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- PDB-4zdw: Crystal structure of the Rab GTPase Sec4p mutant - S29V in comple... -

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Basic information

Entry
Database: PDB / ID: 4zdw
TitleCrystal structure of the Rab GTPase Sec4p mutant - S29V in complex with Sec2p and GDP
Components
  • Rab guanine nucleotide exchange factor SEC2
  • Ras-related protein SEC4
KeywordsGTP binding protein / GTPase / GDP bound / Rab Sec4p / Sec2p
Function / homology
Function and homology information


ascospore-type prospore membrane formation / Golgi to plasma membrane transport vesicle / ascospore-type prospore assembly / Anchoring of the basal body to the plasma membrane / membrane addition at site of cytokinesis / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / cell tip / incipient cellular bud site / vesicle fusion ...ascospore-type prospore membrane formation / Golgi to plasma membrane transport vesicle / ascospore-type prospore assembly / Anchoring of the basal body to the plasma membrane / membrane addition at site of cytokinesis / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / cell tip / incipient cellular bud site / vesicle fusion / cellular bud tip / Golgi to plasma membrane transport / cellular bud neck / mating projection tip / phosphatidylinositol-4-phosphate binding / sporulation resulting in formation of a cellular spore / transport vesicle membrane / exocytosis / protein secretion / transport vesicle / Neutrophil degranulation / guanyl-nucleotide exchange factor activity / autophagy / protein transport / vesicle / mitochondrial outer membrane / endosome / GTPase activity / GTP binding / endoplasmic reticulum / mitochondrion / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4880 / GDP/GTP exchange factor Sec2, N-terminal / Guanine nucleotide exchange factor RAB3IL/RAB3IP/Sec2 / GDP/GTP exchange factor Sec2p / : / ARF-like small GTPases; ARF, ADP-ribosylation factor / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Rho (Ras homology) subfamily of Ras-like small GTPases ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #4880 / GDP/GTP exchange factor Sec2, N-terminal / Guanine nucleotide exchange factor RAB3IL/RAB3IP/Sec2 / GDP/GTP exchange factor Sec2p / : / ARF-like small GTPases; ARF, ADP-ribosylation factor / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Ras-related protein SEC4 / Rab guanine nucleotide exchange factor SEC2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsRinadi, F.C. / Collins, R.N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM069596 United States
CitationJournal: Bmc Struct.Biol. / Year: 2015
Title: New insights into the molecular mechanism of the Rab GTPase Sec4p activation.
Authors: Rinaldi, F.C. / Packer, M. / Collins, R.
History
DepositionApr 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras-related protein SEC4
B: Rab guanine nucleotide exchange factor SEC2
C: Rab guanine nucleotide exchange factor SEC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7124
Polymers41,2693
Non-polymers4431
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-62 kcal/mol
Surface area20200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.900, 119.280, 122.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsTrimer according to Gel filtration

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Components

#1: Protein Ras-related protein SEC4 / Suppressor of RHO3 protein 6


Mass: 19134.889 Da / Num. of mol.: 1 / Mutation: S29V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SEC4, SRO6, YFL005W / Plasmid: ppSUMO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P07560
#2: Protein Rab guanine nucleotide exchange factor SEC2 / GDP-GTP exchange factor SEC2


Mass: 11067.187 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SEC2, YNL272C, N0641 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P17065
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.34 Å3/Da / Density % sol: 76.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Crystals were grown by mixing protein complex with a reservoir solution containing 24% PEG 3350, 0.2 M Sodium Citrate in a 1:1 ratio and with the addition of 10mM GDP to the drop.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 6, 2009 / Details: mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.9→85.44 Å / Num. obs: 19416 / % possible obs: 99.8 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.084 / Net I/av σ(I): 5.1 / Net I/σ(I): 13.4
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 3.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EQB

2eqb


Resolution: 2.9→85.44 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.869 / SU B: 38.788 / SU ML: 0.337 / Cross valid method: THROUGHOUT / ESU R: 0.597 / ESU R Free: 0.377 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.29527 879 5.1 %RANDOM
Rwork0.25802 ---
obs0.25993 16492 89.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.868 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å2-0 Å2-0 Å2
2--0.65 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 2.9→85.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2823 0 28 16 2867
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022876
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6131.9853867
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0925344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.95825.649154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.26715576
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7771522
X-RAY DIFFRACTIONr_chiral_restr0.1110.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022117
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.976 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.512 22 -
Rwork0.326 385 -
obs--29.73 %
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)
14.0513-0.3474-1.7721.83470.17464.58120.10130.6896-0.1678-0.43180.1287-0.5856-0.10020.5966-0.230.25740.1060.08370.6052-0.10570.3454-25.7645-22.6123-18.6267
210.2794-4.361410.99522.238-4.834712.29760.5532-0.2945-0.4071-0.37130.00470.16040.6898-0.3482-0.55790.10010.0434-0.02140.08950.04430.0506-27.6483-27.940711.6846
36.011-3.65836.22892.3766-3.93826.8575-0.02270.35770.6335-0.0851-0.3983-0.30990.0740.44160.42110.15460.0831-0.06320.22580.00720.188-25.9688-22.860912.6412
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 186
2X-RAY DIFFRACTION2B52 - 139
3X-RAY DIFFRACTION3C52 - 139

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