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- PDB-2gzd: Crystal Structure of Rab11 in Complex with Rab11-FIP2 -

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Basic information

Entry
Database: PDB / ID: 2gzd
TitleCrystal Structure of Rab11 in Complex with Rab11-FIP2
Components
  • Rab11 family-interacting protein 2
  • Ras-related protein Rab-11A
KeywordsPROTEIN TRANSPORT / G protein folds / a-helical coiled coil
Function / homology
Function and homology information


TRAM-dependent toll-like receptor 4 signaling pathway / regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / regulation of multivesicular body size / regulation of endocytic recycling / early endosome to recycling endosome transport / postsynaptic recycling endosome / establishment of protein localization to organelle / establishment of vesicle localization / positive regulation of mitotic cytokinetic process ...TRAM-dependent toll-like receptor 4 signaling pathway / regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / regulation of multivesicular body size / regulation of endocytic recycling / early endosome to recycling endosome transport / postsynaptic recycling endosome / establishment of protein localization to organelle / establishment of vesicle localization / positive regulation of mitotic cytokinetic process / plasma membrane to endosome transport / regulation of cilium assembly / exosomal secretion / regulated exocytosis / melanosome transport / amyloid-beta clearance by transcytosis / protein transmembrane transport / astral microtubule organization / VxPx cargo-targeting to cilium / neurotransmitter receptor transport, endosome to postsynaptic membrane / regulation of vesicle-mediated transport / RAB geranylgeranylation / myosin V binding / Golgi to plasma membrane protein transport / multivesicular body assembly / dynein light intermediate chain binding / protein localization to cilium / establishment of protein localization to membrane / protein localization to cell surface / insulin secretion involved in cellular response to glucose stimulus / TBC/RABGAPs / syntaxin binding / mitotic metaphase chromosome alignment / establishment of cell polarity / positive regulation of epithelial cell migration / exocytosis / cleavage furrow / phagocytic cup / centriolar satellite / mitotic spindle assembly / phagocytosis / vesicle-mediated transport / transport vesicle / Anchoring of the basal body to the plasma membrane / positive regulation of G2/M transition of mitotic cell cycle / centriole / phagocytic vesicle / multivesicular body / small monomeric GTPase / G protein activity / positive regulation of GTPase activity / trans-Golgi network membrane / regulation of cytokinesis / cell projection / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / positive regulation of protein localization to plasma membrane / cytoplasmic vesicle membrane / trans-Golgi network / recycling endosome / small GTPase binding / spindle pole / Vasopressin regulates renal water homeostasis via Aquaporins / recycling endosome membrane / endocytic vesicle membrane / neuron projection development / cytoplasmic vesicle / microtubule binding / vesicle / endosome / Golgi membrane / intracellular membrane-bounded organelle / GTPase activity / centrosome / glutamatergic synapse / GTP binding / protein kinase binding / Golgi apparatus / protein homodimerization activity / protein-containing complex / extracellular exosome / nucleoplasm / identical protein binding / cytosol
Similarity search - Function
Rab11-family interacting protein class I / Rab-binding domain FIP-RBD / FIP-RBD, C-terminal domain superfamily / FIP domain / FIP-RBD domain profile. / small GTPase Rab1 family profile. / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. ...Rab11-family interacting protein class I / Rab-binding domain FIP-RBD / FIP-RBD, C-terminal domain superfamily / FIP domain / FIP-RBD domain profile. / small GTPase Rab1 family profile. / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / C2 domain superfamily / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Ras-related protein Rab-11A / Rab11 family-interacting protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsKhan, A.R.
CitationJournal: Structure / Year: 2006
Title: Crystal structure of rab11 in complex with rab11 family interacting protein 2.
Authors: Jagoe, W.N. / Lindsay, A.J. / Read, R.J. / McCoy, A.J. / McCaffrey, M.W. / Khan, A.R.
History
DepositionMay 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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.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 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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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 2
D: Rab11 family-interacting protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8648
Polymers63,7694
Non-polymers1,0954
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-63 kcal/mol
Surface area19130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.364, 91.149, 113.099
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: 1 / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUAA7 - 1737 - 173
21GLUGLUBB7 - 1737 - 173
12HISHISCC473 - 50068 - 95
22HISHISDD473 - 50068 - 95

NCS ensembles :
ID
1
2
DetailsThe biological unit consists of two molecules of Rab11 and two molecules of Rab11-FIP2, with the Rab11-FIP2 molecule forming a central parallel coiled coil nearly coincident with the crystallographic c-axis.

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Components

#1: Protein Ras-related protein Rab-11A / Rab-11 / YL8


Mass: 19547.830 Da / Num. of mol.: 2 / Fragment: G protein domain / Mutation: Q70L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB11a / Plasmid: pET-28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62491, small monomeric GTPase
#2: Protein Rab11 family-interacting protein 2 / Rab11-FIP2 / NRip11


Mass: 12336.811 Da / Num. of mol.: 2 / Fragment: Rab11-FIP2 Rab-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pMAL-c2x / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q7L804
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 54.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5
Details: Ammonium phosphate buffer, between 0.1 and 0.5 M concentration, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97865 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 6, 2005
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97865 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. all: 24131 / Num. obs: 24064 / % possible obs: 99.72 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 13 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 8.8
Reflection shellResolution: 2.44→2.53 Å / Redundancy: 10 % / Rmerge(I) obs: 0.421 / Num. unique all: 2565 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Rab11 in complex with Rab11-FIP in the trigonal space group

Resolution: 2.44→50 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.876 / SU B: 8.166 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.321 / ESU R Free: 0.261 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27888 1290 5.1 %RANDOM
Rwork0.22628 ---
all0.22886 25403 --
obs0.22886 24064 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.23 Å2
Baniso -1Baniso -2Baniso -3
1--3.45 Å20 Å20 Å2
2--0.58 Å20 Å2
3---2.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.261 Å0.321 Å
Refinement stepCycle: LAST / Resolution: 2.44→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3258 0 66 78 3402
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223384
X-RAY DIFFRACTIONr_angle_refined_deg1.9741.9844595
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.5125402
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.28223.374163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.59415587
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0531531
X-RAY DIFFRACTIONr_chiral_restr0.1340.2524
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022509
X-RAY DIFFRACTIONr_nbd_refined0.240.21560
X-RAY DIFFRACTIONr_nbtor_refined0.3040.22283
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.2175
X-RAY DIFFRACTIONr_metal_ion_refined0.0490.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1450.213
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3130.24
X-RAY DIFFRACTIONr_mcbond_it1.1541.52093
X-RAY DIFFRACTIONr_mcangle_it1.85723253
X-RAY DIFFRACTIONr_scbond_it2.48831514
X-RAY DIFFRACTIONr_scangle_it3.7324.51342
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1328medium positional0.430.5
2C239medium positional0.350.5
1A1328medium thermal0.892
2C239medium thermal0.732
LS refinement shellResolution: 2.44→50 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 1290 -
Rwork0.227 1717 -
obs-24064 98.5 %

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