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- PDB-6if3: Complex structure of Rab35 and its effector ACAP2 -

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Basic information

Entry
Database: PDB / ID: 6if3
TitleComplex structure of Rab35 and its effector ACAP2
Components
  • Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 2
  • Ras-related protein Rab-35
KeywordsENDOCYTOSIS / Rab35 / ACAP2 / complex / cryatal structure
Function / homology
Function and homology information


actin filament-based process / Rab protein signal transduction / plasma membrane to endosome transport / 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 ...actin filament-based process / Rab protein signal transduction / plasma membrane to endosome transport / 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 / endosomal transport / intercellular bridge / mitotic cytokinesis / antigen processing and presentation / clathrin-coated pit / ruffle / phosphatidylinositol-4,5-bisphosphate binding / GTPase activator activity / cellular response to nerve growth factor stimulus / clathrin-coated endocytic vesicle membrane / protein localization / recycling endosome membrane / GDP binding / neuron projection development / melanosome / protein transport / endosome membrane / GTPase activity / GTP binding / extracellular exosome / membrane / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Rab35 / Arf GTPase activating protein / ArfGAP domain superfamily / Putative GTPase activating protein for Arf / ARF GTPase-activating proteins domain profile. / Putative GTP-ase activating proteins for the small GTPase, ARF / ARFGAP/RecO-like zinc finger / Domain of unknown function DUF3447 / AH/BAR domain superfamily / ARF-like small GTPases; ARF, ADP-ribosylation factor ...Rab35 / Arf GTPase activating protein / ArfGAP domain superfamily / Putative GTPase activating protein for Arf / ARF GTPase-activating proteins domain profile. / Putative GTP-ase activating proteins for the small GTPase, ARF / ARFGAP/RecO-like zinc finger / Domain of unknown function DUF3447 / AH/BAR domain superfamily / ARF-like small GTPases; ARF, ADP-ribosylation factor / small GTPase Rab1 family profile. / Ankyrin repeat-containing domain / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / PH domain / 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 / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 2 / Ras-related protein Rab-35
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLin, L. / Zhu, J. / Zhang, R.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31600607 China
CitationJournal: Structure / Year: 2019
Title: Rab35/ACAP2 and Rab35/RUSC2 Complex Structures Reveal Molecular Basis for Effector Recognition by Rab35 GTPase.
Authors: Lin, L. / Shi, Y. / Wang, M. / Wang, C. / Zhu, J. / Zhang, R.
History
DepositionSep 18, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 22, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first
Revision 1.3Nov 22, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 2
B: Ras-related protein Rab-35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6434
Polymers40,0962
Non-polymers5472
Water7,026390
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-27 kcal/mol
Surface area15950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.741, 53.468, 144.008
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 2 / Centaurin-beta-2 / Cnt-b2


Mass: 19000.137 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACAP2, CENTB2, KIAA0041 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15057
#2: Protein Ras-related protein Rab-35 / GTP-binding protein RAY / Ras-related protein Rab-1C


Mass: 21095.869 Da / Num. of mol.: 1 / Mutation: Q67L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB35, RAB1C, RAY / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15286
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 2.15 Å3/Da / Density % sol: 42.74 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: Potassium sodium tartrate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 54675 / % possible obs: 96.7 % / Redundancy: 10.4 % / Biso Wilson estimate: 19.55 Å2 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.035 / Rrim(I) all: 0.122 / Χ2: 1.219 / Net I/σ(I): 5.2 / Num. measured all: 570145
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.534.90.58419130.8010.2390.6360.5768.8
1.53-1.555.30.56522950.7680.2280.6140.56881.8
1.55-1.585.30.51724580.8380.2170.5640.58488.3
1.58-1.626.60.52526770.8710.1990.5650.59796.6
1.62-1.657.60.51927430.8870.1890.5540.59298.9
1.65-1.698.70.50127910.9150.1730.5310.60899.9
1.69-1.739.50.46828090.950.1560.4940.621100
1.73-1.7810.20.46427780.9420.1490.4880.64699.8
1.78-1.8310.60.40727850.9690.1290.4270.68399.6
1.83-1.8910.30.36627940.9720.1180.3860.7399.9
1.89-1.9612.40.3228000.980.0940.3340.82599.9
1.96-2.0412.60.2728150.9830.0790.2820.91599.9
2.04-2.1312.60.2228260.9870.0640.2291.07699.9
2.13-2.2412.50.18328140.990.0530.1911.204100
2.24-2.3811.70.15928050.990.0480.1671.3799.8
2.38-2.56130.13828510.9930.040.1441.509100
2.56-2.8213.30.11928770.9950.0340.1241.63100
2.82-3.23130.10128540.9960.0290.1061.92999.9
3.23-4.0712.40.08529130.9970.0250.0892.499.8
4.07-5012.10.07730770.9970.0230.082.47699.9

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TW8, 3JUE

3tw8

3jue


Resolution: 1.5→28.049 Å / FOM work R set: 0.8541 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2051 2759 5.06 %
Rwork0.1721 51720 -
obs0.1738 54479 96.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.36 Å2 / Biso mean: 27.04 Å2 / Biso min: 12.5 Å2
Refinement stepCycle: final / Resolution: 1.5→28.049 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2606 0 33 390 3029
Biso mean--20.36 38.7 -
Num. residues----336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112736
X-RAY DIFFRACTIONf_angle_d1.2553724
X-RAY DIFFRACTIONf_chiral_restr0.057424
X-RAY DIFFRACTIONf_plane_restr0.007485
X-RAY DIFFRACTIONf_dihedral_angle_d17.5291017
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.52590.3538930.3231878197171
1.5259-1.55360.3371160.29792167228382
1.5536-1.58350.31131320.27632328246088
1.5835-1.61580.29271270.25292546267397
1.6158-1.65090.29471590.23962571273099
1.6509-1.68930.2761290.219226182747100
1.6893-1.73160.25691440.211926682812100
1.7316-1.77840.25911480.207826322780100
1.7784-1.83070.25051470.200326272774100
1.8307-1.88980.23751360.187226442780100
1.8898-1.95730.21231400.173326412781100
1.9573-2.03570.18411380.172526712809100
2.0357-2.12830.20951370.163926722809100
2.1283-2.24040.19211380.166626762814100
2.2404-2.38070.19611340.160826482782100
2.3807-2.56440.19721370.16527082845100
2.5644-2.82230.18451700.162426862856100
2.8223-3.23020.17731480.150626952843100
3.2302-4.06770.16951330.143427682901100
4.0677-28.05360.20241530.168428763029100
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)
17.39140.27991.65724.2633-3.54036.3957-0.0623-0.26040.24490.2701-0.0074-0.0589-0.28440.05860.06210.1330.0028-0.00190.1182-0.05670.1567-14.304145.91817.9145
24.7825-3.22940.2044.362-0.14358.7329-0.333-0.0539-0.12240.4150.10320.11760.13550.07340.15410.1827-0.00740.01820.12790.00880.1332-17.147237.966122.1799
31.3589-0.04810.01632.38470.27342.4888-0.00740.02060.03770.0823-0.00270.01620.01380.00840.01860.1182-0.00420.01550.1328-0.01280.1202-17.113835.65028.4218
46.61491.124-3.72646.5265-0.9628.2157-0.27370.4115-0.0007-0.20950.03930.18930.3621-0.31990.24680.2158-0.0270.00460.1209-0.00470.1087-22.037925.12924.3302
54.9549-2.78950.60636.21310.35993.231-0.03690.0856-0.32770.113-0.02110.04930.15320.10930.04610.1349-0.01830.01260.1495-0.02610.1099-16.393524.9009-5.9817
64.77981.1555-0.01041.955-2.69955.9989-0.07060.1998-0.6184-0.27320.1189-0.3310.26670.36840.06370.1785-0.01080.02690.266-0.05290.2752-3.985327.1752-6.8363
75.428-5.1269-5.76835.06534.9667.6520.95970.20781.6827-0.6184-0.5498-0.4172-1.0053-1.3294-0.56820.37570.06230.0540.6036-0.06640.5403-17.304541.8542-6.1466
84.4103-2.78392.0294.1713-1.47312.1586-0.1338-0.13520.04860.12620.0253-0.07670.0601-0.08530.11920.18250.01860.03030.1568-0.03040.0884-11.985615.0619-18.0824
91.6289-1.88930.07263.94320.69440.8443-0.0058-0.05220.02940.1074-0.05290.02380.0863-0.10770.05310.16520.00080.01280.18310.00330.1529-14.833914.4451-15.8791
105.0004-4.8753-3.95795.23853.86862.92920.07880.18480.2422-0.13740.0328-0.2074-0.1491-0.0378-0.14850.1718-0.01060.01570.14990.02940.1438-12.179729.7367-18.732
118.79031.66243.49881.76281.37423.3215-0.34620.26340.3575-0.48780.09870.0635-0.43090.01780.26350.2549-0.0034-0.00320.16420.0070.1363-14.450626.0365-31.2741
122.7261-0.8839-1.45652.21450.42593.5742-0.12480.525-0.0657-0.338-0.06160.0784-0.0786-0.2810.17040.2408-0.0053-0.0090.1922-0.01950.1572-15.875617.8862-35.8568
136.32120.90871.01471.88390.36742.5960.02120.049-0.3420.0266-0.0354-0.10550.21730.20520.00570.24480.04450.02360.1666-0.0320.1927-8.59510.0483-27.0799
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 605 through 627 )A605 - 627
2X-RAY DIFFRACTION2chain 'A' and (resid 628 through 637 )A628 - 637
3X-RAY DIFFRACTION3chain 'A' and (resid 638 through 695 )A638 - 695
4X-RAY DIFFRACTION4chain 'A' and (resid 696 through 709 )A696 - 709
5X-RAY DIFFRACTION5chain 'A' and (resid 710 through 738 )A710 - 738
6X-RAY DIFFRACTION6chain 'A' and (resid 739 through 757 )A739 - 757
7X-RAY DIFFRACTION7chain 'A' and (resid 758 through 769 )A758 - 769
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 30 )B2 - 30
9X-RAY DIFFRACTION9chain 'B' and (resid 31 through 64 )B31 - 64
10X-RAY DIFFRACTION10chain 'B' and (resid 65 through 82 )B65 - 82
11X-RAY DIFFRACTION11chain 'B' and (resid 83 through 109 )B83 - 109
12X-RAY DIFFRACTION12chain 'B' and (resid 110 through 142 )B110 - 142
13X-RAY DIFFRACTION13chain 'B' and (resid 143 through 178 )B143 - 178

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