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- PDB-1zc3: Crystal structure of the Ral-binding domain of Exo84 in complex w... -

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Basic information

Entry
Database: PDB / ID: 1zc3
TitleCrystal structure of the Ral-binding domain of Exo84 in complex with the active RalA
Components
  • Ras-related protein Ral-A
  • exocyst complex protein Exo84
KeywordsSIGNALING PROTEIN / exocytosis / small GTPase / GTP-binding protein
Function / homology
Function and homology information


Insulin processing / VxPx cargo-targeting to cilium / membrane raft localization / exocyst / Edg-2 lysophosphatidic acid receptor binding / establishment of protein localization to mitochondrion / regulation of exocytosis / endosome organization / Golgi to plasma membrane transport / Flemming body ...Insulin processing / VxPx cargo-targeting to cilium / membrane raft localization / exocyst / Edg-2 lysophosphatidic acid receptor binding / establishment of protein localization to mitochondrion / regulation of exocytosis / endosome organization / Golgi to plasma membrane transport / Flemming body / regulation of postsynaptic neurotransmitter receptor internalization / positive regulation of filopodium assembly / positive regulation of epidermal growth factor receptor signaling pathway / myosin binding / positive regulation of mitochondrial fission / cell leading edge / exocytosis / cleavage furrow / extracellular matrix disassembly / p38MAPK events / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / phosphatidylinositol binding / small monomeric GTPase / neural tube closure / synaptic membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / regulation of actin cytoskeleton organization / cytoplasmic vesicle membrane / Schaffer collateral - CA1 synapse / receptor internalization / G protein activity / small GTPase binding / chemotaxis / GDP binding / late endosome / protein localization / protein transport / ATPase binding / growth cone / Ras protein signal transduction / cell division / focal adhesion / GTPase activity / ubiquitin protein ligase binding / GTP binding / perinuclear region of cytoplasm / cell surface / signal transduction / mitochondrion / extracellular exosome / plasma membrane
Similarity search - Function
Exocyst component Exo84, C-terminal / Exocyst complex component Exo84 / Exocyst component Exo84, C-terminal, subdomain 2 / Exocyst component Exo84, C-terminal, subdomain 1 / Exocyst component 84 C-terminal / Vps51/EXO84/COG1 N-terminal / Cullin repeat-like-containing domain superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Small GTPase, Ras-type ...Exocyst component Exo84, C-terminal / Exocyst complex component Exo84 / Exocyst component Exo84, C-terminal, subdomain 2 / Exocyst component Exo84, C-terminal, subdomain 1 / Exocyst component 84 C-terminal / Vps51/EXO84/COG1 N-terminal / Cullin repeat-like-containing domain superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / 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 / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Roll / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Exocyst complex component 8 / Ras-related protein Ral-A
Similarity search - Component
Biological speciesHomo sapiens (human)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsJin, R. / Junutula, J.R. / Matern, H.T. / Ervin, K.E. / Scheller, R.H. / Brunger, A.T.
CitationJournal: Embo J. / Year: 2005
Title: Exo84 and Sec5 are competitive regulatory Sec6/8 effectors to the RalA GTPase.
Authors: Jin, R. / Junutula, J.R. / Matern, H.T. / Ervin, K.E. / Scheller, R.H. / Brunger, A.T.
History
DepositionApr 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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: exocyst complex protein Exo84
C: Ras-related protein Ral-A
D: exocyst complex protein Exo84
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9598
Polymers66,8664
Non-polymers1,0934
Water7,440413
1
A: Ras-related protein Ral-A
D: exocyst complex protein Exo84
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9794
Polymers33,4332
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: exocyst complex protein Exo84
C: Ras-related protein Ral-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9794
Polymers33,4332
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.469, 113.795, 71.012
Angle α, β, γ (deg.)90.00, 102.86, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a complex between Ral and Exo84-RBD. The interaction as seen in the asymmetric unit is only a crystal contact. A functional complex is formed between symmetry related chains A and D, or chains B and C.

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Components

#1: Protein Ras-related protein Ral-A


Mass: 20009.396 Da / Num. of mol.: 2 / Mutation: Q72L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RALA, RAL / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P11233
#2: Protein exocyst complex protein Exo84


Mass: 13423.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O54924
#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


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


Mass: 18.015 Da / Num. of mol.: 413 / 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: 3.17 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18-22% PEG3350, 0.1-0.2 M ammonium sulfate, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2004
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.95→35 Å / Num. all: 59351 / Num. obs: 57036 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.085
Reflection shellResolution: 1.95→2.02 Å / Rmerge(I) obs: 0.469 / % possible all: 70.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→35 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 267842.63 / 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
Rfree0.23 5333 10.2 %RANDOM
Rwork0.206 ---
all0.22 54868 --
obs0.22 52234 95.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.4711 Å2 / ksol: 0.335337 e/Å3
Displacement parametersBiso mean: 36.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å2-1.98 Å2
2---4.25 Å20 Å2
3---3.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4598 0 66 413 5077
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it2.251.5
X-RAY DIFFRACTIONc_mcangle_it3.432
X-RAY DIFFRACTIONc_scbond_it3.472
X-RAY DIFFRACTIONc_scangle_it5.092.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.304 755 10 %
Rwork0.276 6769 -
obs-7524 82.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2gnp.parwater.top
X-RAY DIFFRACTION3ion.paramgnp.top
X-RAY DIFFRACTION4water_rep.paramion.top

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