[English] 日本語
Yorodumi
- PDB-1tu3: Crystal Structure of Rab5 complex with Rabaptin5 C-terminal Domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tu3
TitleCrystal Structure of Rab5 complex with Rabaptin5 C-terminal Domain
Components
  • Rab GTPase binding effector protein 1
  • Ras-related protein Rab-5A
KeywordsPROTEIN TRANSPORT / Rab5 / Rabaptin5 / effector-binding
Function / homology
Function and homology information


regulation of endosome size / cytoplasmic side of early endosome membrane / protein localization to ciliary membrane / synaptic vesicle recycling / amyloid-beta clearance by transcytosis / modulation by host of viral process / regulation of filopodium assembly / Golgi to plasma membrane transport / RAB geranylgeranylation / regulation of autophagosome assembly ...regulation of endosome size / cytoplasmic side of early endosome membrane / protein localization to ciliary membrane / synaptic vesicle recycling / amyloid-beta clearance by transcytosis / modulation by host of viral process / regulation of filopodium assembly / Golgi to plasma membrane transport / RAB geranylgeranylation / regulation of autophagosome assembly / early endosome to late endosome transport / RAB GEFs exchange GTP for GDP on RABs / early phagosome / TBC/RABGAPs / regulation of synaptic vesicle exocytosis / regulation of postsynaptic neurotransmitter receptor internalization / Synthesis of PIPs at the plasma membrane / positive regulation of exocytosis / Respiratory syncytial virus (RSV) attachment and entry / endocytic vesicle / canonical Wnt signaling pathway / phagocytosis / vesicle-mediated transport / phagocytic vesicle / ruffle / somatodendritic compartment / axon terminus / Prevention of phagosomal-lysosomal fusion / endomembrane system / GTPase activator activity / small monomeric GTPase / intracellular protein transport / growth factor activity / regulation of long-term neuronal synaptic plasticity / clathrin-coated endocytic vesicle membrane / terminal bouton / recycling endosome / receptor internalization / synaptic vesicle membrane / phagocytic vesicle membrane / endocytosis / GDP binding / synaptic vesicle / melanosome / protein transport / actin cytoskeleton / Clathrin-mediated endocytosis / G protein activity / Factors involved in megakaryocyte development and platelet production / early endosome membrane / membrane fusion / early endosome / endosome / endosome membrane / protein domain specific binding / membrane raft / axon / neuronal cell body / GTPase activity / intracellular membrane-bounded organelle / apoptotic process / dendrite / GTP binding / glutamatergic synapse / protein homodimerization activity / protein-containing complex / extracellular exosome / nucleoplasm / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Rabaptin / Rabaptin, GTPase-Rab5 binding domain / Rabaptin coiled-coil domain / Rabaptin / Rabaptin-like protein / Single helix bin / small GTPase Rab1 family 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 ...Rabaptin / Rabaptin, GTPase-Rab5 binding domain / Rabaptin coiled-coil domain / Rabaptin / Rabaptin-like protein / Single helix bin / small GTPase Rab1 family 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 / Rab subfamily of small GTPases / 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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Rab-5A / Rab GTPase-binding effector protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsZhu, G. / Zhai, P. / Liu, J. / Terzyan, S. / Li, G. / Zhang, X.C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: Structural basis of Rab5-Rabaptin5 interaction in endocytosis
Authors: Zhu, G. / Zhai, P. / Liu, J. / Terzyan, S. / Li, G. / Zhang, X.C.
History
DepositionJun 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ras-related protein Rab-5A
B: Ras-related protein Rab-5A
C: Ras-related protein Rab-5A
D: Ras-related protein Rab-5A
E: Ras-related protein Rab-5A
F: Rab GTPase binding effector protein 1
G: Rab GTPase binding effector protein 1
H: Rab GTPase binding effector protein 1
I: Rab GTPase binding effector protein 1
J: Rab GTPase binding effector protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,70820
Polymers140,97510
Non-polymers2,73310
Water4,107228
1
A: Ras-related protein Rab-5A
B: Ras-related protein Rab-5A
F: Rab GTPase binding effector protein 1
G: Rab GTPase binding effector protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4838
Polymers56,3904
Non-polymers1,0934
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ras-related protein Rab-5A
D: Ras-related protein Rab-5A
H: Rab GTPase binding effector protein 1
I: Rab GTPase binding effector protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4838
Polymers56,3904
Non-polymers1,0934
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Ras-related protein Rab-5A
J: Rab GTPase binding effector protein 1
hetero molecules

E: Ras-related protein Rab-5A
J: Rab GTPase binding effector protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4838
Polymers56,3904
Non-polymers1,0934
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)112.4, 83.5, 144.9
Angle α, β, γ (deg.)90.00, 102.2, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Ras-related protein Rab-5A


Mass: 19118.766 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB5A, RAB5 / Plasmid: pET11A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P20339
#2: Protein
Rab GTPase binding effector protein 1 / Rabaptin-5 / Rabaptin-5alpha / Rabaptin-4


Mass: 9076.241 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RABEP1, RABPT5, RABPT5A / Plasmid: pGEX6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15276
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 47.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG3350, ammonium bromide, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9186 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 22, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9186 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 54048 / Num. obs: 54048 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 11.3
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.3 / % possible all: 89.4

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1N6H

1n6h


Resolution: 2.31→29.72 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 423796.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1035 2 %RANDOM
Rwork0.222 ---
all0.222 51979 --
obs0.222 51979 90.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.6721 Å2 / ksol: 0.304902 e/Å3
Displacement parametersBiso mean: 65.7 Å2
Baniso -1Baniso -2Baniso -3
1-10.45 Å20 Å27.42 Å2
2---0.88 Å20 Å2
3----9.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.32 Å
Luzzati d res low-6 Å
Luzzati sigma a0.44 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.31→29.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8342 0 165 228 8735
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.641.5
X-RAY DIFFRACTIONc_mcangle_it6.612
X-RAY DIFFRACTIONc_scbond_it6.852
X-RAY DIFFRACTIONc_scangle_it9.122.5
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.425 79 2.3 %
Rwork0.352 3321 -
obs--58.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2GNP.PARGNP.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more