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- PDB-6f6p: Crystal structure of tetrameric human Rabin8 GEF domain -

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Basic information

Entry
Database: PDB / ID: 6f6p
TitleCrystal structure of tetrameric human Rabin8 GEF domain
Components(Rab-3A-interacting protein) x 2
KeywordsHYDROLASE / Rabin8 / GEF / guanine nucleotide exchange factor / tetramer / RAB3I
Function / homology
Function and homology information


ciliary basal body-plasma membrane docking / Golgi to plasma membrane transport vesicle / protein localization to motile cilium / protein localization to organelle / negative regulation of filopodium assembly / VxPx cargo-targeting to cilium / proximal dendrite / BBSome-mediated cargo-targeting to cilium / Golgi to plasma membrane transport / positive regulation of cilium assembly ...ciliary basal body-plasma membrane docking / Golgi to plasma membrane transport vesicle / protein localization to motile cilium / protein localization to organelle / negative regulation of filopodium assembly / VxPx cargo-targeting to cilium / proximal dendrite / BBSome-mediated cargo-targeting to cilium / Golgi to plasma membrane transport / positive regulation of cilium assembly / RAB GEFs exchange GTP for GDP on RABs / protein targeting to membrane / exocytosis / cilium assembly / Anchoring of the basal body to the plasma membrane / ciliary basal body / trans-Golgi network membrane / guanyl-nucleotide exchange factor activity / protein transport / lamellipodium / GTPase binding / centrosome / perinuclear region of cytoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
GDP/GTP exchange factor Sec2, N-terminal / Guanine nucleotide exchange factor RAB3IL/RAB3IP/Sec2 / GDP/GTP exchange factor Sec2p
Similarity search - Domain/homology
Rab-3A-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å
AuthorsLorentzen, E. / Vetter, M.
Funding support Denmark, 1items
OrganizationGrant numberCountry
NNFNNF15OC0014164 Denmark
CitationJournal: Proteins / Year: 2018
Title: Crystal structure of tetrameric human Rabin8 GEF domain.
Authors: Vetter, M. / Boegholm, N. / Christensen, A. / Bhogaraju, S. / Andersen, M.B. / Lorentzen, A. / Lorentzen, E.
History
DepositionDec 6, 2017Deposition site: PDBE / Processing site: PDBE
SupersessionDec 13, 2017ID: 5OAG
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rab-3A-interacting protein
B: Rab-3A-interacting protein
C: Rab-3A-interacting protein
D: Rab-3A-interacting protein


Theoretical massNumber of molelcules
Total (without water)47,9954
Polymers47,9954
Non-polymers00
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, dimers and tetramers by AUC and SEC
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10840 Å2
ΔGint-118 kcal/mol
Surface area25850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.322, 77.000, 137.258
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Rab-3A-interacting protein / Rab3A-interacting protein / Rabin-3 / SSX2-interacting protein


Mass: 11994.736 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB3IP, RABIN8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96QF0
#2: Protein Rab-3A-interacting protein / Rab3A-interacting protein / Rabin-3 / SSX2-interacting protein


Mass: 12010.736 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB3IP, RABIN8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96QF0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.61 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.3 / Details: 50 mM Tris pH 7.3 and 40% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→68.6 Å / Num. obs: 19008 / % possible obs: 99.8 % / Redundancy: 8.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.094 / Net I/σ(I): 11.2
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 8.7 % / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 962 / CC1/2: 0.992 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.45→68.6 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 40.58
RfactorNum. reflection% reflection
Rfree0.3049 933 4.91 %
Rwork0.271 --
obs0.2729 19008 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.45→68.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2972 0 0 184 3156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023001
X-RAY DIFFRACTIONf_angle_d0.3344020
X-RAY DIFFRACTIONf_dihedral_angle_d10.3861930
X-RAY DIFFRACTIONf_chiral_restr0.025475
X-RAY DIFFRACTIONf_plane_restr0.002527
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.57920.43521300.36232525X-RAY DIFFRACTION99
2.5792-2.74080.42841190.34332555X-RAY DIFFRACTION99
2.7408-2.95240.39271400.31912523X-RAY DIFFRACTION99
2.9524-3.24950.41921330.30082536X-RAY DIFFRACTION99
3.2495-3.71970.29241390.26452582X-RAY DIFFRACTION100
3.7197-4.68630.24711220.21632635X-RAY DIFFRACTION100
4.6863-68.65590.26211500.26692719X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 45.4853 Å / Origin y: 38.3367 Å / Origin z: 68.6932 Å
111213212223313233
T0.6927 Å20.0072 Å20.0145 Å2-0.3484 Å20.0806 Å2--0.6966 Å2
L0.0525 °20.0173 °20.0136 °2-3.5942 °2-1.4594 °2--0.6655 °2
S0.0125 Å °0.0201 Å °0.1206 Å °-0.1167 Å °0.1104 Å °0.1377 Å °-0.0012 Å °-0.0581 Å °-0.1628 Å °
Refinement TLS groupSelection details: all

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