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- PDB-6ekk: Crystal structure of GEF domain of DENND 1A in complex with Rab G... -

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Basic information

Entry
Database: PDB / ID: 6ekk
TitleCrystal structure of GEF domain of DENND 1A in complex with Rab GTPase Rab35-GDP bound state.
Components
  • DENN domain-containing protein 1A
  • Ras-related protein Rab-35
KeywordsTRANSCRIPTION / DENND1A- DENN domain-containing protein 1A RAB35- Ras-related protein Rab-35
Function / homology
Function and homology information


regulation of Rab protein signal transduction / Rab protein signal transduction / plasma membrane to endosome transport / phosphatidylinositol phosphate binding / protein localization to endosome / clathrin-coated endocytic vesicle / clathrin-coated vesicle membrane / cell projection membrane / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs ...regulation of Rab protein signal transduction / Rab protein signal transduction / plasma membrane to endosome transport / phosphatidylinositol phosphate binding / protein localization to endosome / clathrin-coated endocytic vesicle / clathrin-coated vesicle membrane / cell projection membrane / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / phosphatidylinositol-3-phosphate binding / endocytic recycling / TBC/RABGAPs / clathrin-coated vesicle / endosomal transport / antigen processing and presentation / mitotic cytokinesis / intercellular bridge / clathrin-coated pit / phosphatidylinositol-4,5-bisphosphate binding / guanyl-nucleotide exchange factor activity / small monomeric GTPase / cell projection / clathrin-coated endocytic vesicle membrane / cellular response to nerve growth factor stimulus / endocytosis / recycling endosome membrane / neuron projection development / GDP binding / intracellular protein localization / melanosome / protein transport / G protein activity / presynaptic membrane / endosome membrane / intracellular membrane-bounded organelle / GTPase activity / GTP binding / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
Longin module / DENN domain-containing protein 1A/1B/1C / Rab35 / dDENN domain / uDENN domain / uDENN domain / Domain always found upstream of DENN domain, found in a variety of signalling proteins / cDENN domain / dDENN domain / DENN domain, C-terminal lobe ...Longin module / DENN domain-containing protein 1A/1B/1C / Rab35 / dDENN domain / uDENN domain / uDENN domain / Domain always found upstream of DENN domain, found in a variety of signalling proteins / cDENN domain / dDENN domain / DENN domain, C-terminal lobe / DENN (AEX-3) domain / Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN / Domain always found downstream of DENN domain, found in a variety of signalling proteins / Tripartite DENN domain / Tripartite DENN domain profile. / : / ARF-like small GTPases; ARF, ADP-ribosylation factor / Small GTPase Rab domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Beta-Lactamase / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Ras-related protein Rab-35 / DENN domain-containing protein 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsSrikannathasan, V. / Szykowska, A. / Tallant, C. / Strain-Damerell, C. / Kopec, J. / Kupinska, K. / Mukhopadhyay, S. / Gavin, M. / Wang, D. / Chalk, R. ...Srikannathasan, V. / Szykowska, A. / Tallant, C. / Strain-Damerell, C. / Kopec, J. / Kupinska, K. / Mukhopadhyay, S. / Gavin, M. / Wang, D. / Chalk, R. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / von Delft, F. / Huber, K.
CitationJournal: To be published
Title: Crystal structure of DENND1A-RAB35 complex with GDP bound state.
Authors: Srikannathasan, V.
History
DepositionSep 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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: DENN domain-containing protein 1A
B: DENN domain-containing protein 1A
C: Ras-related protein Rab-35
D: Ras-related protein Rab-35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,41523
Polymers130,1684
Non-polymers2,24819
Water15,493860
1
A: DENN domain-containing protein 1A
C: Ras-related protein Rab-35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,16011
Polymers65,0842
Non-polymers1,0769
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-58 kcal/mol
Surface area22950 Å2
MethodPISA
2
B: DENN domain-containing protein 1A
D: Ras-related protein Rab-35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,25612
Polymers65,0842
Non-polymers1,17210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-88 kcal/mol
Surface area23460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.700, 67.990, 101.710
Angle α, β, γ (deg.)80.500, 76.800, 67.060
Int Tables number1
Space group name H-MP1

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein DENN domain-containing protein 1A / Connecdenn 1 / Connecdenn / Protein FAM31A


Mass: 45006.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Chain A- DENND1AA (UNIPROT Q8TEH3) Chain B- RAB35 (UNIPROT - Q15286)
Source: (gene. exp.) Homo sapiens (human) / Gene: DENND1A, FAM31A, KIAA1608 / Plasmid: pFB-CT10HF-LIC / Details (production host): C-terminal TAg / Cell (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8TEH3
#2: Protein Ras-related protein Rab-35 / GTP-binding protein RAY / Ras-related protein Rab-1C


Mass: 20077.725 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB35, RAB1C, RAY / Plasmid: pNIC28-Bsa4 / Details (production host): N-terminal his tag / Cell (production host): Escherichia Coli BL21 DE3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15286

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Non-polymers , 4 types, 879 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 860 / 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: 2.64 Å3/Da / Density % sol: 53.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 25%PEG3350, 0.2M AMS, 0.1M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 13, 2017
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.82→50.452 Å / Num. obs: 115286 / % possible obs: 95.7 % / Redundancy: 3.4 % / Net I/σ(I): 8.5
Reflection shellResolution: 1.82→1.87 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TW8

3tw8


Resolution: 1.82→50.452 Å / SU ML: 0.25 / Cross valid method: NONE / σ(F): 1.96 / Phase error: 26.78
RfactorNum. reflection% reflection
Rfree0.2323 5773 5.01 %
Rwork0.1935 --
obs0.1954 115262 96.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 130.5 Å2 / Biso mean: 36.0058 Å2 / Biso min: 17.14 Å2
Refinement stepCycle: final / Resolution: 1.82→50.452 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8664 0 133 860 9657
Biso mean--49.64 45.07 -
Num. residues----1106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089085
X-RAY DIFFRACTIONf_angle_d1.10412376
X-RAY DIFFRACTIONf_chiral_restr0.0431398
X-RAY DIFFRACTIONf_plane_restr0.0051583
X-RAY DIFFRACTIONf_dihedral_angle_d14.4383223
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.82-1.84070.34281880.37623655384396
1.8407-1.86230.39551950.36243595379096
1.8623-1.88510.32071880.33183633382196
1.8851-1.90890.32932230.31993598382196
1.9089-1.9340.34112020.29813611381396
1.934-1.96050.32741970.2793624382196
1.9605-1.98850.30222210.27133663388496
1.9885-2.01820.27341820.25983590377296
2.0182-2.04980.30192090.24333593380296
2.0498-2.08340.2691890.2343641383096
2.0834-2.11930.24351840.22263669385396
2.1193-2.15780.22961820.21723630381296
2.1578-2.19930.26482020.20963599380196
2.1993-2.24420.28931760.21093592376895
2.2442-2.2930.24691920.20873654384696
2.293-2.34640.21531740.1953638381296
2.3464-2.4050.24162110.19733619383096
2.405-2.47010.22721870.19453601378896
2.4701-2.54270.25852050.19963649385496
2.5427-2.62480.21842020.19193587378996
2.6248-2.71860.22881860.18963657384396
2.7186-2.82750.24991930.19223671386497
2.8275-2.95610.23981870.19563697388497
2.9561-3.1120.24091500.18423717386797
3.112-3.30690.19871850.17683699388498
3.3069-3.56220.21321900.17653687387798
3.5622-3.92050.20651950.15973726392198
3.9205-4.48750.19372090.15363709391898
4.4875-5.65260.18391710.15763761393298
5.6526-50.4710.22581980.18373724392298
Refinement TLS params.Method: refined / Origin x: 17.726 Å / Origin y: 9.6475 Å / Origin z: 25.363 Å
111213212223313233
T0.2146 Å20.0077 Å20.0341 Å2-0.1859 Å2-0.0001 Å2--0.2031 Å2
L0.2772 °20.0677 °20.2242 °2-0.1059 °20.0364 °2--0.4261 °2
S0.018 Å °-0.0057 Å °-0.001 Å °0.0447 Å °-0.0049 Å °0.0262 Å °-0.0351 Å °-0.0063 Å °-0.0127 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 390
2X-RAY DIFFRACTION1allB2 - 394
3X-RAY DIFFRACTION1allC3 - 178
4X-RAY DIFFRACTION1allD4 - 177
5X-RAY DIFFRACTION1allE1 - 9
6X-RAY DIFFRACTION1allF1 - 8
7X-RAY DIFFRACTION1allK1 - 2
8X-RAY DIFFRACTION1allS1 - 643
9X-RAY DIFFRACTION1allW1 - 312

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