[English] 日本語
Yorodumi
- PDB-6ekk: Crystal structure of GEF domain of DENND 1A in complex with Rab G... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ekk
TitleCrystal structure of GEF domain of DENND 1A in complex with Rab GTPase Rab35-GDP bound state.
Components
  • DENN domain-containing protein 1A
  • Ras-related protein Rab-35
KeywordsTRANSCRIPTION / DENND1A- DENN domain-containing protein 1A RAB35- Ras-related protein Rab-35
Function / homology
Function and homology information


regulation of Rab protein signal transduction / Rab protein signal transduction / plasma membrane to endosome transport / phosphatidylinositol phosphate binding / protein localization to endosome / clathrin-coated vesicle membrane / cell projection membrane / clathrin-coated endocytic vesicle / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs ...regulation of Rab protein signal transduction / Rab protein signal transduction / plasma membrane to endosome transport / phosphatidylinositol phosphate binding / protein localization to endosome / clathrin-coated vesicle membrane / cell projection membrane / clathrin-coated endocytic vesicle / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / phosphatidylinositol-3-phosphate binding / endocytic recycling / TBC/RABGAPs / clathrin-coated vesicle / endosomal transport / intercellular bridge / mitotic cytokinesis / synaptic vesicle endocytosis / antigen processing and presentation / clathrin-coated pit / phosphatidylinositol-4,5-bisphosphate binding / guanyl-nucleotide exchange factor activity / cellular response to nerve growth factor stimulus / clathrin-coated endocytic vesicle membrane / protein localization / small GTPase binding / positive regulation of GTPase activity / SH3 domain binding / endocytosis / recycling endosome membrane / neuron projection development / GDP binding / melanosome / protein transport / presynaptic membrane / endosome membrane / intracellular membrane-bounded organelle / GTPase activity / dendrite / neuronal cell body / GTP binding / extracellular exosome / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
DENN domain-containing protein 1A/1B/1C / dDENN domain / uDENN domain / Rab35 / uDENN domain / Domain always found upstream of DENN domain, found in a variety of signalling proteins / cDENN domain / dDENN domain / DENN domain, C-terminal lobe / DENN (AEX-3) domain ...DENN domain-containing protein 1A/1B/1C / dDENN domain / uDENN domain / Rab35 / uDENN domain / Domain always found upstream of DENN domain, found in a variety of signalling proteins / cDENN domain / dDENN domain / DENN domain, C-terminal lobe / DENN (AEX-3) domain / Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN / Domain always found downstream of DENN domain, found in a variety of signalling proteins / Tripartite DENN domain / Tripartite DENN domain profile. / ARF-like small GTPases; ARF, ADP-ribosylation factor / small GTPase Rab1 family 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 / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Ras-related protein Rab-35 / DENN domain-containing protein 1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsSrikannathasan, V. / Szykowska, A. / Tallant, C. / Strain-Damerell, C. / Kopec, J. / Kupinska, K. / Mukhopadhyay, S. / Gavin, M. / Wang, D. / Chalk, R. ...Srikannathasan, V. / Szykowska, A. / Tallant, C. / Strain-Damerell, C. / Kopec, J. / Kupinska, K. / Mukhopadhyay, S. / Gavin, M. / Wang, D. / Chalk, R. / Burgess-Brown, N.A. / Arrowsmith, C.H. / Edwards, A. / Bountra, C. / von Delft, F. / Huber, K.
CitationJournal: To be published
Title: Crystal structure of DENND1A-RAB35 complex with GDP bound state.
Authors: Srikannathasan, V.
History
DepositionSep 26, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DENN domain-containing protein 1A
B: DENN domain-containing protein 1A
C: Ras-related protein Rab-35
D: Ras-related protein Rab-35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,41523
Polymers130,1684
Non-polymers2,24819
Water15,493860
1
A: DENN domain-containing protein 1A
C: Ras-related protein Rab-35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,16011
Polymers65,0842
Non-polymers1,0769
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-58 kcal/mol
Surface area22950 Å2
MethodPISA
2
B: DENN domain-containing protein 1A
D: Ras-related protein Rab-35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,25612
Polymers65,0842
Non-polymers1,17210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-88 kcal/mol
Surface area23460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.700, 67.990, 101.710
Angle α, β, γ (deg.)80.500, 76.800, 67.060
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 2 types, 4 molecules ABCD

#1: Protein DENN domain-containing protein 1A / Connecdenn 1 / Connecdenn / Protein FAM31A


Mass: 45006.172 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Chain A- DENND1AA (UNIPROT Q8TEH3) Chain B- RAB35 (UNIPROT - Q15286)
Source: (gene. exp.) Homo sapiens (human) / Gene: DENND1A, FAM31A, KIAA1608 / Plasmid: pFB-CT10HF-LIC / Details (production host): C-terminal TAg / Cell (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8TEH3
#2: Protein Ras-related protein Rab-35 / GTP-binding protein RAY / Ras-related protein Rab-1C


Mass: 20077.725 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB35, RAB1C, RAY / Plasmid: pNIC28-Bsa4 / Details (production host): N-terminal his tag / Cell (production host): Escherichia Coli BL21 DE3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15286

-
Non-polymers , 4 types, 879 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 860 / 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: 2.64 Å3/Da / Density % sol: 53.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 25%PEG3350, 0.2M AMS, 0.1M Bis-Tris pH 5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 13, 2017
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.82→50.452 Å / Num. obs: 115286 / % possible obs: 95.7 % / Redundancy: 3.4 % / Net I/σ(I): 8.5
Reflection shellResolution: 1.82→1.87 Å

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TW8

3tw8


Resolution: 1.82→50.452 Å / SU ML: 0.25 / Cross valid method: NONE / σ(F): 1.96 / Phase error: 26.78
RfactorNum. reflection% reflection
Rfree0.2323 5773 5.01 %
Rwork0.1935 --
obs0.1954 115262 96.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 130.5 Å2 / Biso mean: 36.0058 Å2 / Biso min: 17.14 Å2
Refinement stepCycle: final / Resolution: 1.82→50.452 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8664 0 133 860 9657
Biso mean--49.64 45.07 -
Num. residues----1106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089085
X-RAY DIFFRACTIONf_angle_d1.10412376
X-RAY DIFFRACTIONf_chiral_restr0.0431398
X-RAY DIFFRACTIONf_plane_restr0.0051583
X-RAY DIFFRACTIONf_dihedral_angle_d14.4383223
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.82-1.84070.34281880.37623655384396
1.8407-1.86230.39551950.36243595379096
1.8623-1.88510.32071880.33183633382196
1.8851-1.90890.32932230.31993598382196
1.9089-1.9340.34112020.29813611381396
1.934-1.96050.32741970.2793624382196
1.9605-1.98850.30222210.27133663388496
1.9885-2.01820.27341820.25983590377296
2.0182-2.04980.30192090.24333593380296
2.0498-2.08340.2691890.2343641383096
2.0834-2.11930.24351840.22263669385396
2.1193-2.15780.22961820.21723630381296
2.1578-2.19930.26482020.20963599380196
2.1993-2.24420.28931760.21093592376895
2.2442-2.2930.24691920.20873654384696
2.293-2.34640.21531740.1953638381296
2.3464-2.4050.24162110.19733619383096
2.405-2.47010.22721870.19453601378896
2.4701-2.54270.25852050.19963649385496
2.5427-2.62480.21842020.19193587378996
2.6248-2.71860.22881860.18963657384396
2.7186-2.82750.24991930.19223671386497
2.8275-2.95610.23981870.19563697388497
2.9561-3.1120.24091500.18423717386797
3.112-3.30690.19871850.17683699388498
3.3069-3.56220.21321900.17653687387798
3.5622-3.92050.20651950.15973726392198
3.9205-4.48750.19372090.15363709391898
4.4875-5.65260.18391710.15763761393298
5.6526-50.4710.22581980.18373724392298
Refinement TLS params.Method: refined / Origin x: 17.726 Å / Origin y: 9.6475 Å / Origin z: 25.363 Å
111213212223313233
T0.2146 Å20.0077 Å20.0341 Å2-0.1859 Å2-0.0001 Å2--0.2031 Å2
L0.2772 °20.0677 °20.2242 °2-0.1059 °20.0364 °2--0.4261 °2
S0.018 Å °-0.0057 Å °-0.001 Å °0.0447 Å °-0.0049 Å °0.0262 Å °-0.0351 Å °-0.0063 Å °-0.0127 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 390
2X-RAY DIFFRACTION1allB2 - 394
3X-RAY DIFFRACTION1allC3 - 178
4X-RAY DIFFRACTION1allD4 - 177
5X-RAY DIFFRACTION1allE1 - 9
6X-RAY DIFFRACTION1allF1 - 8
7X-RAY DIFFRACTION1allK1 - 2
8X-RAY DIFFRACTION1allS1 - 643
9X-RAY DIFFRACTION1allW1 - 312

+
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