[English] 日本語
Yorodumi
- PDB-2ocy: Complex of the guanine exchange factor Sec2p and the Rab GTPase Sec4p -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ocy
TitleComplex of the guanine exchange factor Sec2p and the Rab GTPase Sec4p
Components
  • Rab guanine nucleotide exchange factor SEC2
  • Ras-related protein SEC4
KeywordsENDOCYTOSIS/EXOCYTOSIS / Rab / GEF / guanine exchange factor / coiled-coil / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


ascospore-type prospore assembly / Golgi to plasma membrane transport vesicle / Anchoring of the basal body to the plasma membrane / membrane addition at site of cytokinesis / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / cell tip / incipient cellular bud site / vesicle fusion / cellular bud tip ...ascospore-type prospore assembly / Golgi to plasma membrane transport vesicle / Anchoring of the basal body to the plasma membrane / membrane addition at site of cytokinesis / RAB geranylgeranylation / RAB GEFs exchange GTP for GDP on RABs / cell tip / incipient cellular bud site / vesicle fusion / cellular bud tip / Golgi to plasma membrane transport / vesicle docking involved in exocytosis / cellular bud neck / regulation of exocytosis / mating projection tip / phosphatidylinositol-4-phosphate binding / transport vesicle membrane / exocytosis / protein secretion / transport vesicle / Neutrophil degranulation / guanyl-nucleotide exchange factor activity / protein localization to plasma membrane / autophagy / protein transport / vesicle / mitochondrial outer membrane / endosome / GTPase activity / GTP binding / endoplasmic reticulum / mitochondrion / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Helix Hairpins - #910 / GDP/GTP exchange factor Sec2, N-terminal / Guanine nucleotide exchange factor RAB3IL/RAB3IP/Sec2 / GDP/GTP exchange factor Sec2p / 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 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases ...Helix Hairpins - #910 / GDP/GTP exchange factor Sec2, N-terminal / Guanine nucleotide exchange factor RAB3IL/RAB3IP/Sec2 / GDP/GTP exchange factor Sec2p / 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 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Helix non-globular / Rab subfamily of small GTPases / Special / 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
Ras-related protein SEC4 / Rab guanine nucleotide exchange factor SEC2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.3 Å
AuthorsReinisch, K.M. / Dong, G.
CitationJournal: Mol.Cell / Year: 2007
Title: A Catalytic Coiled Coil: Structural Insights into the Activation of the Rab GTPase Sec4p by Sec2p.
Authors: Dong, G. / Medkova, M. / Novick, P. / Reinisch, K.M.
History
DepositionDec 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Rab guanine nucleotide exchange factor SEC2
B: Rab guanine nucleotide exchange factor SEC2
C: Ras-related protein SEC4


Theoretical massNumber of molelcules
Total (without water)55,3293
Polymers55,3293
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9450 Å2
ΔGint-93 kcal/mol
Surface area28750 Å2
MethodPISA
2
A: Rab guanine nucleotide exchange factor SEC2
B: Rab guanine nucleotide exchange factor SEC2
C: Ras-related protein SEC4

A: Rab guanine nucleotide exchange factor SEC2
B: Rab guanine nucleotide exchange factor SEC2
C: Ras-related protein SEC4


Theoretical massNumber of molelcules
Total (without water)110,6586
Polymers110,6586
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area25280 Å2
ΔGint-215 kcal/mol
Surface area51120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.999, 92.999, 295.909
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Detailsthe coordinates reflect the biologically relevant assembly, which consists of two sec2 chains and one Sec4 chain.

-
Components

#1: Protein Rab guanine nucleotide exchange factor SEC2 / GDP-GTP exchange factor SEC2


Mass: 18018.746 Da / Num. of mol.: 2 / Fragment: residues 17-167
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SEC2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P17065
#2: Protein Ras-related protein SEC4 / Suppressor of RHO3 protein 6


Mass: 19291.531 Da / Num. of mol.: 1 / Fragment: residues 18-187
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SEC4, SRO6 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P07560

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.34 Å3/Da / Density % sol: 63.15 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 100 mM sodium acetate (pH 5.0), 200 mM calcium acetate, 20% PEG 400, 10mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 160 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9794
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2006
RadiationMonochromator: single crystal side bounce monochromator, Kohzu HLD8-24
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. all: 11817 / Num. obs: 11817 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 14.5
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 3 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1124 / Rsym value: 0.327 / % possible all: 96.7

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
SHARPphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.3→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.325 1114 -random
Rwork0.25 ---
obs0.25 11817 97.7 %-
all-12095 --
Refinement stepCycle: LAST / Resolution: 3.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3592 0 0 0 3592
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_bond_d0.007
LS refinement shellResolution: 3.3→3.35 Å /
RfactorNum. reflection
Rfree0.455 27
Rwork0.383 -
obs-349

+
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