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- PDB-3bbp: Rab6-GTP:GCC185 Rab binding domain complex -

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Basic information

Entry
Database: PDB / ID: 3bbp
TitleRab6-GTP:GCC185 Rab binding domain complex
Components
  • GRIP and coiled-coil domain-containing protein 2
  • Ras-related protein Rab-6A
KeywordsProtein Transport/Splicing / Golgi complex / GRIP domain / Rab GTPase / Arl GTPase / Golgin / Rab effector / CLASP protein / Acetylation / Alternative splicing / ER-Golgi transport / Golgi apparatus / GTP-binding / Lipoprotein / Membrane / Methylation / Nucleotide-binding / Phosphorylation / Prenylation / Protein transport / Transport / Coiled coil / Cytoplasm / Polymorphism / Protein Transport-Splicing COMPLEX
Function / homology
Function and homology information


regulation of protein exit from endoplasmic reticulum / recycling endosome to Golgi transport / peptidyl-cysteine methylation / minus-end-directed organelle transport along microtubule / late endosome to Golgi transport / protein localization to Golgi membrane / endosome to plasma membrane transport vesicle / microtubule anchoring / early endosome to Golgi transport / microtubule organizing center organization ...regulation of protein exit from endoplasmic reticulum / recycling endosome to Golgi transport / peptidyl-cysteine methylation / minus-end-directed organelle transport along microtubule / late endosome to Golgi transport / protein localization to Golgi membrane / endosome to plasma membrane transport vesicle / microtubule anchoring / early endosome to Golgi transport / microtubule organizing center organization / Retrograde transport at the Trans-Golgi-Network / acrosomal membrane / Golgi ribbon formation / protein localization to Golgi apparatus / Pre-NOTCH Processing in Golgi / intra-Golgi vesicle-mediated transport / protein targeting to lysosome / RAB geranylgeranylation / myosin V binding / 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 / endomembrane system / localization / secretory granule membrane / trans-Golgi network membrane / intracellular protein transport / trans-Golgi network / neuron projection development / cytoplasmic vesicle / protein domain specific binding / Golgi membrane / GTPase activity / Neutrophil degranulation / endoplasmic reticulum membrane / GTP binding / Golgi apparatus / extracellular exosome / nucleoplasm / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
GCC2, Rab binding domain / Rab binding domain / GRIP domain / GRIP domain / GRIP domain profile. / golgin-97, RanBP2alpha,Imh1p and p230/golgin-245 / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases ...GCC2, Rab binding domain / Rab binding domain / GRIP domain / GRIP domain / GRIP domain profile. / golgin-97, RanBP2alpha,Imh1p and p230/golgin-245 / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Ras-related protein Rab-6A / GRIP and coiled-coil domain-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSchweizer Burguete, A. / Fenn, T.D. / Brunger, A.T. / Pfeffer, S.R.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2008
Title: Rab and Arl GTPase family members cooperate in the localization of the golgin GCC185.
Authors: Burguete, A.S. / Fenn, T.D. / Brunger, A.T. / Pfeffer, S.R.
History
DepositionNov 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras-related protein Rab-6A
B: Ras-related protein Rab-6A
C: Ras-related protein Rab-6A
D: GRIP and coiled-coil domain-containing protein 2
E: GRIP and coiled-coil domain-containing protein 2
F: GRIP and coiled-coil domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,66212
Polymers96,0196
Non-polymers1,6426
Water0
1
A: Ras-related protein Rab-6A
B: Ras-related protein Rab-6A
D: GRIP and coiled-coil domain-containing protein 2
E: GRIP and coiled-coil domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1088
Polymers64,0134
Non-polymers1,0954
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ras-related protein Rab-6A
F: GRIP and coiled-coil domain-containing protein 2
hetero molecules

C: Ras-related protein Rab-6A
F: GRIP and coiled-coil domain-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1088
Polymers64,0134
Non-polymers1,0954
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
3
D: GRIP and coiled-coil domain-containing protein 2
E: GRIP and coiled-coil domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)16,3072
Polymers16,3072
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
MethodPISA
4
A: Ras-related protein Rab-6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4013
Polymers23,8531
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
B: Ras-related protein Rab-6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4013
Polymers23,8531
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
C: Ras-related protein Rab-6A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4013
Polymers23,8531
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
F: GRIP and coiled-coil domain-containing protein 2


Theoretical massNumber of molelcules
Total (without water)8,1531
Polymers8,1531
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)168.599, 168.599, 168.955
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

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


Mass: 23853.113 Da / Num. of mol.: 3 / Mutation: Q72L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB6A, RAB6 / Plasmid: pET47b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P20340
#2: Protein GRIP and coiled-coil domain-containing protein 2 / Golgi coiled-coil protein GCC185 / Ran-binding protein 2-like 4 / RanBP2L4 / CTCL tumor antigen se1- ...Golgi coiled-coil protein GCC185 / Ran-binding protein 2-like 4 / RanBP2L4 / CTCL tumor antigen se1-1 / CLL-associated antigen KW-11 / Renal carcinoma antigen NY-REN-53


Mass: 8153.262 Da / Num. of mol.: 3 / Fragment: UNP residues 1446-1511
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GCC2, KIAA0336, RANBP2L4 / Plasmid: pGEX-6P1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: Q8IWJ2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM

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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: 3.61 Å3/Da / Density % sol: 65.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350, 200mM CNNaS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
22981
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL7-110.9785
SYNCHROTRONSSRL BL11-120.9791
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDMay 4, 2007
ADSC QUANTUM 3152CCDMay 20, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97851
20.97911
ReflectionResolution: 3→50 Å / Num. all: 28379 / Num. obs: 28379 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.25 / Rsym value: 0.183 / Net I/σ(I): 10.1

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2GIL

2gil


Resolution: 3→50 Å / Cross valid method: random / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.268 1271 -
Rwork0.228 --
obs0.228 25240 88.4 %
all-25240 -
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4757 0 99 0 4856

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