[English] 日本語
Yorodumi
- PDB-3tkl: Crystal structure of the GTP-bound Rab1a in complex with the coil... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tkl
TitleCrystal structure of the GTP-bound Rab1a in complex with the coiled-coil domain of LidA from Legionella pneumophila
Components
  • LidA protein, substrate of the Dot/Icm system
  • Ras-related protein Rab-1A
KeywordsPROTEIN TRANSPORT/PROTEIN BINDING / Vesicle trafficking / PROTEIN TRANSPORT-PROTEIN BINDING complex
Function / homology
Function and homology information


positive regulation of glycoprotein metabolic process / growth hormone secretion / COPII-coated vesicle cargo loading / melanosome transport / vesicle transport along microtubule / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / Golgi Cisternae Pericentriolar Stack Reorganization / COPII-mediated vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic ...positive regulation of glycoprotein metabolic process / growth hormone secretion / COPII-coated vesicle cargo loading / melanosome transport / vesicle transport along microtubule / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / Golgi Cisternae Pericentriolar Stack Reorganization / COPII-mediated vesicle transport / COPI-dependent Golgi-to-ER retrograde traffic / transport vesicle membrane / virion assembly / Golgi organization / autophagosome assembly / endoplasmic reticulum to Golgi vesicle-mediated transport / COPI-mediated anterograde transport / vesicle-mediated transport / endomembrane system / substrate adhesion-dependent cell spreading / small monomeric GTPase / positive regulation of interleukin-8 production / intracellular protein transport / autophagy / endocytosis / melanosome / cell migration / G protein activity / early endosome / defense response to bacterium / cadherin binding / Golgi membrane / GTPase activity / GTP binding / endoplasmic reticulum / Golgi apparatus / extracellular exosome / cytosol
Similarity search - Function
Helix Hairpins - #990 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / : / ARF-like small GTPases; ARF, ADP-ribosylation factor / small GTPase Rab1 family profile. / Helix Hairpins / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Helix non-globular / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Rho (Ras homology) subfamily of Ras-like small GTPases ...Helix Hairpins - #990 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / : / ARF-like small GTPases; ARF, ADP-ribosylation factor / small GTPase Rab1 family profile. / Helix Hairpins / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Helix non-globular / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Special / 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 / : / Ras-related protein Rab-1A
Similarity search - Component
Biological speciesHomo sapiens (human)
Legionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.183 Å
AuthorsCheng, W. / Yin, K. / Lu, D. / Li, B. / Zhu, D. / Chen, Y. / Zhang, H. / Xu, S. / Chai, J. / Gu, L.
CitationJournal: Plos Pathog. / Year: 2012
Title: Structural insights into a unique Legionella pneumophila effector LidA recognizing both GDP and GTP bound Rab1 in their active state
Authors: Cheng, W. / Yin, K. / Lu, D. / Li, B. / Zhu, D. / Chen, Y. / Zhang, H. / Xu, S. / Chai, J. / Gu, L.
History
DepositionAug 27, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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_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-1A
B: LidA protein, substrate of the Dot/Icm system
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9494
Polymers52,4012
Non-polymers5472
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-23 kcal/mol
Surface area18390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.823, 49.709, 61.702
Angle α, β, γ (deg.)90.00, 99.27, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Ras-related protein Rab-1A / YPT1-related protein


Mass: 21766.635 Da / Num. of mol.: 1 / Fragment: UNP residues 1-191
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB1 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P62820
#2: Protein LidA protein, substrate of the Dot/Icm system


Mass: 30634.645 Da / Num. of mol.: 1 / Fragment: Coiled-coil domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Strain: Corby / Gene: lidA / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A5IFX1
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 1.86 Å3/Da / Density % sol: 33.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 25% PEG3350, 0.7% butanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 14, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.183→50 Å / Num. all: 20017 / Num. obs: 20017 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 25.74 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 23.88
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 4.65 / Num. unique all: 991 / Rsym value: 0.295 / % possible all: 98.7

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FOL

2fol


Resolution: 2.183→31.785 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.25 / σ(F): 1.35 / σ(I): 0 / Phase error: 25.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2515 1020 5.1 %RANDOM
Rwork0.1909 ---
all0.194 19986 --
obs0.194 19986 98.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.449 Å2 / ksol: 0.372 e/Å3
Displacement parametersBiso max: 89.92 Å2 / Biso mean: 32.0164 Å2 / Biso min: 14.28 Å2
Baniso -1Baniso -2Baniso -3
1--0.5706 Å20 Å21.216 Å2
2---1.076 Å20 Å2
3---1.6466 Å2
Refinement stepCycle: LAST / Resolution: 2.183→31.785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2902 0 33 111 3046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092980
X-RAY DIFFRACTIONf_angle_d1.0924015
X-RAY DIFFRACTIONf_chiral_restr0.068454
X-RAY DIFFRACTIONf_plane_restr0.004504
X-RAY DIFFRACTIONf_dihedral_angle_d17.2351156
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1827-2.29780.28391270.20642537266492
2.2978-2.44170.27091350.196327152850100
2.4417-2.63010.31571590.209227142873100
2.6301-2.89470.26011460.216827422888100
2.8947-3.31310.29051500.193327522902100
3.3131-4.17270.21921470.175127502897100
4.1727-31.78880.21991560.18142756291298

+
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