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- PDB-8wf6: 14-3-3 zeta complexed with S559 phosphorylated peptide derived fr... -

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Basic information

Entry
Database: PDB / ID: 8wf6
Title14-3-3 zeta complexed with S559 phosphorylated peptide derived from GPIb alpha cytoplasmic domain
Components
  • 14-3-3 protein zeta/delta
  • S559 phosphorylated peptide
KeywordsBLOOD CLOTTING / Complex / 14-3-3 zeta / GPIb alpha
Function / homology
Function and homology information


thrombin-activated receptor activity / glycoprotein Ib-IX-V complex / synaptic target recognition / Golgi reassembly / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / positive regulation of leukocyte tethering or rolling / blood coagulation, intrinsic pathway / NOTCH4 Activation and Transmission of Signal to the Nucleus / respiratory system process ...thrombin-activated receptor activity / glycoprotein Ib-IX-V complex / synaptic target recognition / Golgi reassembly / Enhanced binding of GP1BA variant to VWF multimer:collagen / Defective binding of VWF variant to GPIb:IX:V / positive regulation of leukocyte tethering or rolling / blood coagulation, intrinsic pathway / NOTCH4 Activation and Transmission of Signal to the Nucleus / respiratory system process / establishment of Golgi localization / Defective F9 activation / Platelet Adhesion to exposed collagen / regulation of synapse maturation / tube formation / Rap1 signalling / positive regulation of platelet activation / negative regulation of protein localization to nucleus / megakaryocyte development / KSRP (KHSRP) binds and destabilizes mRNA / GP1b-IX-V activation signalling / regulation of blood coagulation / Platelet Aggregation (Plug Formation) / Regulation of localization of FOXO transcription factors / phosphoserine residue binding / Interleukin-3, Interleukin-5 and GM-CSF signaling / Activation of BAD and translocation to mitochondria / protein targeting / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / cellular response to glucose starvation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / release of sequestered calcium ion into cytosol / negative regulation of TORC1 signaling / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / protein sequestering activity / ERK1 and ERK2 cascade / negative regulation of innate immune response / hippocampal mossy fiber to CA3 synapse / extracellular matrix / regulation of ERK1 and ERK2 cascade / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / TP53 Regulates Metabolic Genes / Negative regulation of NOTCH4 signaling / lung development / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / regulation of protein stability / cell morphogenesis / platelet activation / blood coagulation / protein localization / melanosome / angiogenesis / DNA-binding transcription factor binding / vesicle / transmembrane transporter binding / blood microparticle / cell surface receptor signaling pathway / cell adhesion / cadherin binding / protein domain specific binding / protein phosphorylation / external side of plasma membrane / focal adhesion / glutamatergic synapse / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / negative regulation of transcription by RNA polymerase II / cell surface / signal transduction / RNA binding / extracellular space / extracellular exosome / nucleoplasm / identical protein binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Leucine-rich repeats, bacterial type / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. ...: / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Leucine-rich repeats, bacterial type / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / 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 / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
SUCCINIC ACID / Platelet glycoprotein Ib alpha chain / 14-3-3 protein zeta/delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsShu, Z.M. / Zhou, A.W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of GPIb-IX Complex
Authors: Shu, Z.M. / Zhou, A.W.
History
DepositionSep 19, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein zeta/delta
B: 14-3-3 protein zeta/delta
Q: S559 phosphorylated peptide
R: S559 phosphorylated peptide
C: 14-3-3 protein zeta/delta
D: 14-3-3 protein zeta/delta
E: S559 phosphorylated peptide
F: S559 phosphorylated peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,59510
Polymers117,3598
Non-polymers2362
Water32418
1
A: 14-3-3 protein zeta/delta
B: 14-3-3 protein zeta/delta
Q: S559 phosphorylated peptide
R: S559 phosphorylated peptide


Theoretical massNumber of molelcules
Total (without water)58,6804
Polymers58,6804
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-30 kcal/mol
Surface area21990 Å2
MethodPISA
2
C: 14-3-3 protein zeta/delta
D: 14-3-3 protein zeta/delta
E: S559 phosphorylated peptide
F: S559 phosphorylated peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9166
Polymers58,6804
Non-polymers2362
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-30 kcal/mol
Surface area22000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.310, 112.240, 83.920
Angle α, β, γ (deg.)90.000, 97.520, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
14-3-3 protein zeta/delta / Protein kinase C inhibitor protein 1 / KCIP-1


Mass: 27864.168 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAZ / Production host: Escherichia coli (E. coli) / References: UniProt: P63104
#2: Protein/peptide
S559 phosphorylated peptide


Mass: 1475.629 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P07359
#3: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.84 Å3/Da / Density % sol: 56.64 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 2% Tacsimate pH7.0, 0.1M Hepes pH7.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Dec 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.47→37.41 Å / Num. obs: 46953 / % possible obs: 99.8 % / Redundancy: 6.7 % / Biso Wilson estimate: 49.96 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.9
Reflection shellResolution: 2.47→2.53 Å / Num. unique obs: 3461 / CC1/2: 0.771

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.47→31.4 Å / SU ML: 0.3187 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.7458
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2384 2276 4.86 %
Rwork0.1965 44600 -
obs0.1985 46876 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 66.59 Å2
Refinement stepCycle: LAST / Resolution: 2.47→31.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7126 0 16 18 7160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00167231
X-RAY DIFFRACTIONf_angle_d0.39529763
X-RAY DIFFRACTIONf_chiral_restr0.031115
X-RAY DIFFRACTIONf_plane_restr0.00281259
X-RAY DIFFRACTIONf_dihedral_angle_d4.07541007
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.47-2.520.33591300.29132784X-RAY DIFFRACTION99.86
2.52-2.580.30031310.25912781X-RAY DIFFRACTION99.76
2.58-2.650.29491460.25332799X-RAY DIFFRACTION99.93
2.65-2.720.33091350.25292772X-RAY DIFFRACTION99.86
2.72-2.80.31611310.25512807X-RAY DIFFRACTION99.9
2.8-2.890.31421580.2412757X-RAY DIFFRACTION99.9
2.89-2.990.25831300.22022809X-RAY DIFFRACTION99.86
2.99-3.110.25691450.2232783X-RAY DIFFRACTION99.83
3.11-3.250.28171570.2232773X-RAY DIFFRACTION99.93
3.25-3.420.30781360.21662780X-RAY DIFFRACTION99.79
3.42-3.640.2271380.20342780X-RAY DIFFRACTION99.86
3.64-3.920.22221540.1852789X-RAY DIFFRACTION99.8
3.92-4.310.19031460.16082774X-RAY DIFFRACTION99.73
4.31-4.930.20161510.15742807X-RAY DIFFRACTION99.6
4.93-6.210.2381380.19982789X-RAY DIFFRACTION99.32
6.21-31.40.18831500.16372816X-RAY DIFFRACTION98.37
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)
13.761097357311.255890866081.507951569462.444221063831.475751088072.71380803824-0.3041192351040.649255632230.0851276418154-0.3615790525460.340859555936-0.417369623903-0.2951236902450.490024941624-0.05034117427710.443385661864-0.06597682901390.04906361466770.6347596809680.03759659559710.50589270872437.94227.77134.656
22.415505697920.80394170594-0.6816344333532.4958667454-0.5289423019042.08607379669-0.08527186105140.2635530648390.18189436764-0.1159687791780.1321945733860.2517873483050.100013189077-0.272873758452-0.03347401616220.4480458107180.0398114973541-0.02577056600540.6296595640380.007377847431190.3618222637273.63911.28633.732
34.957428906094.2044382814-3.292562524227.82608063876-0.04104333288873.96287118653-1.46099895806-0.951735659441-1.152351430431.623598005381.31992344237-0.3085057065380.08939086867211.231234589150.09694494646910.531518081710.184137885122-0.01397018326920.6527989271490.008655047485480.2789644705137.73910.6640.739
40.403520446179-1.04830339562-1.45723873423.041509940054.02104360245.4332245542-1.33349032361-1.07946843355-0.9211132486380.3719522228610.3464302499183.07311676039-0.668497091027-1.984877491060.9076726147960.5131681065660.0808619785035-0.02825806298041.01415047074-0.1387129253960.97059394291933.68727.07942.363
52.29261335011-0.6133733789130.2948634852582.08589179687-0.6050886413510.942325004134-0.0482289257122-0.0406908570857-0.2237663389230.02740750075450.07156874728360.5417268861720.0291617007274-0.0980969141167-0.01281583953010.304464111847-0.02649903319630.03259192401050.3262804077760.009994539335260.512773353516-20.90125.846-2.541
63.25378652446-0.661239843506-0.7056787088112.570823115520.2313350864611.56940756349-0.002347463203430.006533299058540.149161001261-0.06321395546150.00952173746443-0.218165447968-0.0472548834240.0542878428289-0.01143487541810.294582762203-0.0438669211099-0.01144592288510.3250206770230.01685117084780.31800020508913.2649.563-4.258
74.33778694538-3.463588084982.156152176115.494951855920.8414362476623.47948266831-0.525934129274-0.319951683006-0.004488501542270.2165988754660.1399084652240.7542192171730.189986521171-1.720263460760.3587336088150.3570497049670.01769904412030.07571491811980.6494774653360.0313019914810.2983811106149.98610.543-10.875
88.23004070652-6.133416158940.08147943926917.35267667772-2.895940607236.0987542442-0.385940997478-0.191537535893-0.0777441919471-0.1192881990070.0590874094489-0.781701131022-0.4874306125062.21481784350.3303046085570.366571572487-0.1029122815540.02620900161660.577433026572-0.07470850073710.452331786918-17.94425.326-9.497
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:230 )A1 - 230
2X-RAY DIFFRACTION2( CHAIN B AND RESID 1:232 )B1 - 232
3X-RAY DIFFRACTION3( CHAIN Q AND RESID 6:11 )Q6 - 11
4X-RAY DIFFRACTION4( CHAIN R AND RESID 5:11 )R5 - 11
5X-RAY DIFFRACTION5( CHAIN C AND ( RESID 1:230 OR RESID 301:301 ) )C1 - 230
6X-RAY DIFFRACTION5( CHAIN C AND ( RESID 1:230 OR RESID 301:301 ) )C301
7X-RAY DIFFRACTION6( CHAIN D AND ( RESID 2:231 OR RESID 301:301 ) )D2 - 231
8X-RAY DIFFRACTION6( CHAIN D AND ( RESID 2:231 OR RESID 301:301 ) )D301
9X-RAY DIFFRACTION7( CHAIN E AND RESID 6:10 )E6 - 10
10X-RAY DIFFRACTION8( CHAIN F AND RESID 6:10 )F6 - 10

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