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- PDB-4tkn: Structure of the SNX17 FERM domain bound to the second NPxF motif... -

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Basic information

Entry
Database: PDB / ID: 4tkn
TitleStructure of the SNX17 FERM domain bound to the second NPxF motif of KRIT1
Components
  • Krev interaction trapped protein 1
  • Sorting nexin-17
KeywordsPROTEIN TRANSPORT/SIGNALING PROTEIN / FERM domain / NPxY motif / NPxF motif / PROTEIN TRANSPORT-SIGNALING PROTEIN complex
Function / homology
Function and homology information


GTPase regulator activity / cardiac septum development / endothelium development / integrin activation / cholesterol catabolic process / coronary vasculature development / endocytic recycling / negative regulation of endothelial cell migration / regulation of establishment of cell polarity / low-density lipoprotein particle receptor binding ...GTPase regulator activity / cardiac septum development / endothelium development / integrin activation / cholesterol catabolic process / coronary vasculature development / endocytic recycling / negative regulation of endothelial cell migration / regulation of establishment of cell polarity / low-density lipoprotein particle receptor binding / aorta development / endosomal transport / small GTPase-mediated signal transduction / negative regulation of endothelial cell proliferation / regulation of endocytosis / regulation of angiogenesis / negative regulation of endothelial cell apoptotic process / phosphatidylinositol-4,5-bisphosphate binding / receptor-mediated endocytosis / phosphatidylinositol binding / negative regulation of angiogenesis / cell redox homeostasis / kidney development / intracellular protein transport / cell-cell junction / cytoplasmic vesicle / microtubule binding / angiogenesis / cytoskeleton / early endosome / endosome membrane / endosome / signaling receptor binding / intracellular membrane-bounded organelle / Golgi apparatus / signal transduction / protein-containing complex / extracellular space / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Acyl-CoA Binding Protein - #60 / Sorting nexin-17 / SNX17, atypical FERM-like domain / Sorting nexin-17/31, FERM domain / : / : / Sorting Nexin 17 FERM C-terminal domain / Sortin nexin 17/31, FERM domain, F2 lobe / Sortin nexin 17/27/31, FERM domain, F1 lobe / KRIT, N-terminal NPxY motif-rich region ...Acyl-CoA Binding Protein - #60 / Sorting nexin-17 / SNX17, atypical FERM-like domain / Sorting nexin-17/31, FERM domain / : / : / Sorting Nexin 17 FERM C-terminal domain / Sortin nexin 17/31, FERM domain, F2 lobe / Sortin nexin 17/27/31, FERM domain, F1 lobe / KRIT, N-terminal NPxY motif-rich region / Krev interaction trapped protein 1, FERM domain C-lobe / KRIT, N-terminal NPxY motif-rich domain superfamily / NUDIX, or N-terminal NPxY motif-rich, region of KRIT / SNX17/27/31 / Ankyrin repeats (many copies) / Ras-associating (RA) domain profile. / Acyl-CoA Binding Protein / Ras-associating (RA) domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / FERM central domain / PH-domain like / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Ubiquitin-like (UB roll) / PH-like domain superfamily / Roll / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Krev interaction trapped protein 1 / Sorting nexin-17
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsStiegler, A.L. / Zhang, R. / Liu, W. / Boggon, T.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01 NS085078 United States
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural Determinants for Binding of Sorting Nexin 17 (SNX17) to the Cytoplasmic Adaptor Protein Krev Interaction Trapped 1 (KRIT1).
Authors: Stiegler, A.L. / Zhang, R. / Liu, W. / Boggon, T.J.
History
DepositionMay 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sorting nexin-17
B: Sorting nexin-17
C: Sorting nexin-17
D: Krev interaction trapped protein 1
E: Krev interaction trapped protein 1
F: Krev interaction trapped protein 1


Theoretical massNumber of molelcules
Total (without water)103,1796
Polymers103,1796
Non-polymers00
Water86548
1
A: Sorting nexin-17
D: Krev interaction trapped protein 1


Theoretical massNumber of molelcules
Total (without water)34,3932
Polymers34,3932
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-12 kcal/mol
Surface area14320 Å2
MethodPISA
2
B: Sorting nexin-17
E: Krev interaction trapped protein 1


Theoretical massNumber of molelcules
Total (without water)34,3932
Polymers34,3932
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-13 kcal/mol
Surface area13820 Å2
MethodPISA
3
C: Sorting nexin-17
F: Krev interaction trapped protein 1


Theoretical massNumber of molelcules
Total (without water)34,3932
Polymers34,3932
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-11 kcal/mol
Surface area14820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.924, 191.202, 46.593
Angle α, β, γ (deg.)90.000, 110.250, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-403-

HOH

21C-402-

HOH

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Components

#1: Protein Sorting nexin-17 /


Mass: 32469.051 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNX17, KIAA0064 / Plasmid: pET / Production host: Escherichia coli (E. coli) / References: UniProt: Q15036
#2: Protein/peptide Krev interaction trapped protein 1 / Krev interaction trapped 1 / Cerebral cavernous malformations 1 protein


Mass: 1924.094 Da / Num. of mol.: 3 / Fragment: UNP residues 225-237
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRIT1, CCM1 / Plasmid: pGEX-6p1 / Production host: Escherichia coli (E. coli) / References: UniProt: O00522
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.39 Å3/Da / Density % sol: 48.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.9 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 5% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 18042 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 15 % / Biso Wilson estimate: 86.81 Å2 / Rmerge(I) obs: 0.241 / Net I/σ(I): 10.8
Reflection shellResolution: 3→3.12 Å / Redundancy: 14.4 % / Mean I/σ(I) obs: 2.3 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
Cootmodel building
PDB_EXTRACT3.14data extraction
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GXB chain A

4gxb


Resolution: 3→47.88 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 31.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2681 1794 10.02 %Random selection
Rwork0.2181 16107 --
obs0.223 17901 92.51 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 249.35 Å2 / Biso mean: 126.1331 Å2 / Biso min: 65.5 Å2
Refinement stepCycle: final / Resolution: 3→47.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6371 0 0 48 6419
Biso mean---87.08 -
Num. residues----788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056476
X-RAY DIFFRACTIONf_angle_d1.2458739
X-RAY DIFFRACTIONf_chiral_restr0.0681014
X-RAY DIFFRACTIONf_plane_restr0.0051095
X-RAY DIFFRACTIONf_dihedral_angle_d13.6062437
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3-3.08130.39181160.3444916103269
3.0813-3.17190.3421200.31291134125486
3.1719-3.27430.36061260.30541167129387
3.2743-3.39130.33491400.26521218135891
3.3913-3.5270.28311330.26111204133790
3.527-3.68750.29871380.24111281141995
3.6875-3.88180.28391380.23881261139994
3.8818-4.12490.2531410.20911250139196
4.1249-4.44320.22891480.18871306145498
4.4432-4.88990.21221450.16631334147999
4.8899-5.59660.24191480.20261336148499
5.5966-7.04750.2951480.24161332148099
7.0475-47.88580.25991530.198513681521100
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)
15.93411.8461-1.66873.6217-2.29495.2308-0.2314-0.86990.40260.2969-0.1483-0.76980.31360.56480.31480.90670.4112-0.40811.1205-0.34941.22723.948652.50716.4354
27.7017-1.7958-0.09485.18960.4383.1844-0.3982-0.29891.3504-0.09810.4941-0.0845-0.0659-0.0539-0.16850.7390.1651-0.27970.9031-0.23781.116.105853.35196.7182
37.9157-0.7491-5.38445.663-3.37588.706-0.0776-0.752-0.4281-0.0544-0.03080.34660.1302-0.19060.12020.70740.1283-0.15250.6402-0.00070.60413.439833.6044.1595
48.07723.04671.83585.99443.48348.4704-0.11520.36390.585-0.04780.4248-0.2156-1.31190.3871-0.14390.7019-0.00960.1120.59590.02221.154537.470222.055232.8367
54.42461.1585-1.08164.696-6.19158.47550.58130.1698-0.4930.0072-0.1812-0.45940.00180.0968-0.35960.71390.0649-0.06240.7248-0.21091.278131.63111.292229.4177
62.8717-3.54542.21395.2983-3.01371.77050.4755-0.2161-1.50420.16471.70421.49170.1216-1.7744-2.04560.610.05170.1221.23570.11161.47314.65710.680637.4712
77.0556-3.3107-0.51557.64693.42214.50770.30310.6623-0.5274-0.5969-0.40530.7656-0.1782-0.69460.03290.82650.13930.00580.81840.0360.889312.078920.368732.2459
83.25591.7795-2.11717.0260.93515.52060.2180.3493-0.08290.2502-0.07030.74910.3246-0.4857-0.04031.12-0.4062-0.43131.09080.45671.29744.8259-29.179643.6969
95.002-2.8034-1.35866.69351.93062.00060.1027-0.56970.66730.6356-0.221-0.85510.0637-0.5686-0.06481.1892-0.5636-0.6891.13120.34371.508811.6845-18.699147.0174
108.33810.58081.92183.96162.48164.10640.70050.543-0.3541-0.20910.4355-0.2311-0.02890.2635-1.10741.1307-0.179-0.20310.74170.11981.333817.5653-8.187440.1204
116.28274.993-2.59385.30.81875.41980.521-0.46020.14920.0494-0.45080.871-0.4726-0.1471-0.15420.6890.1374-0.28830.75440.15391.1822-0.0412-4.603629.8927
127.9672-2.7701-1.99963.34910.30427.45010.6964-0.78861.01340.1499-1.16061.1607-0.3743-1.67280.35730.7195-0.1275-0.15611.0283-0.08221.4526-2.9463-6.603236.8048
132.94660.48622.33117.8117-3.65913.96540.80840.9363-1.65011.73780.6418-0.6595-1.777-1.1851-0.64590.94870.2526-0.24740.9408-0.15671.06614.248925.414511.6365
142.12980.78710.35139.8813-4.68122.461-0.5039-0.90960.0854-0.3314-1.15490.65071.45351.99332.01860.97930.25160.21831.26260.14411.24529.546924.806424.6601
155.97211.51852.25923.91211.17022.7335-0.2476-2.28612.23040.8142-0.8268-0.57870.49980.83680.45140.72830.11360.29881.35410.52651.6881-11.1809-4.641637.2681
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 113 through 217 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 218 through 293 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 294 through 388 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 113 through 207 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 208 through 275 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 276 through 310 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 311 through 388 )B0
8X-RAY DIFFRACTION8chain 'C' and (resid 113 through 192 )C0
9X-RAY DIFFRACTION9chain 'C' and (resid 193 through 233 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 234 through 293 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 294 through 355 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 356 through 388 )C0
13X-RAY DIFFRACTION13chain 'D' and (resid 227 through 236 )D0
14X-RAY DIFFRACTION14chain 'E' and (resid 227 through 235 )E0
15X-RAY DIFFRACTION15chain 'F' and (resid 227 through 235 )F0

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