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- PDB-2fu5: structure of Rab8 in complex with MSS4 -

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Basic information

Entry
Database: PDB / ID: 2fu5
Titlestructure of Rab8 in complex with MSS4
Components
  • Guanine nucleotide exchange factor MSS4
  • Ras-related protein Rab-8A
KeywordsSIGNALING PROTEIN / MSS4:Rab8 protein complex / GEF:GTPase nucleotide free complex / nucleotide exchange via unfolding of nucleotide binding region
Function / homology
Function and homology information


VxPx cargo-targeting to cilium / TBC/RABGAPs / neurotransmitter receptor transport to postsynaptic membrane / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / small GTPase binding => GO:0031267 / Golgi vesicle fusion to target membrane / vesicle-mediated transport in synapse / regulation of protein transport / post-Golgi vesicle-mediated transport ...VxPx cargo-targeting to cilium / TBC/RABGAPs / neurotransmitter receptor transport to postsynaptic membrane / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / small GTPase binding => GO:0031267 / Golgi vesicle fusion to target membrane / vesicle-mediated transport in synapse / regulation of protein transport / post-Golgi vesicle-mediated transport / neurotransmitter receptor transport, endosome to postsynaptic membrane / Anchoring of the basal body to the plasma membrane / Regulation of PLK1 Activity at G2/M Transition / myosin V binding / vesicle docking involved in exocytosis / regulation of exocytosis / trans-Golgi network transport vesicle / non-motile cilium / ciliary base / small GTPase-mediated signal transduction / cilium assembly / protein secretion / phagocytic vesicle / centriole / axonogenesis / guanyl-nucleotide exchange factor activity / ciliary basal body / regulation of autophagy / protein localization to plasma membrane / regulation of long-term neuronal synaptic plasticity / cytoplasmic vesicle membrane / cilium / recycling endosome / autophagy / cellular response to insulin stimulus / recycling endosome membrane / phagocytic vesicle membrane / GDP binding / regulation of protein localization / synaptic vesicle / protein transport / midbody / cytoplasmic vesicle / dendritic spine / membrane fusion / postsynaptic density / endosome / GTPase activity / centrosome / neuronal cell body / glutamatergic synapse / synapse / dendrite / GTP binding / protein kinase binding / Golgi apparatus / zinc ion binding / membrane / plasma membrane / cytosol
Similarity search - Function
Mss4 / Mss4 protein / MSS4 domain profile. / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / Mss4/translationally controlled tumour-associated TCTP / Mss4-like superfamily / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / small GTPase Rab1 family profile. / Beta Complex / Small GTPase ...Mss4 / Mss4 protein / MSS4 domain profile. / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / Mss4/translationally controlled tumour-associated TCTP / Mss4-like superfamily / Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A / small GTPase Rab1 family profile. / Beta Complex / Small GTPase / Ras family / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Guanine nucleotide exchange factor MSS4 / Ras-related protein Rab-8A
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsItzen, A. / Pylypenko, O. / Goody, R.S. / Rak, A.
CitationJournal: Embo J. / Year: 2006
Title: Nucleotide exchange via local protein unfolding-structure of Rab8 in complex with MSS4
Authors: Itzen, A. / Pylypenko, O. / Goody, R.S. / Alexandrov, K. / Rak, A.
History
DepositionJan 26, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Guanine nucleotide exchange factor MSS4
B: Guanine nucleotide exchange factor MSS4
C: Ras-related protein Rab-8A
D: Ras-related protein Rab-8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5898
Polymers68,3024
Non-polymers2874
Water5,423301
1
A: Guanine nucleotide exchange factor MSS4
D: Ras-related protein Rab-8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2954
Polymers34,1512
Non-polymers1442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-12 kcal/mol
Surface area14400 Å2
MethodPISA
2
B: Guanine nucleotide exchange factor MSS4
C: Ras-related protein Rab-8A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2954
Polymers34,1512
Non-polymers1442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-12 kcal/mol
Surface area13330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.920, 49.850, 83.480
Angle α, β, γ (deg.)102.88, 97.46, 90.12
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Guanine nucleotide exchange factor MSS4 / Rab-interacting factor / Mss4


Mass: 13198.093 Da / Num. of mol.: 2 / Fragment: residues 11-123
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RABIF, MSS4, RASGRF3 / Plasmid: pET19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P47224
#2: Protein Ras-related protein Rab-8A / Oncogene c-mel / Rab8


Mass: 20953.076 Da / Num. of mol.: 2 / Fragment: residues 1-183
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Rab8a, Mel, Rab8 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P55258
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.41 Å3/Da / Density % sol: 48.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 20% PEG3350, 50mM TrisHCL pH 9.0, 0.2M magnesium acetate, 0.15% (w/v) 1,2,3-heptanetriole, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→19.17 Å / Num. all: 40718 / Num. obs: 40718 / % possible obs: 94.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 2→2.05 Å / % possible all: 74.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ProDCdata collection
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1hxr

1hxr


Resolution: 2→19.17 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.903 / SU B: 3.901 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.175 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25213 2036 5 %RANDOM
Rwork0.1969 ---
all0.19964 38678 --
obs0.19964 38678 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.426 Å2
Refinement stepCycle: LAST / Resolution: 2→19.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4162 0 2 309 4473
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224232
X-RAY DIFFRACTIONr_angle_refined_deg1.3251.9485669
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4175503
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.43623.876209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.55115786
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3211533
X-RAY DIFFRACTIONr_chiral_restr0.1010.2621
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023135
X-RAY DIFFRACTIONr_nbd_refined0.2080.21741
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22818
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.2320
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1590.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.227
X-RAY DIFFRACTIONr_mcbond_it1.1231.52633
X-RAY DIFFRACTIONr_mcangle_it1.82424067
X-RAY DIFFRACTIONr_scbond_it2.16531835
X-RAY DIFFRACTIONr_scangle_it3.2994.51602
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.296 117
Rwork0.226 2235

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