2320
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212221
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.962992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8725274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.09124.2100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.63415408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2941516
X-RAY DIFFRACTIONr_chiral_restr0.0910.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021642
X-RAY DIFFRACTIONr_nbd_refined0.2240.2867
X-RAY DIFFRACTIONr_nbtor_refined0.2960.21490
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2143
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.286
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.213
X-RAY DIFFRACTIONr_mcbond_it1.0841.51420
X-RAY DIFFRACTIONr_mcangle_it1.84822208
X-RAY DIFFRACTIONr_scbond_it2.4043886
X-RAY DIFFRACTIONr_scangle_it3.9034.5784
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 64 -
Rwork0.252 1039 -
all-1103 -
obs--100 %

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