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- PDB-6qdt: Crystal structure of 14-3-3sigma in complex with a RapGef2 pT740 ... -

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Basic information

Entry
Database: PDB / ID: 6qdt
TitleCrystal structure of 14-3-3sigma in complex with a RapGef2 pT740 phosphopeptide
Components
  • 14-3-3 protein sigma
  • Rap guanine nucleotide exchange factor 2
KeywordsCHAPERONE / Neuron Regeneration / PPI / phosphorylation
Function / homology
Function and homology information


negative regulation of melanin biosynthetic process / forebrain neuron development / brain-derived neurotrophic factor receptor signaling pathway / positive regulation of dendritic cell apoptotic process / Rap protein signal transduction / diacylglycerol binding / microvillus assembly / negative regulation of dendrite morphogenesis / establishment of endothelial intestinal barrier / beta-1 adrenergic receptor binding ...negative regulation of melanin biosynthetic process / forebrain neuron development / brain-derived neurotrophic factor receptor signaling pathway / positive regulation of dendritic cell apoptotic process / Rap protein signal transduction / diacylglycerol binding / microvillus assembly / negative regulation of dendrite morphogenesis / establishment of endothelial intestinal barrier / beta-1 adrenergic receptor binding / regulation of cell junction assembly / WW domain binding / cellular response to cGMP / nerve growth factor signaling pathway / positive regulation of cAMP-mediated signaling / ventricular system development / positive regulation of vasculogenesis / positive regulation of neuron migration / phosphatidic acid binding / establishment of endothelial barrier / positive regulation of cAMP-dependent protein kinase activity / small GTPase-mediated signal transduction / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / blood vessel development / keratinocyte development / keratinization / plasma membrane => GO:0005886 / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / endocytic vesicle / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / bicellular tight junction / negative regulation of keratinocyte proliferation / positive regulation of protein kinase activity / neuropeptide signaling pathway / establishment of skin barrier / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / adenylate cyclase-activating adrenergic receptor signaling pathway / cAMP binding / cellular response to cAMP / RHO GTPases activate PKNs / protein kinase A signaling / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / cAMP-mediated signaling / GTPase activator activity / guanyl-nucleotide exchange factor activity / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / positive regulation of protein export from nucleus / release of cytochrome c from mitochondria / cellular response to nerve growth factor stimulus / positive regulation of GTPase activity / stem cell proliferation / protein localization to plasma membrane / PDZ domain binding / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / negative regulation of protein kinase activity / neuron migration / regulation of synaptic plasticity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of neuron projection development / intrinsic apoptotic signaling pathway in response to DNA damage / neuron projection development / MAPK cascade / cell-cell junction / late endosome / positive regulation of protein binding / RAF/MAP kinase cascade / positive regulation of cell growth / positive regulation of ERK1 and ERK2 cascade / regulation of cell cycle / intracellular signal transduction / cadherin binding / neuron projection / G protein-coupled receptor signaling pathway / apical plasma membrane / negative regulation of cell population proliferation / neuronal cell body / synapse / calcium ion binding / protein kinase binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / signal transduction / protein-containing complex / extracellular space / extracellular exosome / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Rap guanine nucleotide exchange factor 2 / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras-like guanine nucleotide exchange factor ...Rap guanine nucleotide exchange factor 2 / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras-like guanine nucleotide exchange factor / Ras guanine nucleotide exchange factor domain superfamily / RasGEF domain / Ras guanine-nucleotide exchange factors catalytic domain profile. / Guanine nucleotide exchange factor for Ras-like small GTPases / Ras guanine-nucleotide exchange factors catalytic domain / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 protein sigma / Cyclic nucleotide-monophosphate binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / PDZ domain / RmlC-like jelly roll fold / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Ubiquitin-like domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
14-3-3 protein sigma / Rap guanine nucleotide exchange factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.702 Å
AuthorsAndrei, S.A. / Kaplan, A. / Fournier, A.E. / Ottman, C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific ResearchECHO -STIP 717.014.001 Netherlands
CitationJournal: Cell Chem Biol / Year: 2020
Title: Polypharmacological Perturbation of the 14-3-3 Adaptor Protein Interactome Stimulates Neurite Outgrowth.
Authors: Kaplan, A. / Andrei, S.A. / van Regteren Altena, A. / Simas, T. / Banerjee, S.L. / Kato, N. / Bisson, N. / Higuchi, Y. / Ottmann, C. / Fournier, A.E.
History
DepositionJan 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein sigma
B: Rap guanine nucleotide exchange factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0639
Polymers27,8722
Non-polymers1907
Water7,476415
1
A: 14-3-3 protein sigma
B: Rap guanine nucleotide exchange factor 2
hetero molecules

A: 14-3-3 protein sigma
B: Rap guanine nucleotide exchange factor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,12618
Polymers55,7454
Non-polymers38114
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5260 Å2
ΔGint-126 kcal/mol
Surface area23760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.657, 112.411, 62.749
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-305-

NA

21A-420-

HOH

31A-791-

HOH

41A-803-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein 14-3-3 protein sigma / Epithelial cell marker protein 1 / Stratifin


Mass: 26542.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli (E. coli) / References: UniProt: P31947
#2: Protein/peptide Rap guanine nucleotide exchange factor 2 / Cyclic nucleotide ras GEF / CNrasGEF / Neural RAP guanine nucleotide exchange protein / nRap GEP / ...Cyclic nucleotide ras GEF / CNrasGEF / Neural RAP guanine nucleotide exchange protein / nRap GEP / PDZ domain-containing guanine nucleotide exchange factor 1 / PDZ-GEF1 / RA-GEF-1 / Ras/Rap1-associating GEF-1


Mass: 1329.485 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9Y4G8

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Non-polymers , 4 types, 422 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 415 / 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: 2.61 Å3/Da / Density % sol: 52.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.19 M CaCl2, 5% v/v glycerol, 28 % PEG 400, 0.095 M HEPES, pH 7.1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5419 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Nov 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 1.62→41.866 Å / Num. obs: 32913 / % possible obs: 88.2 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.071 / Rrim(I) all: 0.132 / Net I/σ(I): 8.6
Reflection shellResolution: 1.62→1.66 Å

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.24 Å41.87 Å
Translation5.24 Å41.87 Å

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Processing

Software
NameVersionClassification
xia2data scaling
PHASER2.8.2phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JC3

4jc3


Resolution: 1.702→41.866 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.78
RfactorNum. reflection% reflection
Rfree0.1918 1541 4.94 %
Rwork0.1618 --
obs0.1633 31210 96.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 146.51 Å2 / Biso mean: 19.1745 Å2 / Biso min: 4.86 Å2
Refinement stepCycle: final / Resolution: 1.702→41.866 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1886 0 7 415 2308
Biso mean--23.48 31.82 -
Num. residues----240
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7021-1.7570.2589960.2421986208272
1.757-1.81980.23291300.21822461259189
1.8198-1.89270.24691340.20482762289699
1.8927-1.97880.22811560.18362721287799
1.9788-2.08310.1931340.161827982932100
2.0831-2.21360.1911450.154527582903100
2.2136-2.38450.1731490.148127832932100
2.3845-2.62450.1781420.154328022944100
2.6245-3.00410.20771470.151528202967100
3.0041-3.78450.16641670.134228122979100
3.7845-41.87870.18081410.164629663107100
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)
12.37210.6396-0.33673.06550.13682.4181-0.01090.0068-0.0419-0.08180.01130.01830.0809-0.03730.00360.04680.0035-0.00170.04790.00460.042932.192613.6166-8.2539
20.98290.9081-0.87024.574-3.88614.4258-0.0511-0.0741-0.05250.28870.17330.2671-0.0764-0.1771-0.16230.09810.02850.04160.06590.01260.090424.61777.17819.1267
32.5142.5333-2.75452.6896-3.3085.07840.0417-0.2428-0.63170.6958-0.20120.81220.4302-0.7950.1910.4253-0.12830.11430.29890.00390.451327.1087-12.085726.4511
40.30130.1227-0.03043.2713-1.25750.9947-0.0447-0.00440.00930.15270.0453-0.0966-0.0368-0.00050.00610.07480.0260.00430.0775-0.00310.062831.366515.456810.0179
53.9581-2.07311.67395.1071-2.6325.5626-0.1213-0.13570.1710.27610.0509-0.1705-0.19640.05880.04880.06820.00310.00230.0762-0.04090.067625.870327.705215.753
61.8777-0.81340.96521.612-1.13693.53870.03140.0216-0.0795-0.06010.04610.11790.1439-0.1959-0.06460.05760.00320.00340.0837-0.00690.093810.406524.442110.3094
72.4706-2.67112.4027.33311.76389.424-0.33430.7931-0.0978-0.63660.05430.58530.89-0.29930.2180.23850.0057-0.0540.2845-0.02340.269215.408514.43779.9928
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -4 through 37 )A-4 - 37
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 70 )A38 - 70
3X-RAY DIFFRACTION3chain 'A' and (resid 71 through 79 )A71 - 79
4X-RAY DIFFRACTION4chain 'A' and (resid 80 through 139 )A80 - 139
5X-RAY DIFFRACTION5chain 'A' and (resid 140 through 161 )A140 - 161
6X-RAY DIFFRACTION6chain 'A' and (resid 162 through 231 )A162 - 231
7X-RAY DIFFRACTION7chain 'B' and (resid 591 through 595 )B591 - 595

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