[English] 日本語
Yorodumi
- PDB-3swv: Crystal Structure of a domain of Brefeldin A-inhibited guanine nu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3swv
TitleCrystal Structure of a domain of Brefeldin A-inhibited guanine nucleotide-exchange protein 2 (Brefeldin A-inhibited GEP 2) from Homo sapiens (Human), Northeast Structural Genomics Consortium target id HR5562A
ComponentsBrefeldin A-inhibited guanine nucleotide-exchange protein 2
KeywordsMETAL BINDING PROTEIN / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG / Guanine-nucleotide releasing factor / Phosphoprotein / Nucleotide-binding protein / Metal-binding protein
Function / homology
Function and homology information


endomembrane system organization / symmetric synapse / receptor recycling / axonemal microtubule / endosome organization / GABA receptor binding / Golgi to plasma membrane transport / regulation of ARF protein signal transduction / microtubule organizing center / myosin binding ...endomembrane system organization / symmetric synapse / receptor recycling / axonemal microtubule / endosome organization / GABA receptor binding / Golgi to plasma membrane transport / regulation of ARF protein signal transduction / microtubule organizing center / myosin binding / exocytosis / protein kinase A regulatory subunit binding / Association of TriC/CCT with target proteins during biosynthesis / asymmetric synapse / GABA-ergic synapse / guanyl-nucleotide exchange factor activity / trans-Golgi network / recycling endosome / positive regulation of tumor necrosis factor production / protein transport / presynapse / cytoplasmic vesicle / dendritic spine / intracellular signal transduction / Golgi membrane / intracellular membrane-bounded organelle / centrosome / glutamatergic synapse / perinuclear region of cytoplasm / Golgi apparatus / membrane / cytosol
Similarity search - Function
Sec7/BIG1-like, C-terminal domain / BIG2 C-terminal domain / Mon2/Sec7/BIG1-like, HDS / Mon2/Sec7/BIG1-like, HDS / Mon2/Sec7/BIG1-like, dimerisation and cyclophilin-binding domain / Mon2/Sec7/BIG1-like, dimerisation and cyclophilin-binding domain / Mon2/Sec7/BIG1-like, HUS domain / Mon2/Sec7/BIG1-like, HUS domain / Arf Nucleotide-binding Site Opener; domain 2 / Arf Nucleotide-binding Site Opener,domain 2 ...Sec7/BIG1-like, C-terminal domain / BIG2 C-terminal domain / Mon2/Sec7/BIG1-like, HDS / Mon2/Sec7/BIG1-like, HDS / Mon2/Sec7/BIG1-like, dimerisation and cyclophilin-binding domain / Mon2/Sec7/BIG1-like, dimerisation and cyclophilin-binding domain / Mon2/Sec7/BIG1-like, HUS domain / Mon2/Sec7/BIG1-like, HUS domain / Arf Nucleotide-binding Site Opener; domain 2 / Arf Nucleotide-binding Site Opener,domain 2 / Annexin V; domain 1 - #20 / Sec7 domain / Sec7, C-terminal domain superfamily / Sec7 domain superfamily / Sec7 domain / SEC7 domain profile. / Sec7 domain / Annexin V; domain 1 / Armadillo-like helical / Armadillo-type fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Brefeldin A-inhibited guanine nucleotide-exchange protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsSeetharaman, J. / Su, M. / Forouhar, F. / Wang, D. / Janjua, H. / Cunningham, K. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. ...Seetharaman, J. / Su, M. / Forouhar, F. / Wang, D. / Janjua, H. / Cunningham, K. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of a domain of Brefeldin A-inhibited guanine nucleotide-exchange protein 2 (BrefeldinA-inhibited GEP 2) from Homo sapiens (Human), Northeast Structural Genomics Consortium target id HR5562A
Authors: Seetharaman, J. / Su, M. / Forouhar, F. / Wang, D. / Janjua, H. / Cunningham, K. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJul 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Brefeldin A-inhibited guanine nucleotide-exchange protein 2


Theoretical massNumber of molelcules
Total (without water)23,7891
Polymers23,7891
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.939, 53.939, 75.725
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

-
Components

#1: Protein Brefeldin A-inhibited guanine nucleotide-exchange protein 2 / Brefeldin A-inhibited GEP 2


Mass: 23788.945 Da / Num. of mol.: 1 / Fragment: SEC7 domain residues 635-836
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARFGEF2, ARFGEP2, BIG2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y6D5

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.99 %
Crystal growTemperature: 291 K / pH: 5
Details: 15% PEG1000, 0.1M sodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONNSLS X4A10.979
SYNCHROTRONNSLS X6A20.979
Detector
TypeIDDetectorDate
ADSC QUANTUM 4r1CCDDec 1, 2009
ADSC QUANTUM 2102CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHx-ray1
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.26
ReflectionResolution: 3→50 Å / Num. obs: 9252 / % possible obs: 94.8 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Rmerge(I) obs: 0.069 / Rsym value: 0.063 / Net I/σ(I): 8.9
Reflection shellResolution: 3→3.11 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.309 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 3→20 Å / σ(F): 2 / Stereochemistry target values: ENGH & HUBER / Details: twinning fraction = 0.260 twin law = -h, -k, l
RfactorNum. reflectionSelection details
Rfree0.262 814 RANDOM
Rwork0.203 --
obs0.203 7363 -
all-8177 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.374 Å20 Å20 Å2
2--5.374 Å20 Å2
3----10.747 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1531 0 0 0 1531
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d1.18
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_deg2.08
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.1421.5
X-RAY DIFFRACTIONc_mcangle_it2.0522
X-RAY DIFFRACTIONc_scbond_it1.2232
X-RAY DIFFRACTIONc_scangle_it2.1092.5
LS refinement shellResolution: 3→20 Å / Num. reflection Rfree: 814
Xplor fileSerial no: 1 / Param file: protein_rep.param

+
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://pdbjlvh1.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