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- PDB-2d7c: Crystal structure of human Rab11 in complex with FIP3 Rab-binding... -

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Basic information

Entry
Database: PDB / ID: 2d7c
TitleCrystal structure of human Rab11 in complex with FIP3 Rab-binding domain
Components
  • Rab11 family-interacting protein 3
  • Ras-related protein Rab-11A
KeywordsPROTEIN TRANSPORT / GTP-ase / coiled-coil / Structural Genomics
Function / homology
Function and homology information


: / regulation of protein localization to centrosome / protein localization to cleavage furrow / synaptic vesicle endosomal processing / : / postsynaptic recycling endosome membrane / regulation of endocytic recycling / establishment of protein localization to organelle / negative regulation of adiponectin secretion / postsynaptic recycling endosome ...: / regulation of protein localization to centrosome / protein localization to cleavage furrow / synaptic vesicle endosomal processing / : / postsynaptic recycling endosome membrane / regulation of endocytic recycling / establishment of protein localization to organelle / negative regulation of adiponectin secretion / postsynaptic recycling endosome / positive regulation of mitotic cytokinetic process / establishment of vesicle localization / plasma membrane to endosome transport / regulation of cilium assembly / amyloid-beta clearance by transcytosis / regulation of protein transport / presynaptic endosome / neurotransmitter receptor transport, endosome to postsynaptic membrane / exosomal secretion / vesicle-mediated transport in synapse / VxPx cargo-targeting to cilium / regulation of vesicle-mediated transport / protein transmembrane transport / myosin V binding / RAB geranylgeranylation / astral microtubule organization / positive regulation of cilium assembly / multivesicular body assembly / protein localization to cilium / melanosome transport / endocytic recycling / Golgi to plasma membrane protein transport / establishment of protein localization to membrane / TBC/RABGAPs / protein localization to cell surface / syntaxin binding / dynein light intermediate chain binding / mitotic metaphase chromosome alignment / exocytosis / cleavage furrow / positive regulation of epithelial cell migration / mitotic spindle assembly / positive regulation of G2/M transition of mitotic cell cycle / endocytic vesicle / transport vesicle / intercellular bridge / phagocytic vesicle / vesicle-mediated transport / multivesicular body / Anchoring of the basal body to the plasma membrane / cytoplasmic vesicle membrane / trans-Golgi network membrane / small monomeric GTPase / regulation of cytokinesis / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / centriole / trans-Golgi network / regulation of long-term neuronal synaptic plasticity / recycling endosome / Schaffer collateral - CA1 synapse / small GTPase binding / centriolar satellite / recycling endosome membrane / neuron projection development / spindle pole / endocytic vesicle membrane / Vasopressin regulates renal water homeostasis via Aquaporins / synaptic vesicle membrane / G protein activity / cytoplasmic vesicle / midbody / molecular adaptor activity / microtubule binding / intracellular membrane-bounded organelle / vesicle / protein-macromolecule adaptor activity / endosome / cilium / ciliary basal body / Golgi membrane / cell division / GTPase activity / calcium ion binding / centrosome / GTP binding / protein-containing complex binding / glutamatergic synapse / Golgi apparatus / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular exosome / nucleoplasm / identical protein binding / plasma membrane / cytosol
Similarity search - Function
: / Rab11-FIP3-like domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2440 / Rab-binding domain FIP-RBD / FIP-RBD, C-terminal domain superfamily / FIP domain / FIP-RBD domain profile. / : / Small GTPase Rab domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases ...: / Rab11-FIP3-like domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2440 / Rab-binding domain FIP-RBD / FIP-RBD, C-terminal domain superfamily / FIP domain / FIP-RBD domain profile. / : / Small GTPase Rab domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / EF-hand domain pair / Rab subfamily of small GTPases / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Rab11 family-interacting protein 3 / Ras-related protein Rab-11A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsShiba, T. / Koga, H. / Shin, H.W. / Kawasaki, M. / Kato, R. / Nakayama, K. / Wakatsuki, S.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Structural basis for Rab11-dependent membrane recruitment of a family of Rab11-interacting protein 3 (FIP3)/Arfophilin-1.
Authors: Shiba, T. / Koga, H. / Shin, H.W. / Kawasaki, M. / Kato, R. / Nakayama, K. / Wakatsuki, S.
History
DepositionNov 16, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 26, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_label_seq_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 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ras-related protein Rab-11A
B: Ras-related protein Rab-11A
C: Rab11 family-interacting protein 3
D: Rab11 family-interacting protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2139
Polymers47,9234
Non-polymers1,2905
Water7,386410
1
A: Ras-related protein Rab-11A
C: Rab11 family-interacting protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7045
Polymers23,9622
Non-polymers7433
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-22 kcal/mol
Surface area11040 Å2
MethodPISA
2
B: Ras-related protein Rab-11A
D: Rab11 family-interacting protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5094
Polymers23,9622
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-21 kcal/mol
Surface area11300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.717, 120.565, 36.249
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein Ras-related protein Rab-11A / Rab-11


Mass: 18871.107 Da / Num. of mol.: 2 / Fragment: residues 7-173 / Mutation: Q70L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX6P-1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P62491
#2: Protein/peptide Rab11 family-interacting protein 3 / Rab11-FIP3 / EF hands-containing Rab-interacting protein / Eferin


Mass: 5090.523 Da / Num. of mol.: 2 / Fragment: Rab-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX6P-1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O75154

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Non-polymers , 4 types, 415 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.48 Å3/Da / Density % sol: 50.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20% iso-propanol, 3% (w/v) PEG 4000, 0.05M MES-NaOH, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-6A10.9789, 0.9793, 0.9600
SYNCHROTRONPhoton Factory AR-NW12A21
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDOct 5, 2004
ADSC QUANTUM 2102CCDOct 28, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)MADMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.97931
30.961
411
ReflectionResolution: 1.75→50 Å / Num. all: 49404 / Num. obs: 49356 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.3
Reflection shellResolution: 1.75→1.81 Å / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 4.3 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
SOLVEphasing
CNS1refinement
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.75→40 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 2457 -RANDOM
Rwork0.202 ---
all0.203 49404 --
obs0.203 49090 99.9 %-
Refinement stepCycle: LAST / Resolution: 1.75→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3356 0 78 410 3844
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.19

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