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- PDB-4dbb: The PTB domain of Mint1 is autoinhibited by a helix in the C-term... -

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Basic information

Entry
Database: PDB / ID: 4dbb
TitleThe PTB domain of Mint1 is autoinhibited by a helix in the C-terminal linker region
ComponentsAmyloid beta A4 precursor protein-binding family A member 1
KeywordsPROTEIN TRANSPORT / X11S/MINTS / PTB DOMAIN / CHIMERA PROTEIN
Function / homology
Function and homology information


gamma-aminobutyric acid secretion / Dopamine Neurotransmitter Release Cycle / glutamate secretion / synaptic vesicle exocytosis / presynaptic active zone membrane / phosphatidylinositol-4,5-bisphosphate binding / presynaptic modulation of chemical synaptic transmission / locomotory behavior / establishment of localization in cell / PDZ domain binding ...gamma-aminobutyric acid secretion / Dopamine Neurotransmitter Release Cycle / glutamate secretion / synaptic vesicle exocytosis / presynaptic active zone membrane / phosphatidylinositol-4,5-bisphosphate binding / presynaptic modulation of chemical synaptic transmission / locomotory behavior / establishment of localization in cell / PDZ domain binding / intracellular protein transport / Schaffer collateral - CA1 synapse / multicellular organism growth / amyloid-beta binding / regulation of gene expression / chemical synaptic transmission / in utero embryonic development / dendritic spine / glutamatergic synapse / protein-containing complex binding / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / protein-containing complex / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain ...Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
ACETIC ACID / ISOPROPYL ALCOHOL / Amyloid-beta A4 precursor protein-binding family A member 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.901 Å
AuthorsTomchick, D.R. / Rizo, J. / Ho, A. / Xu, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Autoinhibition of Mint1 adaptor protein regulates amyloid precursor protein binding and processing.
Authors: Matos, M.F. / Xu, Y. / Dulubova, I. / Otwinowski, Z. / Richardson, J.M. / Tomchick, D.R. / Rizo, J. / Ho, A.
History
DepositionJan 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Database references
Revision 1.2Jun 28, 2017Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Source and taxonomy / Structure summary
Category: diffrn_radiation_wavelength / entity ...diffrn_radiation_wavelength / entity / entity_name_com / entity_src_gen / pdbx_distant_solvent_atoms / software / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_fragment / _entity_name_com.name ..._entity.pdbx_fragment / _entity_name_com.name / _software.name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)18,8698
Polymers18,4091
Non-polymers4607
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.729, 64.729, 115.155
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-802-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Amyloid beta A4 precursor protein-binding family A member 1 / Adapter protein X11alpha / Neuron-specific X11 protein / Neuronal Munc18-1-interacting protein 1 / Mint-1


Mass: 18408.863 Da / Num. of mol.: 1
Fragment: PTB DOMAIN, UNP residues 453-643 with deletion of residues 497-508
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Apba1, Mint1, X11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O35430

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Non-polymers , 5 types, 85 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE CHIMERA PROTEIN IS OF PTB DOMAIN OF MINT-1(UNP RESIDUES 453-643) WITH TWO DELETIONS OF RESIDUES ...THE CHIMERA PROTEIN IS OF PTB DOMAIN OF MINT-1(UNP RESIDUES 453-643) WITH TWO DELETIONS OF RESIDUES 499-508 AND 569-585.

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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: 3.25 Å3/Da / Density % sol: 62.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% isopropanol, 25% glycerol, 0.1 M Hepes pH 7.5, 0.15 M NaCl, 0.2 M ammonium acetate, 2 mM TCEP, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE
DetectorType: R-AXIS IV / Detector: IMAGE PLATE / Date: May 10, 2010 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 19927 / Num. obs: 19927 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 13.6 % / Rmerge(I) obs: 0.066 / Χ2: 0.954 / Net I/σ(I): 11.6
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
1.9-1.9211.54670.822197.9
1.92-1.9313.54770.842199.2
1.93-1.9513.84890.886198
1.95-1.9713.54850.883199.40.958
1.97-1.9913.84890.9071980.883
1.99-2.0113.64750.92711000.793
2.01-2.0313.74820.931198.40.672
2.03-2.0513.74850.931199.80.696
2.05-2.0713.74830.935198.60.625
2.07-2.0913.74900.934199.20.537
2.09-2.1113.84830.989199.40.516
2.11-2.1413.74810.9311990.448
2.14-2.1713.64960.9411000.401
2.17-2.1913.84920.9581990.38
2.19-2.2213.94840.971199.20.345
2.22-2.2513.74870.995199.80.301
2.25-2.2813.94860.956199.40.252
2.28-2.3213.74910.96199.40.256
2.32-2.3613.84860.981199.40.234
2.36-2.3913.85000.96611000.199
2.39-2.4413.84860.972199.60.207
2.44-2.4813.94990.974199.60.192
2.48-2.5313.74950.93199.80.171
2.53-2.5813.95010.948199.80.152
2.58-2.6313.74900.951199.80.151
2.63-2.713.85090.942199.80.127
2.7-2.7613.94850.983199.80.117
2.76-2.8413.85060.97211000.089
2.84-2.9213.94920.93411000.077
2.92-3.0213.85000.98711000.063
3.02-3.1213.85080.98911000.055
3.12-3.2513.85071.03311000.051
3.25-3.413.85131.03111000.042
3.4-3.5813.75021.02211000.034
3.58-3.813.75191.01711000.027
3.8-4.0913.75160.97111000.024
4.09-4.513.55171.03911000.022
4.5-5.1613.35250.91211000.021
5.16-6.4913.15520.89811000.022
6.49-5011.95970.98199.20.02

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.901→33.016 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8487 / SU ML: 0.42 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Phase error: 21.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2252 934 5.08 %RANDOM
Rwork0.1966 ---
all0.198 18378 --
obs0.198 18378 92.09 %-
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.598 Å2 / ksol: 0.388 e/Å3
Displacement parametersBiso max: 215.84 Å2 / Biso mean: 59.5601 Å2 / Biso min: 17.42 Å2
Baniso -1Baniso -2Baniso -3
1-0.1306 Å20 Å20 Å2
2--0.1306 Å2-0 Å2
3----0.2613 Å2
Refine analyzeLuzzati sigma a obs: 0.42 Å
Refinement stepCycle: LAST / Resolution: 1.901→33.016 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1195 0 29 78 1302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171241
X-RAY DIFFRACTIONf_angle_d1.4431665
X-RAY DIFFRACTIONf_chiral_restr0.12189
X-RAY DIFFRACTIONf_plane_restr0.008216
X-RAY DIFFRACTIONf_dihedral_angle_d13.27476
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.901-2.00120.2438610.1971351141251
2.0012-2.12660.25021280.19792471259993
2.1266-2.29080.23251520.1842635278799
2.2908-2.52120.21111470.188926502797100
2.5212-2.88590.22391460.19327132859100
2.8859-3.63520.22141430.18927322875100
3.6352-33.02120.2251570.20628923049100
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)
14.35763.59051.11214.55672.69942.29930.78041.5005-0.8766-0.2230.22921.54981.7304-0.937-0.76470.71060.0094-0.18920.60640.05190.56088.0326-11.61347.6782
21.43610.8194-0.13482.1184-0.42561.03880.0307-0.17110.02770.23-0.12310.01120.02790.01520.06990.3007-0.0086-0.06520.14260.02310.218717.408713.842213.8971
34.3253-1.4601-0.423.24140.47253.77790.5073-0.05320.3584-0.0205-0.2535-0.6523-0.46380.4663-0.17650.218-0.0449-0.02810.17040.03380.269519.641920.05787.5857
46.22930.06490.46163.2920.03953.44080.0694-0.3204-0.7711.2122-0.1355-0.46270.92880.3890.27040.5050.0028-0.00520.1520.06880.27522.09040.774914.915
51.93670.27130.05672.41610.72722.14960.0255-0.15610.08060.5574-0.13710.18090.4215-0.17770.07120.3333-0.03040.01470.17390.00130.171414.939310.150512.4987
63.6042-0.22331.46284.0937-0.36283.9447-0.2163-0.60610.31371.22360.2711-0.29930.2216-0.25910.19790.4428-0.0133-0.02820.2010.01910.137916.010314.342217.0193
77.3015-0.0761-3.68842.7785-0.84463.61650.17430.5935-0.73250.2369-0.39070.9620.2052-1.4740.36150.4235-0.14530.05290.604-0.07680.5323.98273.39089.0778
82.00051.09772.24177.89541.4973.09270.0036-0.939-0.03850.3210.20230.277-1.01710.2978-0.30570.6852-0.14770.07481.21140.11220.9015-5.488511.16467.2333
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 455:459)A455 - 459
2X-RAY DIFFRACTION2(chain A and resid 460:480)A460 - 480
3X-RAY DIFFRACTION3(chain A and resid 481:516)A481 - 516
4X-RAY DIFFRACTION4(chain A and resid 517:537)A517 - 537
5X-RAY DIFFRACTION5(chain A and resid 538:563)A538 - 563
6X-RAY DIFFRACTION6(chain A and resid 564:598)A564 - 598
7X-RAY DIFFRACTION7(chain A and resid 599:620)A599 - 620
8X-RAY DIFFRACTION8(chain A and resid 623:640)A623 - 640

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