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- PDB-5nqh: Structure of the human Fe65-PTB2 homodimer -

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Basic information

Entry
Database: PDB / ID: 5nqh
TitleStructure of the human Fe65-PTB2 homodimer
ComponentsAmyloid beta A4 precursor protein-binding family B member 1
KeywordsSIGNALING PROTEIN / Alzheimers disease / phosphotyrosine-binding (PTB) domain / homodimerization
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 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / 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 / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsFeilen, L.P. / Haubrich, K. / Sinning, I. / Konietzko, U. / Kins, S. / Simon, B. / Wild, K.
CitationJournal: Front Mol Neurosci / Year: 2017
Title: Fe65-PTB2 Dimerization Mimics Fe65-APP Interaction.
Authors: Feilen, L.P. / Haubrich, K. / Strecker, P. / Probst, S. / Eggert, S. / Stier, G. / Sinning, I. / Konietzko, U. / Kins, S. / Simon, B. / Wild, K.
History
DepositionApr 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Amyloid beta A4 precursor protein-binding family B member 1
B: Amyloid beta A4 precursor protein-binding family B member 1
C: Amyloid beta A4 precursor protein-binding family B member 1
D: Amyloid beta A4 precursor protein-binding family B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,87615
Polymers61,8394
Non-polymers1,03711
Water1,40578
1
A: Amyloid beta A4 precursor protein-binding family B member 1
C: Amyloid beta A4 precursor protein-binding family B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5809
Polymers30,9192
Non-polymers6617
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-71 kcal/mol
Surface area13500 Å2
MethodPISA
2
B: Amyloid beta A4 precursor protein-binding family B member 1
D: Amyloid beta A4 precursor protein-binding family B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2966
Polymers30,9192
Non-polymers3764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-37 kcal/mol
Surface area13840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.578, 104.279, 60.578
Angle α, β, γ (deg.)90.000, 112.040, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 15459.690 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APBB1, FE65, RIR / Production host: Escherichia coli (E. coli) / References: UniProt: O00213
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.97 Å3/Da / Density % sol: 58.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.08 M sodium acetate, 1.6 M ammonium sulfate, 20 % (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.6→49.44 Å / Num. obs: 19955 / % possible obs: 99.3 % / Redundancy: 6.6 % / Biso Wilson estimate: 39.04 Å2 / Net I/σ(I): 9
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 2.3 / % possible all: 98.3

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3dxc

3dxc


Resolution: 2.6→49.44 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.23
RfactorNum. reflection% reflection
Rfree0.2405 1016 5.1 %
Rwork0.1927 --
obs0.1952 19931 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 153.03 Å2 / Biso mean: 50.7225 Å2 / Biso min: 16.75 Å2
Refinement stepCycle: final / Resolution: 2.6→49.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3832 0 60 78 3970
Biso mean--76.53 44.41 -
Num. residues----501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023973
X-RAY DIFFRACTIONf_angle_d0.5835397
X-RAY DIFFRACTIONf_chiral_restr0.041618
X-RAY DIFFRACTIONf_plane_restr0.003678
X-RAY DIFFRACTIONf_dihedral_angle_d10.5112336
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.73710.39481200.30062703282398
2.7371-2.90860.28141440.25182670281499
2.9086-3.13310.26531410.22762710285199
3.1331-3.44830.23121350.21022700283599
3.4483-3.94710.23441640.178326952859100
3.9471-4.97220.21561520.14782714286699
4.9722-49.44870.21761600.17662723288399
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.6112-0.012-0.54041.9253-0.53432.75120.0213-0.7358-0.45230.2336-0.09010.18020.3193-0.49960.07220.2742-0.06060.01730.4368-0.01140.2553-25.1228-2.6807-7.7178
22.1568-2.3843-1.23413.58310.00095.70.273-0.6877-0.03490.1979-0.0612-0.27680.11440.3742-0.15260.4006-0.1041-0.030.64390.02160.3867-22.3523-0.44052.1714
38.25331.14314.47768.6504-2.18363.37770.55-2.10580.22451.8281-0.0693-0.7558-0.9097-2.0899-0.45990.51430.0017-0.04440.8522-0.20790.5188-33.78687.02490.6691
47.8497-2.12451.796.03840.82374.0866-0.0476-0.19810.3836-0.10810.0205-0.12640.03050.33110.03440.1819-0.0417-0.01830.2291-0.00950.284-28.439-1.4949-9.4316
59.9176-5.71176.55054.8824-4.78314.85730.1157-0.1986-0.5013-0.13740.0232-0.08830.0386-0.0235-0.17490.3108-0.00670.00130.31090.02280.291-45.4309-1.33-15.6401
66.2110.4537-0.80733.12691.30473.34380.1989-0.7729-0.09260.26690.1625-0.3169-0.32270.1051-0.37230.2199-0.06370.02820.2440.0130.2601-60.87478.0947-4.103
75.1630.21441.79565.37232.83143.22250.02650.2134-0.0366-0.1664-0.11890.5433-0.3244-0.78370.1820.3013-0.03980.12930.39060.05240.2667-65.48146.1274-13.4509
85.2424-5.3599-0.64465.51121.17524.4853-0.36640.52650.84341.28060.068-0.6914-0.8599-0.0720.28020.55220.09050.05070.39390.11290.3645-62.16226.773.0595
93.7221-0.6681-0.57593.7337-0.02024.09690.0472-0.0149-0.1877-0.1743-0.03680.1940.13210.1018-0.02630.15520.0009-0.0040.2368-0.01550.2339-59.7371.8204-9.822
106.10974.73060.77154.89321.61443.87970.6937-0.4565-0.73990.75250.73691.16391.4037-1.5687-0.89370.46330.0066-0.00290.48660.07690.4063-67.6169-11.5183-10.8826
113.04870.4137-0.00194.20630.73634.1886-0.01880.15980.2946-0.04480.1044-0.1728-0.21840.3241-0.0490.21840.00750.05330.2169-0.02510.246-56.49516.4985-9.3779
127.9549-1.46965.50133.78250.19175.89190.2458-0.9221-3.18040.35150.4583-0.10890.8740.2002-0.40550.5766-0.01340.2310.72010.04530.9744-45.2706-11.3015-5.1524
133.8453-2.1176-1.5014.80670.49324.2001-0.6384-0.08710.4689-0.72480.85440.14260.33060.5546-0.04110.3919-0.0861-0.02760.38380.0520.3097-41.08753.5876-38.0362
147.03461.07240.74424.08310.00166.6992-0.28970.2248-0.70770.41790.1111-0.04181.2120.07990.04470.5178-0.040.13980.1865-0.04810.3637-48.854-7.265-27.7992
157.9332-1.5144-3.01743.6979-1.97823.58640.07340.5902-0.9607-2.0181-1.2211-1.35621.91542.86491.23011.01620.37030.14531.3680.40070.6354-31.9224-7.3481-33.0837
167.0285-4.737-1.27473.58840.62176.5197-0.3080.45180.59490.42370.1274-0.70360.03611.10290.21630.28190.0338-0.02780.53880.08460.3278-39.39754.7521-43.7799
178.0204-2.1992-0.29672.42250.54620.22350.06370.9184-0.2368-0.3128-0.1280.3570.3491-0.317-0.05390.22970.0025-0.05830.249-0.03630.2731-51.26062.1157-39.3873
186.72282.9767-1.26646.4428-1.43995.2815-0.46790.1587-0.0853-0.4979-0.18930.08520.49730.31050.51170.33880.15230.04540.3313-0.0440.2715-45.8376-0.6594-31.9888
192.126-4.09690.88048.0604-0.60616.930.8520.40510.3469-0.712-0.80530.5489-0.4872-0.45710.01030.3960.07170.00220.5319-0.02120.3114-55.173812.3686-36.2132
202.8838-1.56470.78053.0431-0.64110.9173-0.4255-0.0519-0.158-0.10240.01510.43680.12180.55570.60820.65610.02740.08410.3057-0.07960.4393-57.249631.0466-34.0433
214.88141.89142.38397.1817-1.51422.0726-0.1896-0.18710.30431.03970.39441.2862-0.4115-1.2357-0.28190.5870.10120.20930.40080.16280.6482-69.909432.9127-22.7603
228.02614.35532.63486.75426.72037.273-0.6782-1.80291.12941.7424-1.28630.2452-0.476-0.35390.82510.7636-0.175-0.39160.48780.11870.7528-63.419544.8466-30.9934
237.0156-3.47383.34922.99350.25624.49440.0120.85180.0596-1.1542-0.4265-0.83180.08540.85570.38590.40760.07010.07530.40440.02910.4229-51.347931.2233-34.8924
240.18040.20690.17096.7322-3.42935.8135-0.1952-0.0598-0.15890.71510.19310.6951-0.8730.2970.06970.4038-0.10910.00650.30350.00290.394-61.002126.9981-27.3203
253.9006-2.8932-2.65168.7139-1.28943.4396-0.11850.0188-0.23170.40760.27410.68870.2832-0.1147-0.16780.3212-0.0385-0.00740.26470.0520.3466-62.590727.0711-29.3157
262.86982.838-0.59213.4818-2.55637.3886-0.09190.0369-0.50280.10320.1584-0.14210.13020.233-0.10430.25080.0720.03570.3626-0.06720.3422-53.39172.6254-20.3256
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 539 through 570 )A539 - 570
2X-RAY DIFFRACTION2chain 'A' and (resid 571 through 585 )A571 - 585
3X-RAY DIFFRACTION3chain 'A' and (resid 586 through 599 )A586 - 599
4X-RAY DIFFRACTION4chain 'A' and (resid 600 through 643 )A600 - 643
5X-RAY DIFFRACTION5chain 'A' and (resid 644 through 665 )A644 - 665
6X-RAY DIFFRACTION6chain 'B' and (resid 539 through 552 )B539 - 552
7X-RAY DIFFRACTION7chain 'B' and (resid 553 through 585 )B553 - 585
8X-RAY DIFFRACTION8chain 'B' and (resid 586 through 599 )B586 - 599
9X-RAY DIFFRACTION9chain 'B' and (resid 600 through 626 )B600 - 626
10X-RAY DIFFRACTION10chain 'B' and (resid 627 through 631 )B627 - 631
11X-RAY DIFFRACTION11chain 'B' and (resid 632 through 655 )B632 - 655
12X-RAY DIFFRACTION12chain 'B' and (resid 656 through 666 )B656 - 666
13X-RAY DIFFRACTION13chain 'C' and (resid 539 through 552 )C539 - 552
14X-RAY DIFFRACTION14chain 'C' and (resid 553 through 571 )C553 - 571
15X-RAY DIFFRACTION15chain 'C' and (resid 572 through 578 )C572 - 578
16X-RAY DIFFRACTION16chain 'C' and (resid 579 through 599 )C579 - 599
17X-RAY DIFFRACTION17chain 'C' and (resid 600 through 614 )C600 - 614
18X-RAY DIFFRACTION18chain 'C' and (resid 615 through 643 )C615 - 643
19X-RAY DIFFRACTION19chain 'C' and (resid 644 through 663 )C644 - 663
20X-RAY DIFFRACTION20chain 'D' and (resid 539 through 552 )D539 - 552
21X-RAY DIFFRACTION21chain 'D' and (resid 553 through 570 )D553 - 570
22X-RAY DIFFRACTION22chain 'D' and (resid 571 through 578 )D571 - 578
23X-RAY DIFFRACTION23chain 'D' and (resid 579 through 599 )D579 - 599
24X-RAY DIFFRACTION24chain 'D' and (resid 600 through 619 )D600 - 619
25X-RAY DIFFRACTION25chain 'D' and (resid 620 through 655 )D620 - 655
26X-RAY DIFFRACTION26chain 'D' and (resid 656 through 666 )D656 - 666

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