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- PDB-1uad: Crystal structure of the RalA-GppNHp-Sec5 Ral-binding domain complex -

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Basic information

Entry
Database: PDB / ID: 1uad
TitleCrystal structure of the RalA-GppNHp-Sec5 Ral-binding domain complex
Components
  • Exocyst complex component Sec5Exocyst
  • Ras-related protein Ral-A
KeywordsENDOCYTOSIS/EXOCYTOSIS / small GTP-binding protein / immunogloblin-like fold / beta-sandwich / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


small GTPase binding => GO:0031267 / VxPx cargo-targeting to cilium / membrane raft localization / regulation of entry of bacterium into host cell / exocyst / Edg-2 lysophosphatidic acid receptor binding / establishment of protein localization to mitochondrion / : / Golgi to plasma membrane transport / regulation of exocytosis ...small GTPase binding => GO:0031267 / VxPx cargo-targeting to cilium / membrane raft localization / regulation of entry of bacterium into host cell / exocyst / Edg-2 lysophosphatidic acid receptor binding / establishment of protein localization to mitochondrion / : / Golgi to plasma membrane transport / regulation of exocytosis / Flemming body / regulation of postsynaptic neurotransmitter receptor internalization / positive regulation of filopodium assembly / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of mitochondrial fission / myosin binding / exocytosis / cleavage furrow / vesicle-mediated transport / p38MAPK events / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / small monomeric GTPase / G protein activity / synaptic membrane / neural tube closure / Translocation of SLC2A4 (GLUT4) to the plasma membrane / regulation of actin cytoskeleton organization / Schaffer collateral - CA1 synapse / cytoplasmic vesicle membrane / receptor internalization / GDP binding / chemotaxis / protein transport / ATPase binding / Ras protein signal transduction / cell cycle / cell division / focal adhesion / GTPase activity / ubiquitin protein ligase binding / GTP binding / protein kinase binding / cell surface / signal transduction / mitochondrion / extracellular exosome / plasma membrane
Similarity search - Function
Exocyst complex component EXOC2/Sec5 / Exocyst complex component EXOC2/Sec5, N-terminal domain / Exocyst complex component Sec5 / IPT/TIG domain / IPT domain / Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases ...Exocyst complex component EXOC2/Sec5 / Exocyst complex component EXOC2/Sec5, N-terminal domain / Exocyst complex component Sec5 / IPT/TIG domain / IPT domain / Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / 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 / Immunoglobulin E-set / P-loop containing nucleotide triphosphate hydrolases / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Exocyst complex component 2 / Ras-related protein Ral-A
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsFukai, S. / Matern, H.T. / Scheller, R.H. / Brunger, A.T.
CitationJournal: EMBO J. / Year: 2003
Title: Structural basis of the interaction between RalA and Sec5, a subunit of the Sec6/8 complex
Authors: Fukai, S. / Matern, H.T. / Jagath, J.R. / Scheller, R.H. / Brunger, A.T.
History
DepositionMar 9, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 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_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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.value / _struct_conn.pdbx_dist_value / _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_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_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: Ras-related protein Ral-A
B: Ras-related protein Ral-A
C: Exocyst complex component Sec5
D: Exocyst complex component Sec5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1548
Polymers61,0614
Non-polymers1,0934
Water3,999222
1
A: Ras-related protein Ral-A
C: Exocyst complex component Sec5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0774
Polymers30,5312
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ras-related protein Ral-A
D: Exocyst complex component Sec5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0774
Polymers30,5312
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)117.418, 117.418, 102.676
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein Ras-related protein Ral-A / RalA


Mass: 20024.367 Da / Num. of mol.: 2 / Fragment: residues 9-183
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIL / References: UniProt: P11233
#2: Protein Exocyst complex component Sec5 / Exocyst / rSec5


Mass: 10506.199 Da / Num. of mol.: 2 / Fragment: N-terminal domain, Sec5 Ral-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pGEX2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIL / References: UniProt: O54921
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.86 Å3/Da / Density % sol: 56.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG8000, sodium acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
113-17 mg/mlprotein1drop
250 mMsodium acetate1reservoirpH5.5
37.5-8.5 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 24, 2002
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 40357 / Num. obs: 40357 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 23.4 Å2 / Rsym value: 0.044 / Net I/σ(I): 40.4
Reflection shellResolution: 2.1→2.14 Å / Mean I/σ(I) obs: 3.75 / Rsym value: 0.274 / % possible all: 98.6
Reflection
*PLUS
Num. measured all: 249726 / Rmerge(I) obs: 0.044
Reflection shell
*PLUS
Highest resolution: 2.1 Å / % possible obs: 98.6 % / Rmerge(I) obs: 0.274

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CTQ

1ctq


Resolution: 2.1→41.51 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2588488.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 4051 10 %RANDOM
Rwork0.219 ---
all0.223 40357 --
obs0.219 40357 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.2895 Å2 / ksol: 0.315895 e/Å3
Displacement parametersBiso mean: 45.2 Å2
Baniso -1Baniso -2Baniso -3
1-5.03 Å20 Å20 Å2
2--5.03 Å20 Å2
3----10.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.1→41.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4134 0 66 222 4422
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.541.5
X-RAY DIFFRACTIONc_mcangle_it2.542
X-RAY DIFFRACTIONc_scbond_it1.992
X-RAY DIFFRACTIONc_scangle_it2.932.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.319 675 10.2 %
Rwork0.279 5940 -
obs--98.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4GNP.PARAMGNP.TOP
Refinement
*PLUS
Highest resolution: 2.1 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.143
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.37
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.759

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