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- PDB-3tw8: GEF domain of DENND 1B in complex with Rab GTPase Rab35 -

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Basic information

Entry
Database: PDB / ID: 3tw8
TitleGEF domain of DENND 1B in complex with Rab GTPase Rab35
Components
  • DENN domain-containing protein 1B
  • Ras-related protein Rab-35
KeywordsPROTEIN TRANSPORT / longin domain / Rab GTPase / guanine exchange factor
Function / homology
Function and homology information


T-helper 2 cell cytokine production / guanyl-nucleotide exchange factor activity => GO:0005085 / small GTPase binding => GO:0031267 / Rab protein signal transduction / plasma membrane to endosome transport / phosphatidylinositol phosphate binding / protein localization to endosome / cell projection membrane / clathrin-coated endocytic vesicle / RAB geranylgeranylation ...T-helper 2 cell cytokine production / guanyl-nucleotide exchange factor activity => GO:0005085 / small GTPase binding => GO:0031267 / Rab protein signal transduction / plasma membrane to endosome transport / phosphatidylinositol phosphate binding / protein localization to endosome / cell projection membrane / clathrin-coated endocytic vesicle / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / endocytic recycling / TBC/RABGAPs / clathrin-coated vesicle / endosomal transport / intercellular bridge / mitotic cytokinesis / antigen processing and presentation / regulation of immune response / clathrin-coated pit / phosphatidylinositol-4,5-bisphosphate binding / cellular response to nerve growth factor stimulus / clathrin-coated endocytic vesicle membrane / protein localization / positive regulation of GTPase activity / endocytosis / recycling endosome membrane / GDP binding / neuron projection development / melanosome / protein transport / T cell receptor signaling pathway / endosome membrane / nuclear speck / intracellular membrane-bounded organelle / GTPase activity / GTP binding / extracellular exosome / plasma membrane / cytosol
Similarity search - Function
Longin module / DENN domain, C-terminal lobe / Helix Hairpins - #1000 / DENN domain-containing protein 1A/1B/1C / dDENN domain / uDENN domain / Rab35 / uDENN domain / Domain always found upstream of DENN domain, found in a variety of signalling proteins / cDENN domain ...Longin module / DENN domain, C-terminal lobe / Helix Hairpins - #1000 / DENN domain-containing protein 1A/1B/1C / dDENN domain / uDENN domain / Rab35 / 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 Rab1 family profile. / Helix Hairpins / 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 / Helix non-globular / Rab subfamily of small GTPases / Special / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ras-related protein Rab-35 / DENN domain-containing protein 1B / DENN domain-containing protein 1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsWu, X.D. / Kummel, D. / Reinisch, K.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Insights regarding guanine nucleotide exchange from the structure of a DENN-domain protein complexed with its Rab GTPase substrate.
Authors: Wu, X. / Bradley, M.J. / Cai, Y. / Kummel, D. / De La Cruz, E.M. / Barr, F.A. / Reinisch, K.M.
History
DepositionSep 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2011Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DENN domain-containing protein 1B
B: Ras-related protein Rab-35
C: DENN domain-containing protein 1B
D: Ras-related protein Rab-35


Theoretical massNumber of molelcules
Total (without water)129,8064
Polymers129,8064
Non-polymers00
Water3,369187
1
A: DENN domain-containing protein 1B
B: Ras-related protein Rab-35


Theoretical massNumber of molelcules
Total (without water)64,9032
Polymers64,9032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-15 kcal/mol
Surface area22920 Å2
MethodPISA
2
C: DENN domain-containing protein 1B
D: Ras-related protein Rab-35


Theoretical massNumber of molelcules
Total (without water)64,9032
Polymers64,9032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-13 kcal/mol
Surface area24000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.588, 56.563, 175.305
Angle α, β, γ (deg.)90.00, 95.63, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22C
13A
23C
14A
24C
15A
25C
16A
26C
17A
27C
18B
28D
19B
29D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASPASPVALVAL2AA3 - 203 - 20
211ASPASPVALVAL2CC3 - 203 - 20
112PROPROPHEPHE2AA30 - 5630 - 56
212PROPROPHEPHE2CC30 - 5630 - 56
113THRTHRCYSCYS2AA71 - 8671 - 86
213THRTHRCYSCYS2CC71 - 8671 - 86
114CYSCYSTYRTYR2AA97 - 10897 - 108
214CYSCYSTYRTYR2CC97 - 10897 - 108
124LYSLYSVALVAL2AA110 - 139110 - 139
224LYSLYSVALVAL2CC110 - 139110 - 139
116VALVALTYRTYR1AA265 - 322265 - 322
216VALVALTYRTYR1CC265 - 322265 - 322
118ASPASPPHEPHE2BB6 - 97 - 10
218ASPASPPHEPHE2DD6 - 97 - 10
128LEULEUASPASP2BB11 - 3012 - 31
228LEULEUASPASP2DD11 - 3012 - 31
119TYRTYRLEULEU2BB37 - 17638 - 177
219TYRTYRLEULEU2DD37 - 17638 - 177

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9

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Components

#1: Protein DENN domain-containing protein 1B / Connecdenn 2 / Protein FAM31B


Mass: 44279.684 Da / Num. of mol.: 2 / Fragment: UNP residues 1-391
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DENND1B, C1orf218, FAM31B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6P3S1-2, UniProt: Q6P3S1*PLUS
#2: Protein Ras-related protein Rab-35 / GTP-binding protein RAY / Ras-related protein Rab-1C


Mass: 20623.334 Da / Num. of mol.: 2 / Fragment: UNP residues 1-180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB35, RAB1C, RAY / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15286
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.33 Å3/Da / Density % sol: 47.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1 M Magnesium Formate, 19% PEG 3350, 0.1 M HEPES (pH 7.4), 4mM n-Nonyl-beta-D-glucoside, 289K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 12, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. all: 70529 / Num. obs: 66297 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 3.3 %
Reflection shellResolution: 2.1→2.18 Å / % possible all: 99.3

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Processing

Software
NameVersionClassification
CBASSdata collection
SHARPphasing
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→24.89 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.916 / SU B: 16.653 / SU ML: 0.192 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26871 4502 7 %RANDOM
Rwork0.22667 ---
all0.22957 64040 --
obs0.22957 59538 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.795 Å2
Baniso -1Baniso -2Baniso -3
1-1.48 Å20 Å25.39 Å2
2---2.15 Å20 Å2
3---1.73 Å2
Refinement stepCycle: LAST / Resolution: 2.1→24.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8386 0 0 187 8573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0228214
X-RAY DIFFRACTIONr_bond_other_d0.0040.025480
X-RAY DIFFRACTIONr_angle_refined_deg1.621.95711178
X-RAY DIFFRACTIONr_angle_other_deg1.099313255
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.12551036
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.32124.331344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.325151313
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5731534
X-RAY DIFFRACTIONr_chiral_restr0.0940.21322
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0219124
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021660
X-RAY DIFFRACTIONr_mcbond_it2.59425216
X-RAY DIFFRACTIONr_mcbond_other1.68922097
X-RAY DIFFRACTIONr_mcangle_it3.31238397
X-RAY DIFFRACTIONr_scbond_it4.6154.52998
X-RAY DIFFRACTIONr_scangle_it5.6262781
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A107TIGHT POSITIONAL0.050.05
1A144MEDIUM POSITIONAL0.060.5
1A107TIGHT THERMAL0.30.5
1A144MEDIUM THERMAL0.282
2A157TIGHT POSITIONAL0.050.05
2A235MEDIUM POSITIONAL0.050.5
2A157TIGHT THERMAL0.270.5
2A235MEDIUM THERMAL0.222
3A95TIGHT POSITIONAL0.050.05
3A133MEDIUM POSITIONAL0.050.5
3A95TIGHT THERMAL0.460.5
3A133MEDIUM THERMAL0.252
4A250TIGHT POSITIONAL0.070.05
4A298MEDIUM POSITIONAL0.070.5
4A250TIGHT THERMAL0.340.5
4A298MEDIUM THERMAL0.252
5A1243TIGHT POSITIONAL0.10.05
5A1243TIGHT THERMAL0.330.5
6A668TIGHT POSITIONAL0.050.05
6A668TIGHT THERMAL0.250.5
7A467TIGHT POSITIONAL0.050.05
7A467TIGHT THERMAL0.170.5
8B141TIGHT POSITIONAL0.050.05
8B165MEDIUM POSITIONAL0.050.5
8B141TIGHT THERMAL0.240.5
8B165MEDIUM THERMAL0.192
9B831TIGHT POSITIONAL0.040.05
9B936MEDIUM POSITIONAL0.050.5
9B831TIGHT THERMAL0.220.5
9B936MEDIUM THERMAL0.182
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 335 -
Rwork0.312 4359 -
obs--100 %
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)
12.1280.2766-0.72074.41270.06221.667-0.0865-0.0746-0.11270.63730.1080.23340.05710.0594-0.02150.19660.0505-0.04560.20020.03480.1148105.674610.261859.8758
22.4893-0.0401-0.61422.47460.38332.66960.1385-0.16760.20920.4420.02780.7415-0.1756-0.5814-0.16630.39640.09170.20990.38850.09930.531278.882514.045271.1846
33.28351.2064-1.17853.6227-0.2162.86390.16860.15690.3491-0.24350.0078-0.0043-0.2432-0.1251-0.17640.17320.0738-0.06350.22720.00460.1232123.71129.721726.061
43.7857-0.8111-1.08233.179-0.05532.77640.11790.1992-0.0576-0.4984-0.1453-0.53310.19490.37720.02740.23780.1078-0.03720.38320.04590.2382147.483718.054813.4475
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 374
2X-RAY DIFFRACTION2B5 - 176
3X-RAY DIFFRACTION3C1 - 374
4X-RAY DIFFRACTION4D4 - 177

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