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- PDB-3cwz: Structure of RAB6(GTP)-R6IP1 complex -

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Basic information

Entry
Database: PDB / ID: 3cwz
TitleStructure of RAB6(GTP)-R6IP1 complex
Components
  • Rab6-interacting protein 1
  • Ras-related protein Rab-6A
KeywordsTRANSPORT PROTEIN / Rab6 Interacting Protein 1 / Rab small GTPase / Rab-binding domain / guanosine 5' triphosphate / RUN / RPIP8 / UNC-14 / NESCA PLAT / GOLGI apparatus / Golgi / lipase / lipoxygenase / membrane / lipoprotein / ER-Golgi transport / GTP-binding / Methylation / Nucleotide-binding / Phosphoprotein / Prenylation / Protein transport / Transport
Function / homology
Function and homology information


guanyl-nucleotide exchange factor activity => GO:0005085 / peptidyl-cysteine methylation / minus-end-directed organelle transport along microtubule / protein localization to Golgi membrane / endosome to plasma membrane transport vesicle / RAB GEFs exchange GTP for GDP on RABs / small GTPase binding => GO:0031267 / early endosome to Golgi transport / Retrograde transport at the Trans-Golgi-Network / acrosomal membrane ...guanyl-nucleotide exchange factor activity => GO:0005085 / peptidyl-cysteine methylation / minus-end-directed organelle transport along microtubule / protein localization to Golgi membrane / endosome to plasma membrane transport vesicle / RAB GEFs exchange GTP for GDP on RABs / small GTPase binding => GO:0031267 / early endosome to Golgi transport / Retrograde transport at the Trans-Golgi-Network / acrosomal membrane / retromer complex / protein localization to Golgi apparatus / Pre-NOTCH Processing in Golgi / RAB geranylgeranylation / myosin V binding / intra-Golgi vesicle-mediated transport / COPI-independent Golgi-to-ER retrograde traffic / RAB GEFs exchange GTP for GDP on RABs / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / retrograde transport, endosome to Golgi / TBC/RABGAPs / antigen processing and presentation / localization / endomembrane system / secretory granule membrane / trans-Golgi network membrane / intracellular protein transport / trans-Golgi network / neuron projection development / negative regulation of neuron projection development / cytoplasmic vesicle / protein domain specific binding / Golgi membrane / GTPase activity / Neutrophil degranulation / endoplasmic reticulum membrane / GTP binding / Golgi apparatus / extracellular exosome / membrane / plasma membrane / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #800 / 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 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #800 / 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 / RUN domain / Tripartite DENN domain / Tripartite DENN domain profile. / RUN / RUN domain / RUN domain superfamily / RUN domain / RUN domain profile. / PLAT/LH2 domain / Lipoxygenase-1 / PLAT/LH2 domain / PLAT/LH2 domain superfamily / PLAT/LH2 domain / PLAT domain profile. / small GTPase Rab1 family profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / 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 / Up-down Bundle / Sandwich / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Ras-related protein Rab-6A / DENN domain-containing protein 5A
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsRecacha, R. / Houdusse, A. / Goud, B. / Khan, A.R.
CitationJournal: Structure / Year: 2009
Title: Structural basis for recruitment of Rab6-interacting protein 1 to Golgi via a RUN domain.
Authors: Recacha, R. / Boulet, A. / Jollivet, F. / Monier, S. / Houdusse, A. / Goud, B. / Khan, A.R.
History
DepositionApr 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 14, 2016Group: Structure summary
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_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 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ras-related protein Rab-6A
B: Rab6-interacting protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1654
Polymers65,6172
Non-polymers5472
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.240, 100.240, 299.250
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Ras-related protein Rab-6A / Rab-6


Mass: 21607.662 Da / Num. of mol.: 1 / Fragment: unp residues 8-195 / Mutation: Q72L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB6A, RAB6 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P20340
#2: Protein Rab6-interacting protein 1 / Rab6IP1


Mass: 44009.809 Da / Num. of mol.: 1 / Fragment: unp residues 707-1145
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Description: Vector pHis2 derived from pET15 modified to rTEV cleavage site
Gene: Rab6ip1 / Plasmid: pHis2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6PAL8
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 62.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M HEPES, 2% PEG 4000, 3% MPD, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF BM1410.978
SYNCHROTRONESRF ID14-120.934
Detector
TypeIDDetector
MAR scanner 345 mm plate1IMAGE PLATE
ADSC QUANTUM 2102CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9781
20.9341
ReflectionResolution: 3→50 Å / Num. obs: 18629 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 101.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.3

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 3.2→24.97 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1994733.59 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.302 625 4.1 %RANDOM
Rwork0.246 ---
obs0.246 15427 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.483 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 100.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 3.2→24.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3802 0 33 37 3872
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d2.823
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.343 91 3.6 %
Rwork0.316 2415 -
obs--99.8 %
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 DIFFRACTION4gtp.paramgtp.top

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