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- PDB-7kjo: crystal structure of PLEKHA7 PH domain biding SO4 -

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Basic information

Entry
Database: PDB / ID: 7kjo
Titlecrystal structure of PLEKHA7 PH domain biding SO4
ComponentsPleckstrin homology domain-containing family A member 7
KeywordsCELL ADHESION / PLEKHA7 / PH domain / Pleckstrin homology domain / PIP / inositol-phosphate
Function / homology
Function and homology information


zonula adherens maintenance / epithelial cell-cell adhesion / zonula adherens / pore complex assembly / delta-catenin binding / cell-cell adhesion mediated by cadherin / pore complex / cell junction / centrosome / extracellular exosome ...zonula adherens maintenance / epithelial cell-cell adhesion / zonula adherens / pore complex assembly / delta-catenin binding / cell-cell adhesion mediated by cadherin / pore complex / cell junction / centrosome / extracellular exosome / nucleoplasm / cytosol
Similarity search - Function
PKHA4-7, PH domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily
Similarity search - Domain/homology
Pleckstrin homology domain-containing family A member 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsMarassi, F.M. / Aleshin, A.E. / Liddington, R.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA179087 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA160398 United States
CitationJournal: Structure / Year: 2021
Title: Structural basis for the association of PLEKHA7 with membrane-embedded phosphatidylinositol lipids.
Authors: Aleshin, A.E. / Yao, Y. / Iftikhar, A. / Bobkov, A.A. / Yu, J. / Cadwell, G. / Klein, M.G. / Dong, C. / Bankston, L.A. / Liddington, R.C. / Im, W. / Powis, G. / Marassi, F.M.
History
DepositionOct 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1May 5, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 15, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pleckstrin homology domain-containing family A member 7
B: Pleckstrin homology domain-containing family A member 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7479
Polymers32,0862
Non-polymers6617
Water3,729207
1
A: Pleckstrin homology domain-containing family A member 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3274
Polymers16,0431
Non-polymers2843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Pleckstrin homology domain-containing family A member 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4205
Polymers16,0431
Non-polymers3764
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.830, 64.830, 59.233
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 164 through 236 or resid 258 through 283 or resid 302))
21(chain B and (resid 164 through 283 or resid 303))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROTHRTHR(chain A and (resid 164 through 236 or resid 258 through 283 or resid 302))AA164 - 2366 - 78
12ARGARGVALVAL(chain A and (resid 164 through 236 or resid 258 through 283 or resid 302))AA258 - 283100 - 125
13SO4SO4SO4SO4(chain A and (resid 164 through 236 or resid 258 through 283 or resid 302))AE302
21PROPROVALVAL(chain B and (resid 164 through 283 or resid 303))BB164 - 2836 - 125
22SO4SO4SO4SO4(chain B and (resid 164 through 283 or resid 303))BI303

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Components

#1: Protein Pleckstrin homology domain-containing family A member 7 / PH domain-containing family A member 7


Mass: 16043.245 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLEKHA7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6IQ23
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / 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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.94 Å3/Da / Density % sol: 36.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: protein in 180 mM NaCl and 20 mM sodium phosphate mixed with 25% glycerol, 2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 1.45→45.842 Å / Num. obs: 46929 / % possible obs: 99.2 % / Redundancy: 19 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.2
Reflection shellResolution: 1.45→1.48 Å / Rmerge(I) obs: 0.362 / Num. unique obs: 4283

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UPR

1upr


Resolution: 1.45→45.842 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.1 / Phase error: 17.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1714 4271 5.04 %
Rwork0.153 80519 -
obs0.1539 43487 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.15 Å2 / Biso mean: 31.787 Å2 / Biso min: 12.8 Å2
Refinement stepCycle: final / Resolution: 1.45→45.842 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1695 0 60 207 1962
Biso mean--49.61 40 -
Num. residues----206
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A952X-RAY DIFFRACTION9.446TORSIONAL
12B952X-RAY DIFFRACTION9.446TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4501-1.46660.34421500.3146255795
1.4666-1.48380.27671130.2829267598
1.4838-1.50190.27641570.2615263699
1.5019-1.52090.29591600.2355267798
1.5209-1.54090.24381430.224269199
1.5409-1.56210.2061430.2043265299
1.5621-1.58440.20361590.1893264799
1.5844-1.6080.17991460.1841268299
1.608-1.63310.2221390.1797265599
1.6331-1.65990.22071300.1776271899
1.6599-1.68850.20791400.165268599
1.6885-1.71930.18471450.16592670100
1.7193-1.75230.22461570.1591271099
1.7523-1.78810.19681380.1627265299
1.7881-1.8270.18081340.16272711100
1.827-1.86950.19651360.151269099
1.8695-1.91620.13931420.1502268799
1.9162-1.9680.1811240.1382682100
1.968-2.02590.17161510.13972706100
2.0259-2.09130.17951270.14262729100
2.0913-2.16610.18081250.13942688100
2.1661-2.25280.16631230.13972740100
2.2528-2.35530.17041370.13992655100
2.3553-2.47950.11931490.14422766100
2.4795-2.63480.1611520.14462668100
2.6348-2.83820.1661590.15082705100
2.8382-3.12380.18381530.15782696100
3.1238-3.57570.17581610.13422671100
3.5757-4.50440.13631440.12782693100
4.5044-45.820.16671340.16672725100
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)
11.82590.19271.43493.4568-0.93264.5742-0.0676-0.1969-0.10470.52170.1226-0.1018-0.1432-0.1078-0.06820.20440.01250.00340.2034-0.01760.17846.915168.300731.8568
22.39680.72240.37421.85140.46152.03060.0466-0.09820.14570.2012-0.03250.15020.0083-0.1053-0.00960.1020.00080.01510.1208-0.00280.108940.438570.891230.1702
33.05830.48871.97783.7-0.07223.2971-0.0772-0.14050.02320.3146-0.06620.1102-0.18210.01380.17640.1511-0.02060.010.1756-0.02150.137454.42975.912635.749
43.0947-0.1651-0.46583.05330.26153.37950.01680.23930.3204-0.03440.02070.0929-0.2570.0501-0.01710.1054-0.0391-0.00940.1370.00890.173647.744578.654127.6148
53.1924-0.3451-3.41740.03080.37313.64260.5008-0.19770.081-0.30360.203-0.43-0.04920.3826-0.66350.4181-0.11790.00320.7118-0.01450.283338.357968.290243.4042
61.51190.02350.66851.499-0.12031.7085-0.00690.0642-0.0051-0.13760.09030.06210.01510.0473-0.06760.1084-0.01950.00270.1540.00680.100920.987763.953741.8355
74.82213.4087-0.95519.2201-1.23242.00440.41580.34370.0187-0.947-0.15730.2509-0.3259-0.1163-0.37860.4933-0.0246-0.05260.30120.01250.320711.487861.126.3279
81.832-0.5578-0.17311.5147-0.77561.5681-0.04090.0503-0.0001-0.26440.0820.02280.14960.016-0.00780.1916-0.01720.01360.1884-0.0060.163524.714463.435738.9404
95.6829-1.974-0.79510.96311.34359.5711-0.06570.0147-0.7413-0.08640.0394-0.39370.99170.3447-0.01160.21050.03020.03530.11780.00070.209626.940353.966643.059
101.55650.0762-0.39790.04010.1621.1499-0.06890.29810.1108-0.08020.00630.03150.0359-0.13270.04870.1954-0.00530.01240.23030.01240.202925.141370.741233.5817
111.8987-0.42591.37462.9006-0.48693.9284-0.10990.07730.0241-0.12250.01440.0603-0.1509-0.24290.12030.11840.0108-0.00220.17370.00740.136213.290370.840234.2254
127.04011.7865-2.96052.4435-1.01554.17570.2586-0.29390.6080.0755-0.01630.0793-0.4184-0.0064-0.20850.16270.0260.00810.1419-0.03320.178521.644675.678242.819
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 164 through 181 )A164 - 181
2X-RAY DIFFRACTION2chain 'A' and (resid 182 through 218 )A182 - 218
3X-RAY DIFFRACTION3chain 'A' and (resid 219 through 258 )A219 - 258
4X-RAY DIFFRACTION4chain 'A' and (resid 259 through 283 )A259 - 283
5X-RAY DIFFRACTION5chain 'B' and (resid 159 through 164 )B159 - 164
6X-RAY DIFFRACTION6chain 'B' and (resid 165 through 174 )B165 - 174
7X-RAY DIFFRACTION7chain 'B' and (resid 175 through 181 )B175 - 181
8X-RAY DIFFRACTION8chain 'B' and (resid 182 through 197 )B182 - 197
9X-RAY DIFFRACTION9chain 'B' and (resid 198 through 204 )B198 - 204
10X-RAY DIFFRACTION10chain 'B' and (resid 205 through 218 )B205 - 218
11X-RAY DIFFRACTION11chain 'B' and (resid 219 through 266 )B219 - 266
12X-RAY DIFFRACTION12chain 'B' and (resid 267 through 284 )B267 - 284

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