[English] 日本語
Yorodumi
- PDB-1x03: Crystal structure of endophilin BAR domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1x03
TitleCrystal structure of endophilin BAR domain
ComponentsSH3-containing GRB2-like protein 2
KeywordsTRANSFERASE / BAR domain
Function / homology
Function and homology information


negative regulation of blood-brain barrier permeability / synaptic vesicle uncoating / dendrite extension / Retrograde neurotrophin signalling / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / Recycling pathway of L1 / cellular response to brain-derived neurotrophic factor stimulus / MHC class II antigen presentation / InlB-mediated entry of Listeria monocytogenes into host cell ...negative regulation of blood-brain barrier permeability / synaptic vesicle uncoating / dendrite extension / Retrograde neurotrophin signalling / Lysosome Vesicle Biogenesis / Golgi Associated Vesicle Biogenesis / Recycling pathway of L1 / cellular response to brain-derived neurotrophic factor stimulus / MHC class II antigen presentation / InlB-mediated entry of Listeria monocytogenes into host cell / negative regulation of protein phosphorylation / central nervous system development / cell projection / EGFR downregulation / clathrin-coated endocytic vesicle membrane / Negative regulation of MET activity / neuron projection development / Cargo recognition for clathrin-mediated endocytosis / presynapse / Clathrin-mediated endocytosis / early endosome / Golgi membrane / negative regulation of gene expression / lipid binding / glutamatergic synapse / perinuclear region of cytoplasm / signal transduction / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Endophilin-A, SH3 domain / BAR domain / BAR domain profile. / BAR / Arfaptin homology (AH) domain/BAR domain / BAR domain / AH/BAR domain superfamily / Variant SH3 domain / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Src homology 3 domains ...Endophilin-A, SH3 domain / BAR domain / BAR domain profile. / BAR / Arfaptin homology (AH) domain/BAR domain / BAR domain / AH/BAR domain superfamily / Variant SH3 domain / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.1 Å
AuthorsMasuda, M. / Takeda, S. / Sone, M. / Kamioka, Y. / Mori, H. / Mochizuki, N.
CitationJournal: Embo J. / Year: 2006
Title: Endophilin BAR domain drives membrane curvature by two newly identified structure-based mechanisms
Authors: Masuda, M. / Takeda, S. / Sone, M. / Ohki, T. / Mori, H. / Kamioka, Y. / Mochizuki, N.
History
DepositionMar 14, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 2, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SH3-containing GRB2-like protein 2


Theoretical massNumber of molelcules
Total (without water)29,1261
Polymers29,1261
Non-polymers00
Water0
1
A: SH3-containing GRB2-like protein 2

A: SH3-containing GRB2-like protein 2


Theoretical massNumber of molelcules
Total (without water)58,2522
Polymers58,2522
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-y,z1
Buried area5490 Å2
ΔGint-49 kcal/mol
Surface area22040 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)127.424, 127.424, 99.635
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
DetailsThe biological assembly is a dimer generated by the two fold axis.

-
Components

#1: Protein SH3-containing GRB2-like protein 2 / endophilin A1 / SH3 domain protein 2A / Endophilin 1 / EEN-B1


Mass: 29125.752 Da / Num. of mol.: 1 / Fragment: endophilin BAR domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX6p3 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pLysS
References: UniProt: Q99962, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 277 K / Method: microdialysis / pH: 7.4
Details: NaCl, ethylene glycol, glycerol, benzamizine/HCl, Hepes, DTT, pH 7.4, MICRODIALYSIS, temperature 277K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1901
2901
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL45PX10.9797
SYNCHROTRONSPring-8 BL44B220.9793, 0.9794, 0.9817, 0.9817
Detector
TypeIDDetectorDate
RIGAKU JUPITER1CCDJul 4, 2004
ADSC QUANTUM 2102CCDJun 27, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1DiamondSINGLE WAVELENGTHMx-ray1
2Si 111MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
20.97931
30.97941
40.98171
ReflectionResolution: 3.1→50 Å / Num. all: 14522 / Num. obs: 14464 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.066 / Net I/σ(I): 22.9
Reflection shellResolution: 3.1→3.21 Å / Rmerge(I) obs: 0.363 / Mean I/σ(I) obs: 4.5 / Num. unique all: 1433 / % possible all: 100

-
Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 3.1→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 738 -RANDOM
Rwork0.236 ---
all0.238 14529 --
obs0.238 14449 99.4 %-
Displacement parametersBiso mean: 84.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.66 Å
Refinement stepCycle: LAST / Resolution: 3.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1698 0 0 0 1698
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005675
X-RAY DIFFRACTIONc_angle_deg1.02969
LS refinement shellResolution: 3.1→3.21 Å
RfactorNum. reflection% reflection
Rfree0.366 73 -
Rwork0.423 --
obs-1406 98.7 %

+
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