[English] 日本語
Yorodumi
- PDB-5lpn: Structure of human Rab10 in complex with the bMERB domain of Mical-1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lpn
TitleStructure of human Rab10 in complex with the bMERB domain of Mical-1
Components
  • Protein-methionine sulfoxide oxidase MICAL1
  • Ras-related protein Rab-10
KeywordsENDOCYTOSIS / Mical-1 / DUF3585 / Mical / Rab effector / Rab10 / oxidoreductase
Function / homology
Function and homology information


protein localization to basolateral plasma membrane / establishment of neuroblast polarity / endoplasmic reticulum tubular network organization / establishment of protein localization to endoplasmic reticulum membrane / hippocampal mossy fiber expansion / : / F-actin monooxygenase / F-actin monooxygenase activity / NAD(P)H oxidase (H2O2-forming) / sulfur oxidation ...protein localization to basolateral plasma membrane / establishment of neuroblast polarity / endoplasmic reticulum tubular network organization / establishment of protein localization to endoplasmic reticulum membrane / hippocampal mossy fiber expansion / : / F-actin monooxygenase / F-actin monooxygenase activity / NAD(P)H oxidase (H2O2-forming) / sulfur oxidation / secretory vesicle / endoplasmic reticulum tubular network / regulation of regulated secretory pathway / insulin-responsive compartment / polarized epithelial cell differentiation / NAD(P)H oxidase H2O2-forming activity / regulated exocytosis / exocytic vesicle / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / cadherin binding involved in cell-cell adhesion / myosin V binding / RAB geranylgeranylation / Golgi to plasma membrane transport / actin filament depolymerization / RAB GEFs exchange GTP for GDP on RABs / Golgi to plasma membrane protein transport / establishment of protein localization to membrane / intermediate filament / endosomal transport / antigen processing and presentation / exocytosis / actin filament bundle assembly / intercellular bridge / vesicle-mediated transport / cytoskeleton organization / FAD binding / axonogenesis / cytoplasmic vesicle membrane / secretory granule membrane / small monomeric GTPase / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / actin filament / adherens junction / trans-Golgi network / monooxygenase activity / recycling endosome / SH3 domain binding / small GTPase binding / phagocytic vesicle membrane / recycling endosome membrane / cellular response to insulin stimulus / actin filament binding / GDP binding / actin cytoskeleton / G protein activity / Factors involved in megakaryocyte development and platelet production / actin binding / midbody / cytoskeleton / lysosome / endosome / endosome membrane / cilium / ciliary basal body / Golgi membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / protein kinase binding / negative regulation of apoptotic process / GTP binding / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / extracellular exosome / nucleoplasm / metal ion binding / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Mical, Rossman domain / bMERB domain / Bivalent Mical/EHBP Rab binding domain / bMERB domain profile. / DUF3585 / : / : / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. ...Mical, Rossman domain / bMERB domain / Bivalent Mical/EHBP Rab binding domain / bMERB domain profile. / DUF3585 / : / : / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / FAD-binding domain / FAD binding domain / ARF-like small GTPases; ARF, ADP-ribosylation factor / Small GTPase Rab domain profile. / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain 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 / FAD/NAD(P)-binding domain superfamily / 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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Ras-related protein Rab-10 / [F-actin]-monooxygenase MICAL1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRai, A. / Oprisko, A. / Campos, J. / Fu, Y. / Friese, T. / Itzen, A. / Goody, R.S. / Mueller, M.P. / Gazdag, E.M.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationSFB642, grant A4 Germany
Max Planck Society Germany
CitationJournal: Elife / Year: 2016
Title: bMERB domains are bivalent Rab8 family effectors evolved by gene duplication.
Authors: Rai, A. / Oprisko, A. / Campos, J. / Fu, Y. / Friese, T. / Itzen, A. / Goody, R.S. / Gazdag, E.M. / Muller, M.P.
History
DepositionAug 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Sep 14, 2016Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 10, 2024Group: 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
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.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.value / _struct_conn.pdbx_dist_value / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ras-related protein Rab-10
B: Protein-methionine sulfoxide oxidase MICAL1
C: Ras-related protein Rab-10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3507
Polymers58,2573
Non-polymers1,0934
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-43 kcal/mol
Surface area23450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.390, 59.000, 198.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Ras-related protein Rab-10


Mass: 20202.314 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB10 / Production host: Escherichia coli (E. coli) / References: UniProt: P61026
#2: Protein Protein-methionine sulfoxide oxidase MICAL1 / Molecule interacting with CasL protein 1 / MICAL-1 / NEDD9-interacting protein with calponin ...Molecule interacting with CasL protein 1 / MICAL-1 / NEDD9-interacting protein with calponin homology and LIM domains


Mass: 17852.303 Da / Num. of mol.: 1 / Fragment: UNP residues 918-1067
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MICAL1, MICAL, NICAL / Production host: Escherichia coli (E. coli)
References: UniProt: Q8TDZ2, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of one atom of oxygen into the other donor
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / 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.: 4 / 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: 2.93 Å3/Da / Density % sol: 58.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 6%-10% PEG8000 0.1M Imidazole / PH range: 7.6-8.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99997 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 20, 2015
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99997 Å / Relative weight: 1
ReflectionResolution: 2.8→44.004 Å / Num. obs: 17508 / % possible obs: 99.63 % / Redundancy: 12.7 % / Rmerge(I) obs: 0.118 / Rsym value: 0.123 / Net I/σ(I): 14.12
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.723 / Mean I/σ(I) obs: 3.25 / CC1/2: 0.803 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4lhw and 5szg

4lhw

5szg


Resolution: 2.8→44.004 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 30.75
RfactorNum. reflection% reflection
Rfree0.2866 875 5 %
Rwork0.244 --
obs0.2462 17499 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.8→44.004 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3677 0 66 4 3747
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083793
X-RAY DIFFRACTIONf_angle_d1.1185125
X-RAY DIFFRACTIONf_dihedral_angle_d20.5152282
X-RAY DIFFRACTIONf_chiral_restr0.06589
X-RAY DIFFRACTIONf_plane_restr0.006644
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.97550.36621430.30522705X-RAY DIFFRACTION99
2.9755-3.20510.37291430.29272713X-RAY DIFFRACTION99
3.2051-3.52760.32811410.26922709X-RAY DIFFRACTION99
3.5276-4.03770.27621450.25082757X-RAY DIFFRACTION100
4.0377-5.08590.27471470.21532792X-RAY DIFFRACTION100
5.0859-44.00980.25461560.23062948X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 1.7086 Å / Origin y: 73.9068 Å / Origin z: 216.9504 Å
111213212223313233
T0.339 Å20.0622 Å2-0.0207 Å2-0.3542 Å2-0.0427 Å2--0.3078 Å2
L0.7826 °2-0.5522 °20.2051 °2-0.7247 °2-0.6177 °2--1.0177 °2
S-0.0376 Å °-0.2198 Å °-0.1146 Å °0.2532 Å °0.1731 Å °-0.0524 Å °-0.2518 Å °-0.1436 Å °0.0247 Å °
Refinement TLS groupSelection details: all

+
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