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- PDB-5dse: Crystal Structure of the TTC7B/Hyccin Complex -

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Basic information

Entry
Database: PDB / ID: 5dse
TitleCrystal Structure of the TTC7B/Hyccin Complex
Components
  • Hyccin
  • Tetratricopeptide repeat protein 7B
KeywordsPROTEIN BINDING / PI4P synthesis
Function / homology
Function and homology information


phosphatidylinositol phosphate biosynthetic process / myelination / protein localization to plasma membrane / neuron projection / plasma membrane / cytosol
Similarity search - Function
Hyccin / Tetratricopeptide repeat protein 7, N-terminal / Hyccin / Tetratricopeptide repeat protein 7 N-terminal / Anaphase-promoting complex, cyclosome, subunit 3 / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats ...Hyccin / Tetratricopeptide repeat protein 7, N-terminal / Hyccin / Tetratricopeptide repeat protein 7 N-terminal / Anaphase-promoting complex, cyclosome, subunit 3 / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Tetratricopeptide repeat protein 7B / Hyccin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsWu, X. / Baskin, J.M. / Reinisch, K.M. / De Camilli, P.
CitationJournal: Nat.Cell Biol. / Year: 2016
Title: The leukodystrophy protein FAM126A (hyccin) regulates PtdIns(4)P synthesis at the plasma membrane.
Authors: Baskin, J.M. / Wu, X. / Christiano, R. / Oh, M.S. / Schauder, C.M. / Gazzerro, E. / Messa, M. / Baldassari, S. / Assereto, S. / Biancheri, R. / Zara, F. / Minetti, C. / Raimondi, A. / ...Authors: Baskin, J.M. / Wu, X. / Christiano, R. / Oh, M.S. / Schauder, C.M. / Gazzerro, E. / Messa, M. / Baldassari, S. / Assereto, S. / Biancheri, R. / Zara, F. / Minetti, C. / Raimondi, A. / Simons, M. / Walther, T.C. / Reinisch, K.M. / De Camilli, P.
History
DepositionSep 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Tetratricopeptide repeat protein 7B
B: Hyccin
C: Tetratricopeptide repeat protein 7B
D: Hyccin


Theoretical massNumber of molelcules
Total (without water)257,1614
Polymers257,1614
Non-polymers00
Water91951
1
A: Tetratricopeptide repeat protein 7B
B: Hyccin


Theoretical massNumber of molelcules
Total (without water)128,5802
Polymers128,5802
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-30 kcal/mol
Surface area34390 Å2
MethodPISA
2
C: Tetratricopeptide repeat protein 7B
D: Hyccin


Theoretical massNumber of molelcules
Total (without water)128,5802
Polymers128,5802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-37 kcal/mol
Surface area43400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.779, 168.068, 239.671
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tetratricopeptide repeat protein 7B / / TPR repeat protein 7B / Tetratricopeptide repeat protein 7-like-1 / TPR repeat protein 7-like-1


Mass: 93661.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTC7B, TTC7L1 / Plasmid: pCOLADuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q86TV6
#2: Protein Hyccin / Down-regulated by CTNNB1 protein A / Protein FAM126A


Mass: 34919.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FAM126A, DRCTNNB1A / Plasmid: pGEX-6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BYI3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.35 ul protein + 1.35 ul mother liquor (0.1 M HEPES [pH 7.0-7.4], 4-5% polyethylene glycol [PEG] 8,000) + 0.3 ul 0.2 M 3-(1-Pyridino)-1-propane sulfonate (NDSB-201)
PH range: 7.0-7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.9→29.96 Å / Num. all: 64836 / Num. obs: 64827 / % possible obs: 99.5 % / Redundancy: 6.6 % / Net I/σ(I): 22.8
Reflection shellResolution: 2.9→3 Å / Redundancy: 6.2 % / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1630)refinement
HKL-2000data scaling
SHELXphasing
Cootmodel building
RefinementResolution: 2.9→29.959 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2417 1999 3.08 %Random selection
Rwork0.2123 ---
obs0.2132 64827 99.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→29.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13824 0 0 51 13875
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00314093
X-RAY DIFFRACTIONf_angle_d0.6619077
X-RAY DIFFRACTIONf_dihedral_angle_d12.3995214
X-RAY DIFFRACTIONf_chiral_restr0.0252181
X-RAY DIFFRACTIONf_plane_restr0.0032413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.97250.3321380.27114343X-RAY DIFFRACTION98
2.9725-3.05280.35251400.27164400X-RAY DIFFRACTION99
3.0528-3.14250.33611410.2734441X-RAY DIFFRACTION99
3.1425-3.24380.3131400.27034414X-RAY DIFFRACTION99
3.2438-3.35960.29861410.24734424X-RAY DIFFRACTION99
3.3596-3.49390.29011410.22384442X-RAY DIFFRACTION100
3.4939-3.65270.25121430.22244470X-RAY DIFFRACTION100
3.6527-3.84490.21861410.2064454X-RAY DIFFRACTION100
3.8449-4.08520.21271440.1844495X-RAY DIFFRACTION100
4.0852-4.39970.20581430.17314508X-RAY DIFFRACTION100
4.3997-4.84080.20861440.1744532X-RAY DIFFRACTION100
4.8408-5.53750.24331460.20434577X-RAY DIFFRACTION100
5.5375-6.96220.24251460.2424586X-RAY DIFFRACTION100
6.9622-29.96050.22021510.20864742X-RAY DIFFRACTION99
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)
12.3951.3274-0.52352.4627-0.52180.0869-0.27190.47510.9335-0.00380.1196-0.4935-0.29990.28350.0720.9254-0.1959-0.16270.92980.36131.867162.7402100.1795110.0209
22.4240.65290.80693.06170.43281.7004-0.04980.0916-0.00640.41850.1492-0.64860.08490.1078-0.08080.54950.071-0.02220.4957-0.01930.528533.106261.3678114.3537
30.6083-0.36490.37612.82870.5291.2213-0.0348-0.0335-0.10510.09860.01730.31550.2271-0.25950.00420.4128-0.04220.1250.54360.04520.506112.488353.2355100.1996
40.53610.78910.66081.63371.41811.22950.566-0.91261.25271.6338-0.47590.5501-0.6501-0.2956-0.17171.8608-0.13760.08020.933-0.43171.45136.293691.875139.688
54.71792.6795-0.99963.1416-1.42262.2775-0.14831.03681.88540.28010.38190.6343-0.2134-0.4077-0.26340.95610.0614-0.03140.74270.20921.555938.28991.0759117.6193
63.1312-0.93780.38943.4632-0.32413.08260.0282-0.16740.36341.2048-0.2163-1.0789-0.22550.50780.11960.8156-0.044-0.27380.5441-0.03031.022350.064177.118126.8829
71.97482.5247-1.28036.4824-1.910.96920.0439-0.1139-0.13020.1059-0.1126-0.3092-0.14690.00550.05230.5924-0.02060.0050.61920.13990.495990.259589.07167.4238
89.22982.5213-2.6153.4951-1.40752.30450.2681-0.57490.9594-0.0758-0.2950.4762-0.40010.17450.04730.5008-0.01420.03970.4867-0.06490.494651.519566.304378.899
91.9173-0.2187-0.53221.85150.21651.8294-0.11-0.0735-0.08340.12060.1072-0.07030.2750.02750.00260.43140.003-0.01910.459-0.08010.387138.797433.605584.2702
100.9221-0.3877-1.3122.55210.83223.2363-0.42170.9396-0.5434-0.95950.2761-0.56290.2675-0.04510.11490.9239-0.24160.29250.9665-0.13040.725770.062945.491151.8034
113.15051.2271.27461.5977-0.38021.30050.0674-0.1254-0.15390.3235-0.211-0.1750.2079-0.24860.17290.6003-0.05440.09770.54450.0180.453270.98954.977374.5406
123.865-0.3427-0.66882.8250.6112.9959-0.42681.27810.5445-0.5880.22660.1626-0.4929-0.29880.21440.7112-0.1144-0.07930.79220.13950.476657.311360.896458.9544
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 140:394)
2X-RAY DIFFRACTION2(chain A and resid 395:693)
3X-RAY DIFFRACTION3(chain A and resid 694:843)
4X-RAY DIFFRACTION4(chain B and resid 7:103)
5X-RAY DIFFRACTION5(chain B and resid 104:196)
6X-RAY DIFFRACTION6(chain B and resid 197:287)
7X-RAY DIFFRACTION7(chain C and resid 8:360)
8X-RAY DIFFRACTION8(chain C and resid 361:469)
9X-RAY DIFFRACTION9(chain C and resid 470:843)
10X-RAY DIFFRACTION10(chain D and resid 7:131)
11X-RAY DIFFRACTION11(chain D and resid 132:187)
12X-RAY DIFFRACTION12(chain D and resid 188:287)

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