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- PDB-4f2h: Structure of the minimal Ste5 VWA domain subject to autoinhibitio... -

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Basic information

Entry
Database: PDB / ID: 4f2h
TitleStructure of the minimal Ste5 VWA domain subject to autoinhibition by the Ste5 PH domain
ComponentsProtein STE5
KeywordsSIGNALING PROTEIN / Von Wildebrand Type A / Ste5ms / Coactivation of Fus3
Function / homology
Function and homology information


mating projection tip membrane / invasive growth in response to glucose limitation / pheromone-dependent signal transduction involved in conjugation with cellular fusion / MAP-kinase scaffold activity / mating projection tip / negative regulation of MAPK cascade / phosphatidylinositol-4,5-bisphosphate binding / kinase binding / G-protein beta-subunit binding / positive regulation of protein phosphorylation ...mating projection tip membrane / invasive growth in response to glucose limitation / pheromone-dependent signal transduction involved in conjugation with cellular fusion / MAP-kinase scaffold activity / mating projection tip / negative regulation of MAPK cascade / phosphatidylinositol-4,5-bisphosphate binding / kinase binding / G-protein beta-subunit binding / positive regulation of protein phosphorylation / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Protein Ste5, Fus3-binding domain / Protein Ste5, Fus3-binding domain / Scaffold protein Ste5, Fus3-binding domain / Ste5, Fus3-binding domain superfamily / Scaffold protein Ste5, Fus3-binding region / Protein kinase Fus3-binding / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.192 Å
AuthorsCoyle, S.M. / Zalatan, J.G. / Lim, W.A.
CitationJournal: Science / Year: 2012
Title: Conformational control of the Ste5 scaffold protein insulates against MAP kinase misactivation.
Authors: Zalatan, J.G. / Coyle, S.M. / Rajan, S. / Sidhu, S.S. / Lim, W.A.
History
DepositionMay 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
Revision 1.2Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein STE5


Theoretical massNumber of molelcules
Total (without water)23,6841
Polymers23,6841
Non-polymers00
Water00
1
A: Protein STE5

A: Protein STE5


Theoretical massNumber of molelcules
Total (without water)47,3672
Polymers47,3672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
2
A: Protein STE5

A: Protein STE5

A: Protein STE5

A: Protein STE5


Theoretical massNumber of molelcules
Total (without water)94,7344
Polymers94,7344
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area6980 Å2
ΔGint-24 kcal/mol
Surface area33260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.840, 87.350, 100.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Protein STE5


Mass: 23683.568 Da / Num. of mol.: 1 / Fragment: VWA domain (UNP residues 583-787)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: STE5, NUL3 / Production host: Escherichia coli (E. coli) / References: UniProt: P32917

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.25 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG3350, 0.1 M calcium chloride, 25 mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceTypeIDWavelength (Å)
ROTATING ANODERIGAKU11.5418
ROTATING ANODERIGAKU21.5418
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDJul 3, 2011
ADSC QUANTUM 315r2CCDJul 5, 2011
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21
ReflectionResolution: 3.19→19.7 Å / Num. all: 4884 / Num. obs: 4395 / % possible obs: 90 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.75 % / Rsym value: 0.109 / Net I/σ(I): 25.4
Reflection shellResolution: 3.19→3.28 Å / Redundancy: 4.91 % / Mean I/σ(I) obs: 10.56 / Rsym value: 0.236 / % possible all: 89.9

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FZE

3fze


Resolution: 3.192→19.694 Å / SU ML: 0.82 / σ(F): 2.02 / Phase error: 24.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2566 220 5.01 %
Rwork0.183 --
obs0.1869 4395 90.38 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 24.316 Å2 / ksol: 0.364 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.8312 Å20 Å20 Å2
2--4.7262 Å2-0 Å2
3---1.1051 Å2
Refinement stepCycle: LAST / Resolution: 3.192→19.694 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1536 0 0 0 1536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081564
X-RAY DIFFRACTIONf_angle_d1.9822115
X-RAY DIFFRACTIONf_dihedral_angle_d14.983577
X-RAY DIFFRACTIONf_chiral_restr0.174249
X-RAY DIFFRACTIONf_plane_restr0.003262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.192-4.01620.27521090.18972068X-RAY DIFFRACTION92
4.0162-19.69450.24341110.17782107X-RAY DIFFRACTION89
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)
10.016-0.05480.04220.1491-0.14570.1009-0.06650.01510.1211-0.0006-0.1625-0.1534-0.07680.1063-0.2153-0.4085-0.32530.3095-0.16210.2353-0.1942-4.1609-35.1256-9.1265
20.0084-0.0052-0.00370.0046-0.00120.0023-0.01430.02080.00990.0104-0.02310.02470.00960.0108-0.00290.1865-0.1423-0.02010.36080.17620.3672-24.9042-33.9512-9.6874
30.0381-0.02920.03470.1437-0.09560.08690.23220.21350.4567-0.0340.14780.1945-0.16530.01470.47180.0190.0836-0.06040.05410.17420.1743-15.4067-21.9166-16.058
40.1473-0.0538-0.03560.01880.00240.06990.03770.29890.1415-0.1338-0.05990.00440.011-0.0824-0.04490.08530.02160.0110.18620.0710.1222-7.7634-29.5036-21.7125
50.0405-0.00850.03510.02510.02630.077-0.00760.0409-0.0141-0.0616-0.0935-0.1298-0.0224-0.102-0.07420.0606-0.00080.00030.42560.2060.10673.736-29.8845-23.0854
60.2149-0.09570.05640.0543-0.03690.0589-0.1194-0.05870.10720.0299-0.0488-0.18150.0302-0.0738-0.12760.18820.00760.03710.01570.03260.0337-9.2705-37.4946-11.2567
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 584:616)
2X-RAY DIFFRACTION2chain 'A' and (resseq 617:626)
3X-RAY DIFFRACTION3chain 'A' and (resseq 627:692)
4X-RAY DIFFRACTION4chain 'A' and (resseq 693:721)
5X-RAY DIFFRACTION5chain 'A' and (resseq 722:734)
6X-RAY DIFFRACTION6chain 'A' and (resseq 735:774)

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